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SCIEX CESI 8000 Plus User Manual

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CESI 8000 Plus High Performance
Separation-ESI Module
User Manual
RUO-IDV-05-3897-B
February 2019

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Summary of Contents for SCIEX CESI 8000 Plus

  • Page 1 CESI 8000 Plus High Performance Separation-ESI Module User Manual RUO-IDV-05-3897-B February 2019...
  • Page 2 This document is provided to customers who have purchased SCIEX equipment to use in the operation of such SCIEX equipment. This document is copyright protected and any reproduction of this document or any part of this document is strictly prohibited, except as SCIEX may authorize in writing.

  • Page 3: Table Of Contents

    安全、通知和标签 , 23 综述 , 23 警告、注意、重要事项以及注释的提示 , 24 仪器安全防护措施 , 25 活动部件或尖锐物 , 26 , 26 电气安全 激光安全 （适用于可选激光设备） , 26 1 类激光小心标签 (1 级激光警告标签 ), 26 User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF...
  • Page 4 Élimination des appareils contenant des composants au mercure, 39 Étiquette marque CE, 39 Étiquette marque MRC, 40 Étiquette marque CSA, 40 CHAPTER 4: System Overview, 41 About This Manual, 41 CESI 8000 Plus High Performance Separation-ESI Module User Manual RUO-IDV-05-3897-B | B11949AF...
  • Page 5 CESI 8000 Plus System: Installing OptiMS Cartridge, 53 OptiMS Cartridge Installation, 53 Thermo Scientific Mass Spectrometer: Integration with the CESI 8000 Plus System, 57 Physical Integration with the CESI 8000 Plus System, 57 OptiMS Cartridge Sprayer Tip Installation into a Thermo...
  • Page 6 Dialog, 118 Insert Option, 120 Sequence Dialog, 121 Sequence Table Rows, 123 Fill Down Option, 127 Display Options, 128 Vial Legend, 129 Tray Detail View, 129 Vial Preview, 130 CESI 8000 Plus High Performance Separation-ESI Module User Manual RUO-IDV-05-3897-B | B11949AF...
  • Page 7 Create a Sequence in the Analyst Software, 173 ® Start a Sequence in the Analyst Software, 176 Load Sample and Reagents on the CESI 8000 Plus System, 177 Sample Tray Setup, 177 Create a Sequence in the CESI 8000 Software, 179...
  • Page 8 Analysis, 214 CHAPTER 10: Shutdown Procedures and Decoupling Instruments, 217 Shutdown and Decoupling Overview, 217 Cartridge Removal and the CESI 8000 Plus System Shutdown, 217 Cartridge Removal and Instrument Shutdown, 217 Decoupling the CESI 8000 Plus System, 222 Decoupling from the Thermo Scientific Mass...
  • Page 9 APPENDIX B: Nominal Network Configuration, 235 Overview, 235 Switching from the CESI 8000 Plus System to Different Mass Spectrometer Systems, 236 Switching to the CESI 8000 Plus System from Different Mass Spectrometer Systems, 236 Switching from a SCIEX Mass Spectrometer to Another Mass...
  • Page 10 Troubleshooting and Flow Diagrams, 349 Sample Preparation Considerations for Analysis with CESI- MS, 350 Properties of a Method or Sequence Cannot be Modified or Saved, 350 Blocked Sprayer Tip, 351 CESI 8000 Plus High Performance Separation-ESI Module User Manual RUO-IDV-05-3897-B | B11949AF...
  • Page 11 Contents Possible Cause, 351 Possible Solution, 351 Electrospray Cannot Be Established Between the CESI 8000 Plus System and Mass Spectrometer, 353 Electrospray is Detected at Zero Ion Spray (IS) Voltage while Applying CE Voltage, 354 Unstable Electrospray while Applying CE Voltage and IS...
  • Page 12 Contents CESI 8000 Plus High Performance Separation-ESI Module User Manual RUO-IDV-05-3897-B | B11949AF...

  • Page 13: Safety, Notices And Labels

    CHAPTER 1 Safety, Notices and Labels Overview A description of the symbols and labels that are used on the SCIEX CESI 8000 Plus High Performance Separation-ESI Module, or that are shown in this manual, can be found in this section.

  • Page 14: Alerts For Warning, Caution, Important, And Note

    Important adds benefit to the performance of a piece of equipment or to a process. NOTE Used to call attention to notable information that should be followed during installation, use, or servicing of this equipment. CESI 8000 Plus High Performance Separation-ESI Module User Manual 14 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 15: Instrument Safety Precautions

    • Acknowledge and act upon instrument alarms and error messages. • Keep away from moving parts. • Report any broken parts to your SCIEX representative. • Use the proper tools when troubleshooting. User Manual CESI 8000 Plus High Performance Separation-ESI Module...

  • Page 16: Moving Parts Or Sharp Objects

    • This equipment is used in a manner other than specified. Operate the instrument as instructed in the product manuals. • You introduce software that is not authorized by SCIEX into your computer. Only operate your system’s computer with software authorized by SCIEX.

  • Page 17: Laser Safety (For Optional Laser Device)

    • Always wear assigned personal protective equipment, including powder-free neoprene or nitrile gloves, safety glasses, and a laboratory coat. • Follow required electrical safe work practices. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 17 / 376...

  • Page 18: Safety Symbols And Labels

    This symbol calls attention to important information to read, or is accompanied by another symbol indicating a particular safety hazard. The information is located either on the label with the symbol or in the CESI 8000 Plus documentation. Sharp Object Label This symbol indicates that there are sharp objects, and the operator should use care when accessing this area.

  • Page 19: Mobile Cart Caution Label

    A label cautioning users when moving the cart or adjusting the height of the cart can be found on the CESI 8000 Plus mobile cart. The CESI 8000 instrument is situated on the mobile cart. The OptiMS cartridge spray tip on the CESI 8000 instrument has to be in very close proximity to a mass spectrometer when the system is used.

  • Page 20: Other Instrument Labels

    WEEE (waste, electrical, and electronic equipment). To safely dispose of this equipment, contact a local Customer Service office for complimentary equipment pick- up and recycling. CESI 8000 Plus High Performance Separation-ESI Module User Manual 20 / 376...

  • Page 21: Disposal Of Devices Containing Mercury Components

    The CSA symbol on the CESI 8000 instrument indicates that the instrument has been certified by a Nationally Recognized Testing laboratory (NRTL) to applicable Laboratory Equipment Safety Standards for the United States and Canada. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 21 / 376...
  • Page 22 Safety, Notices and Labels CESI 8000 Plus High Performance Separation-ESI Module User Manual 22 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 23: 安全、通知和标签

    章 2 安全、通知和标签 综述 用于 SCIEX CESI 8000 Plus 高性能分离系统或在本手册中显示的符号和标签的描述可在 本节中找到。 仔细阅读所有说明之前，请勿尝试执行任何操作。在任何情况下如果不知如何处理， 请与您的 SCIEX 代表联系。 SCIEX 强烈要求其客户和员工遵守所有国家健康和安全标准，如防护的使用。此标准 包括但不限于下列事项：操作或维护本仪器或任何其他实验室自动仪器时，请佩戴防 护眼镜、手套和合适的实验室装备。 警告 如果设备的使用未能按照 SCIEX 公司所指定的方式进行，该设备所具备的 保护性能可能受损。 User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 23 / 376...

  • Page 24: 警告、注意、重要事项以及注释的提示

    安全、通知和标签 警告、注意、重要事项以及注释的提示 本文档中的所有警告与注意都包含感叹号，设在三角形中。 感叹号符号是国际通用符号，用于提示在安装、使用、维护和维修前应阅读并理解所 有的安全说明。 警告 “警告”指可能的有害情况，若未加以避免，则会导致死亡或严重伤害。也 可用它来说明有可能出现可能导致错误诊断的错误数据。还可用它来说明 仪器严重损坏的可能性。 注意 “小心”是指如果未能避免可能导致轻微或中度伤害的潜在危险情况。可用 于警示不安全操作。可能用于说明有可能出现可能导致错误诊断的错误数 据。 重要 用于对正在执行的步骤或程序进行有价值的备注。遵循“重要事项”中的建议有助于改善 某件设备或某个程序的性能。 注释 用于提醒在设备安装、使用、或维修过程中应遵照的重要信息。 CESI 8000 Plus High Performance Separation-ESI Module User Manual 24 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 25: 仪器安全防护措施

    • 在计算机中安装了未经 SCIEX 授权的软件。请在系统的计算机上仅运 行 SCIEX 授权的软件。 • 安装的软件并非是具有原始版权的版本。请仅使用具有原始版权的软 件，以防止病毒感染。 注意 如果是从 SCIEX 或 SCIEX 授权分销商之外的另一方购买的本产品，同时 目前也不在 SCIEX 服务维护协议的范围内，则 SCIEX 不能担保该产品具 有最新的强制性工艺修订，也不能担保用户可获得有关该产品的最新信息 公告。如果您从第三方购买了此产品且想要了解这方面的更多信息，请联 系您的 SCIEX 代表。 User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 25 / 376...

  • Page 26: 活动部件或尖锐物

    合 21 CFR 1040 的适用要求。激光束 不可见。 CLASS 1 LASER PRODUCT THIS PRODUCT CONFORMS TO APPLICABLE REQUIREMENTS OF 21 CFR 1040 AT THE DATE OF MANUFACTURE. MANUFACTURED: 726024-C A016350L EPS CESI 8000 Plus High Performance Separation-ESI Module User Manual 26 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 27: 化学品注意事项

    • 当工作中用到易燃材料，如异丙醇、甲醇和其他易燃溶剂时，请避免火源。 • 要小心地使用和处置任何化学品。 如果不遵循处理和处置化学品的适当程序，就 会存在人身伤害的潜在风险。 • 清洗过程中应避免皮肤接触化学品，使用后洗手。 • 请遵守关于生物危害性、有毒或放射性物质的存储、处理和处置的所有当地法 规。 • 此产品的灯含汞。 请勿混入垃圾。 请遵照当地、州/省或联邦法律进行回收或处 置。 安全符号和标签 高压电击危险符号 此符号表示存在高电压和电击危险，并且操作员进入此区域时应小心操作。 注意安全符号 此符号提示您注意阅读重要信息，或者与另一符号结合表明存在特定的安全隐患。信 息位于符号标签上，或者在 CESI 8000 Plus 文档中。 User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 27 / 376...

  • Page 28: 尖锐物标签

    用水和有毒物质强制法令》(California Safe Drinking Water and Toxic Enforcement Act) 提 出 （通常称为 65 号提案 (Proposition 65)，加利福尼亚州颁布） 。有害化学物质的完整 列表请访问： www.P65Warnings.ca.gov. RoHS 通知 这些标签和材料声明表 （有害物质的名称和含量表）必须符合中华人民共和国电子行 业标准 SJ/T11364-2006 《电子信息产品污染控制标识要求》中的要求。 CESI 8000 Plus High Performance Separation-ESI Module User Manual 28 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 29: 中国 Rohs 警告标签

    与用户自行执行的操作过程有关。本手册中，与特定操作过程相关的各种风险可能使 用这些标签和符号，详见该任务操作过程中的“警告”或“注意”部分。 环保标签 (WEEE) 按照欧盟报废电子电气设备 (WEEE) 指令要求，产品上必须标有带叉的有轮垃圾桶符 号。 产品上出现该标志，说明： • 该设备是在 2005 年 8 月 13 日以后投放欧洲市场的，并且 • 设备将不通过欧盟的任何成员国的市政废物收集系统进行处置。 遵循当地城市废物法规条例中的合适处理规定，减少 WEEE （废电子电机设备）对环 境的影响。 为了安全地处理设备，请联系当地的客户服务部进行免费的仪器上门回 收。 User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 29 / 376...

  • Page 30: 处理包含加汞组件的设备

    解并遵守对含加汞组件 （开关、灯、电池、继电器或电极）设备的安全正确处理规定 至关重要。加汞组件指示器标签可能发生变化，具体取决于设备的类型。 CE 标志标签 标志– “CE”标志表示产品上市前经过评估，并已被认定符合欧盟安全、健康和/或环境 保护要求。 RCM 标志标签 RCM 标 记用于符合澳大利亚通信媒体管理局 (ACMA) EMC 要求。 CSA 标识标签 CESI 8000 仪器上的 CSA 符号表明，该仪器被国家认可测试实验室 (NRTL) 认证为符合适 用的美国和加拿大实验室设备安全标准。 CESI 8000 Plus High Performance Separation-ESI Module User Manual 30 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 31: Sécurité, Consignes Et Étiquettes

    Présentation Dans cette section, il est possible de trouver une description des symboles et des étiquettes utilisés sur le Module de séparations hautes performances SCIEX CESI 8000 Plus, ou qui sont indiqués dans ce manuel. N’essayez pas d’exécuter une procédure avant d'avoir lu attentivement toutes les instructions.

  • Page 32: Alertes « Avertissement, Mise En Garde, Important Et Remarque

    NOTE Sert à attirer l’attention sur des informations importantes dont il convient de tenir compte lors de l’installation, l’utilisation ou l'entretien de cet équipement. CESI 8000 Plus High Performance Separation-ESI Module User Manual 32 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 33: Précautions De Sécurité Pour L'instrument

    • Cet équipement est utilisé d’une manière autre que celle spécifiée Utilisez cet instrument conformément aux instructions des manuels du produit. • Vous installez un logiciel non autorisé par SCIEX sur votre ordinateur. N’utilisez l’ordinateur de votre système qu’avec des logiciels agréés par SCIEX.

  • Page 34: Pièces Mobiles Ou Objets Tranchants

    Sécurité, Consignes et étiquettes CAUTION Si vous avez acheté ce produit ailleurs que chez SCIEX ou un distributeur SCIEX autorisé, et s’il ne fait pas l’objet d’un contrat de maintenance SCIEX, SCIEX ne peut garantir que le produit a bénéficié des toutes dernières révisions techniques obligatoires ou que vous recevrez les bulletins d’information les...

  • Page 35: Sécurité Laser (Pour Les Appareils Avec Laser En Option)

    FABRICATION » se situe à proximité de l'étiquette signalétique. Le faisceau laser n'est pas visible. CLASS 1 LASER PRODUCT THIS PRODUCT CONFORMS TO APPLICABLE REQUIREMENTS OF 21 CFR 1040 AT THE DATE OF MANUFACTURE. MANUFACTURED: 726024-C User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 35 / 376...

  • Page 36: Précautions Chimiques

    Symbole « Haute tension, risque de choc électrique » Ce symbole indique la présence de haute tension et d'un risque de choc électrique, et l'opérateur doit faire preuve de précautions lors de l'accès à cette zone. CESI 8000 Plus High Performance Separation-ESI Module User Manual 36 / 376...

  • Page 37: Symbole De Sécurité Attention

    Ce symbole attire l'attention sur des informations importantes à lire, ou est accompagné d'un autre symbole indiquant un danger particulier pour la sécurité. Les informations se trouvent soit sur l'étiquette avec le symbole ou dans la documentation du CESI 8000 Plus. Étiquette Objet tranchant Ce symbole indique la présence d'objets tranchants et l'opération doit faire preuve de...

  • Page 38: Consignes Rohs

    être indiqués par ces étiquettes et symboles et sont précisés dans les Mises en garde ou les Avertissements dans les procédures décrivant la tâche. CESI 8000 Plus High Performance Separation-ESI Module User Manual 38 / 376...

  • Page 39: Étiquette De Recyclage (Weee)

    Marque CE - La marque « CE » indique qu’un produit a été évalué avant d’être placé sur le marché et qu’il a été jugé comme répondant aux exigences de l’Union européenne en matière de sécurité, de santé et/ou de protection de l’environnement. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 39 / 376...

  • Page 40: Étiquette Marque Mrc

    Nationally Recognized Testing laboratory (NRTL - laboratoire national d’essai reconnu) aux Normes sur la sécurité de l’équipement de laboratoire pour les États-Unis et le Canada. CESI 8000 Plus High Performance Separation-ESI Module User Manual 40 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 41: System Overview

    • A photo diode array (PDA) detector that is in the 190 nm to 600 nm range. • A laser-induced fluorescence (LIF) detector that permits high-sensitivity analysis of labeled molecular species. For instructions on using the UV, PDA, or LIF detector, go to the SCIEX web site at www.sciex.com and then click Products >...

  • Page 42: Introduction

    CE in an ultra low-flow format that enhances the sensitivity of mass spectrometry while reducing ion suppression. Within the CESI 8000 Plus system, sample components are separated by an electrical field that is applied between the inlet vial and the OptiMS sprayer (Figure 4.1).

  • Page 43: Instrument

    System Overview This manual will describe the major components of the CESI 8000 Plus system with OptiMS technology, and common procedures such as installation, integration with mass specs, as well as the more commonly used software procedures. Appendices describe care and maintenance of CESI 8000 Plus components, and corrective actions for specific problems that may occur.

  • Page 44: Sample Handling System

    High voltage (HV) from the mass spectrometer connects to the current monitor circuit on the CESI 8000 Plus system through the input HV cable. An output cable delivers the voltage from the outlet side of the current monitor circuit to the OptiMS capillary, required for the electrospray.
  • Page 45 Wear protective eyewear, lab coat, and gloves when opening the sample cover. The CESI-MS vials are pressurized during rinse and separation-with-pressure events. To reduce the risk of breakage and expelled particles, use only SCIEX vials designed for the CESI 8000 Plus system (PN B11648). Inspect every vial for damage before use.

  • Page 46: Syringe Pump, Power Supply, Leds And Interlock

    Syringe Pump, Power Supply, LEDs and Interlock Syringe Pump The CESI 8000 Plus system can generate pressures with an internal pump mechanism. This pump can supply 0.1 psi to 25 psi to perform pressure injections or low-pressure mobilizations. The pump can apply a maximum of 100 psi to move the fluids through the capillary. The pressure can...

  • Page 47: Cartridge And Sample Cover Interlocks

    System Overview Cartridge and Sample Cover Interlocks The hinged doors of the CESI 8000 Plus system have interlock sensors that prevent unsafe access to the inside of the instrument. The outer door is called the sample cover; the second inner door is called the cartridge cover.

  • Page 48: Optims Cartridge

    4.8). These capillaries are shrouded at the inlet ends by protective covers which automatically retract when the OptiMS cartridge is installed in the CESI 8000 Plus system. The spray end (5) is made of PEEK, which is a high performance plastic material that has been tested and proven to be inert under CESI-MS conditions.
  • Page 49 OptiMS cartridge is installed in the CESI 8000 Plus system. The locking mechanism will not retract if the OptiMS cartridge is not installed on the CESI 8000 Plus system.
  • Page 50 System Overview • OptiMS adapter for SCIEX mass spectrometer (Figure 4.10) Figure 4.10 Adapter for SCIEX Nanospray® III Ion Source 1. HV Input Cable 2. HV Output Cable • OptiMS adapter for Thermo Scientific mass spectrometer (Figure 4.11) Figure 4.11 Adapter for Thermo Scientific NanoSpray II ion source 1.

  • Page 51: Integrating The Cesi 8000 Plus System With A Mass Spectrometer

    Integrating the CESI 8000 Plus System with a Mass Spectrometer CESI-MS Integration Procedures This chapter discusses the integration of the CESI 8000 Plus system with the following mass spectrometers: • Thermo Scientific LTQ mass spectrometer series • Thermo Scientific Q Exactive mass spectrometer ®...
  • Page 52 WARNING To prevent a shock hazard, do not touch the mass spectrometer adapter when connected to the CESI 8000 Plus system and the separation voltage is on. CESI 8000 Plus High Performance Separation-ESI Module User Manual 52 / 376...

  • Page 53: Cesi 8000 Plus System: Installing Optims Cartridge

    Integrating the CESI 8000 Plus System with a Mass Spectrometer CESI 8000 Plus System: Installing OptiMS Cartridge The OptiMS interface plate must be installed onto a CESI 8000 Plus system before an OptiMS cartridge can be installed. Refer to Removing and Re-installing OptiMS Interface Plate...
  • Page 54 Integrating the CESI 8000 Plus System with a Mass Spectrometer To install the cartridge body, sit the cartridge’s ends on the aligning blocks of the OptiMS interface plate at a 45 degree angle, and lightly push it in (Figure 5.3).
  • Page 55 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.4 Pivot Cartridge Upwards and Align onto Interface Plate 1. Align “T” Slider into the Groove Figure 5.5 Slide Cartridge All the Way Down 1. Capillaries (appear beneath interface block and within the ejectors)
  • Page 56 Integrating the CESI 8000 Plus System with a Mass Spectrometer Route coolant and capillary tubing through the notched arm (Figure 5.6). Figure 5.6 Routing Coolant and Capillary Tubing Bring the lock down bar to the front of the cartridge and secure cartridge in place by...

  • Page 57: Thermo Scientific Mass Spectrometer: Integration With The Cesi 8000 Plus System

    Ensure that both the CESI 8000 Plus system and controller are connected to electrical power. Connect the GPIB-USB cable to the connector labeled “Controller” on the CESI 8000 Plus system. Plug the other end of the GPIB-USB cable to a USB port on the CESI 8000 Plus controller (Figure 5.8).
  • Page 58 Integrating the CESI 8000 Plus System with a Mass Spectrometer Connect the relay cable to the relay input (labeled I/O) on the CESI 8000 Plus system. Connect the other end of the relay cable to the Thermo Scientific mass spectrometer relay...

  • Page 59: Optims Cartridge Sprayer Tip Installation Into A Thermo Scientific Nanospray Ii Ion Source

    To prevent a shock hazard, ensure that the MS ESI voltage is set to zero and idle. The CESI 8000 Plus system separation voltage should be off. Prior to installing the NanoSpray II ion source, ensure the 1-inch adapter ring is not installed (Figure 5.11).

  • Page 60: Scientific Nanospray Ii Ion

    Integrating the CESI 8000 Plus System with a Mass Spectrometer Additionally, ensure the ion sweep cone has been removed from the mass spectrometer (Figure 5.12). CAUTION The ion sweep cone may be hot. Care must be taken when manipulating it.
  • Page 61 Integrating the CESI 8000 Plus System with a Mass Spectrometer WARNING It is critical to perform Step 2 prior to installation of the adapter. During the installation of the OptiMS spray assembly, the glass tip of the OptiMS sprayer will be exposed. If the ion source stage is too close to the mass spectrometer inlet, then damage to the tip may result.
  • Page 62 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.15 Adapter for Thermo Scientific Mass Spectrometer in Place 1. Thumbscrew 2. Adapter (in place) Remove protective sleeve from OptiMS sprayer’s tip (Figure 5.16). IMPORTANT Save the protective sleeve. It will be needed if the OptiMS cartridge has to be removed and/ or stored for later use.
  • Page 63 WARNING To prevent a shock hazard, ensure that the MS ESI voltage is set to zero and idle. The CESI 8000 Plus system separation voltage should be off. Figure 5.18 HV Cable to Mass Spectrometer Input Cable (Cable-to-Cable) Connection User Manual...
  • Page 64 Integrating the CESI 8000 Plus System with a Mass Spectrometer To expose the HV connectors, slide open the door located on the lower-left corner of the right-side panel of the CESI 8000 Plus system (Figure 5.19). Connect the black ground banana plug from the cable to the matching black receptacle on the panel.

  • Page 65: Establishing Communication Between The Cesi 8000 Plus Controller And The Thermo Scientific Mass Spectrometer

    Integrating the CESI 8000 Plus System with a Mass Spectrometer WARNING To prevent a shock hazard, install the HV Input and Output cables and then check the connections at both ends before turning on the CESI 8000 Plus system. Figure 5.20 High Voltage Panel Connections 1.

  • Page 66: Aligning The Cesi 8000 Plus System With A Thermo Scientific Mass Spectrometer

    Aligning the CESI 8000 Plus System with a Thermo Scientific Mass Spectrometer The level of the buffer vials in the CESI 8000 Plus system must be at the same level as the OptiMS cartridge sprayer tip. This will prevent hydrodynamic (siphoning) flow within the capillaries, which may affect CE-MS separation performance.
  • Page 67 Integrating the CESI 8000 Plus System with a Mass Spectrometer If necessary, use the knob shown in Figure 5.23 to retract the ion source stage all the way back so that the sprayer tip does not collide with the mass spectrometer when moving the stage.
  • Page 68 Integrating the CESI 8000 Plus System with a Mass Spectrometer WARNING It is critical to perform Step 1 prior to moving the CESI 8000 Plus cart towards the stage. This will avoid any potential damage to the tip of the OptiMS sprayer.
  • Page 69 Always press the height adjustments buttons one at a time, never simultaneously. IMPORTANT If the CESI 8000 Plus cart will not power to its lowest height, or if it becomes stuck, then the cart must be re-programmed. Refer to the...
  • Page 70 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.26 Cart Height Adjustment Buttons 1. Cart Up Button 2. Cart Down Button Use the mass spectrometer alignment knobs to make fine adjustments to align the OptiMS sprayer tip to the center of the source inlet on the mass spectrometer (Figure 5.27).

  • Page 71: Sciex Tripletof ® 5600 Mass Spectrometer: Integration With The Cesi 8000

    Integrating the CESI 8000 Plus System with a Mass Spectrometer When the CESI 8000 Plus system is visually aligned to the mass spectrometer, lock the wheels on the CESI 8000 Plus cart by stepping on the locking lever at each caster (Figure 5.28).
  • Page 72 Integrating the CESI 8000 Plus System with a Mass Spectrometer Connect the GPIB-USB cable to the connector labeled “Controller” on the CESI 8000 Plus system. Use spacer if needed. Plug the other end of the GPIB-USB cable to a USB port on the...

  • Page 73: Optims Cartridge Sprayer Tip Installation Into The Sciex Nanospray

    To prevent a shock hazard, ensure that the MS ESI voltage is set to zero and idle. The CESI 8000 Plus separation voltage should be off. To install the mass spectrometer spray end of the OptiMS cartridge into the SCIEX Nanospray® III source, perform the following steps: Install the SCIEX Nanospray®...
  • Page 74 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.32 Pulling Back the SCIEX Assembly WARNING It is critical to perform Step 2 prior to installation of the adapter. During the installation of the OptiMS spray assembly, the glass tip of the OptiMS sprayer will be exposed.
  • Page 75 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.33 Orientation of the Adapter Prior to Installation onto the Ion Source 1. High Voltage (HV) Output Cable ® 3. SCIEX Nanospray III Adapter 2. Hook 4. SCIEX Nanospray ®...
  • Page 76 Integrating the CESI 8000 Plus System with a Mass Spectrometer Remove protective sleeve from the OptiMS sprayer tip (Figure 5.35). IMPORTANT Save the protective sleeve. It will be needed if the OptiMS cartridge has to be removed and/ or stored for later use.
  • Page 77 Integrating the CESI 8000 Plus System with a Mass Spectrometer The OptiMS has a locking mechanism which keeps the OptiMS Spray Assembly securely attached to the adapter. Twist the OptiMS sprayer assembly counter clockwise (Figure 5.37) to lock it into place within the adapter.
  • Page 78 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.38 CESI 8000 Plus System HV Panel WARNING To prevent a shock hazard, ensure that the MS ESI voltage is set to zero and idle. The CESI 8000 Plus separation voltage should be off.
  • Page 79 Connect the red banana ground plug into the matching red receptacle on the panel. Connect the HV cable from the mass spectrometer ion source into the input connection on the CESI 8000 Plus HV panel, and twist 90 degrees clockwise to lock it in place (Figure 5.39 Figure 5.40).

  • Page 80: Establishing Communication Between The Cesi 8000 Plus Controller And The Sciex Mass Spectrometer

    Integrating the CESI 8000 Plus System with a Mass Spectrometer Establishing Communication Between the CESI 8000 Plus Controller and the SCIEX Mass Spectrometer The CESI 8000 Plus controller (PC) communicates with the SCIEX mass spectrometer using an Ethernet cable (Figure 5.30).

  • Page 81: Aligning The Cesi 8000 Plus System With The Sciex Tripletof

    5600 Mass Spectrometer The level of the buffer vials in the CESI 8000 Plus system must be at the same level as the OptiMS cartridge sprayer tip. This will prevent hydrodynamic (siphoning) flow within the capillaries, which may affect CE-MS separation performance. This leveling is done by aligning the height indicator line on the CESI 8000 Plus system with the OptiMS sprayer tip placed at the mass spectrometer adapter.
  • Page 82 Integrating the CESI 8000 Plus System with a Mass Spectrometer Figure 5.43 Move Stage All the Way Back 1. Coarse Z-axis Adjustment Knob 2. Stage IMPORTANT Make sure that the Source Drain assembly on the mass spectrometer is covered. The...
  • Page 83 If the ion source stage is too close to the mass spectrometer inlet, then damage to the tip may result. Move the CESI 8000 Plus cart close, approximately 4 inches (10 cm.) to the ion source stage so that the OptiMS coolant tubes can be fully extended (Figure 5.45).
  • Page 84 Always remove consumable before adjusting the CESI 8000 Plus cart height. Use the up and down height-adjustment buttons on the front of the cart to adjust the height of the cart until the height indicator on the CESI 8000 Plus system is aligned to the OptiMS sprayer tip (Figure 5.47).
  • Page 85 Always press the height adjustments buttons one at a time, never simultaneously. IMPORTANT If the table top of the CESI 8000 Plus cart will not power to its lowest height, or if it becomes stuck, then the cart must be re-programmed. Refer to the...
  • Page 86 When the CESI 8000 Plus system is in visual alignment to the mass spectrometer, lock the wheels on the CESI 8000 Plus cart. This is done by stepping on the locking lever at each caster to lock each wheel in place (Figure 5.49).

  • Page 87: 32 Karat Software Overview

    The 32 Karat software is a full-featured chromatography and capillary electrophoresis software package that provides control of the CESI 8000 Plus system. For the CESI 8000 Plus user, there is no electrophoretic data collected by the 32 Karat software. Only voltage, electrical current, pressure, and power data traces can be collected.

  • Page 88: Controller And Instrument Start Up

    If the instrument is installed on a network, the user name and password will be supplied by the network administrator. 32 Karat software functionality is different when run on a network CESI 8000 Plus High Performance Separation-ESI Module User Manual...

  • Page 89: License Key

    Service Support selection. Instrument Start Up The software can only control the CESI 8000 Plus system after it has completed its startup initialization process. Before starting the CESI 8000 Plus system: • Make sure the cartridge is installed.

  • Page 90: Instruments And Projects

    An instrument is opened online by double-clicking the instrument icon. Open Offline To open an instrument offline, right-click the instrument icon and select CESI 8000 Plus High Performance Separation-ESI Module User Manual 90 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 91: Using The Direct Control Window To Load The Cartridge And Samples

    Using the Direct Control Window to Load the Cartridge and Samples Direct Control Control can be selected from the menu (Figure 6.5). Figure 6.5 Control Menu for Direct Control User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 91 / 376...
  • Page 92 (Figure 6.8). Figure 6.8 Direct Control Window Load Select to move the trays to the front of the sample compartment. CESI 8000 Plus High Performance Separation-ESI Module User Manual 92 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 93: Tripletof ® 5600 Mass Spectrometer Using Aao

    ® ® communicate with the Analyst TF software used by the controller of the SCIEX TripleTOF 5600 mass spectrometer. If AAO is being used, the Direct Control window will display an icon that indicates the mass spectrometer status of the AAO interface (Figure 6.9).

  • Page 94: Methods And Sequences

    ® For AAO configurations (such as for the SCIEX TripleTOF 5600 mass spectrometer), the relay event will echo back to the software to send the start acquisition command through the AAO interface.

  • Page 95: Creating And Editing A Method

    CESI 8000 Software Online Help. Instrument Setup — Initial Conditions Initial Conditions tab is used to set instrument parameters at the start of a method, before the separation begins. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 95 / 376...
  • Page 96 Wait for external trigger a run. These are selected by selecting the appropriate box. If is selected, the CESI 8000 Plus system becomes a slave device and does not start until an external signal is Wait for temperature received. The two options assure that the system has reached the correct operating temperature before beginning a run.

  • Page 97: Instrument Setup - Time Program

    Some events do not have a time option, others can be timed or untimed. Collection of voltage and current data begins with the first User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 97 / 376...

  • Page 98: Separate Dialog

    Figure 6.12 Time Program Event List The following dialogs and field definitions are the ones that should be more commonly used by the CESI 8000 Plus user. For information on more advanced event types, refer to the CESI 8000 Software Online Help.
  • Page 99 Figure 6.14 Tray Selection Dialog User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 99 / 376...

  • Page 100: Rinse Dialog

    The inject event is used to deliver a precisely measured amount of sample into the capillary (Figure 6.16). This step is always untimed, and usually precedes the first separation step. CESI 8000 Plus High Performance Separation-ESI Module User Manual 100 / 376...
  • Page 101 The Allow Override box must be checked in the Sequence Table area (in Figure 6.16) to give the sequence parameters priority over the method parameters. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 101 / 376...

  • Page 102: Stop Data

    For example, type: TestMethod_111518 Click Save C:\32Karat\Projects\Default\Methods The default path at installation is: Your system administrator may have assigned you to a different default path. CESI 8000 Plus High Performance Separation-ESI Module User Manual 102 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 103: Overview Of Creating A Sequence

    Sequence mode is used to append multiple methods together as a sequence. The CESI 8000 Plus system must be online to run samples and acquire data. If you are not online, “offline” appears in the title bar of the instrument window. Close any offline windows before proceeding.

  • Page 104: Programming A Sequence

    , select For Acquisition . Amount Values are not used in this example. Next Click . The Sequence Wizard — Unknowns page displays (Figure 6.21). CESI 8000 Plus High Performance Separation-ESI Module User Manual 104 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 105 Data Path Click the green folder icon, and select , then navigate to the folder. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 105 / 376...
  • Page 106 Number of Unknown Runs in Sequence fields. Next Click . The Sequence Wizard — Vials page displays (Figure 6.24). Figure 6.24 Sequence Wizard — Vials Page CESI 8000 Plus High Performance Separation-ESI Module User Manual 106 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 107 Figure 6.25 Sequence Wizard — Reports Page This page (Figure 6.25) allows you to have reports generated automatically at the end of the sequence run. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 107 / 376...

  • Page 108: Sequence Table

    1, rep 2, etc., appended to the file name. Sample Inject Inlet — Indicates the vial the sample is being injected from if sample is located in the inlet tray. CESI 8000 Plus High Performance Separation-ESI Module User Manual 108 / 376...

  • Page 109: Sequence Validation

    32 Karat Software Overview Sample Inject Outlet — Indicates the vial the sample is being injected from if sample is located in the outlet tray. In the CESI 8000 Plus system the sample is always located in the inlet sample tray.
  • Page 110 32 Karat Software Overview CESI 8000 Plus High Performance Separation-ESI Module User Manual 110 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 111: Cesi 8000 Software

    32 Karat software, the CESI 8000 software has been developed with the routine user in mind. The CESI 8000 software steps the instrument operator through the tasks of running methods and sequences on the CESI 8000 Plus system. Routine users often receive Standard Operating Procedures detailing separation methods, sequences, and report templates developed in the 32 Karat software by method developers.

  • Page 112: Launching The Cesi 8000 Software

    CESI 8000 Software Launching the CESI 8000 Software Launch the CESI 8000 software by double-clicking the CESI 8000 Plus icon on the Windows desktop. The Ready window appears as shown in Figure 7.1. The upper right buttons activate the major functions. Hover the mouse over the buttons to obtain a balloon tip regarding function.

  • Page 113: Login And Logout

    Figure 7.2 Login Dialog NOTE If 32 Karat software security is configured to use the Domain controller, then the system will also prompt for the Domain name. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 113 / 376...

  • Page 114: Lock And Unlock

    When the CESI 8000 software is locked, other users will still be able to access other programs (such as the 32 Karat software) on the system. About Dialog To view the software versions for the CESI 8000 Plus, 32 Karat, and the instrument firmware Copy Version versions, select .

  • Page 115: Run Application

    • Application Selection • Samples and Vials • Run Acquisition Application Selection The first step of Run Application is to select an application (Figure 7.3). User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 115 / 376...
  • Page 116 Instead of using the 32 Karat button in this instance, use the “Show 32 Karat” button at the center bottom of the dialog. CESI 8000 Plus High Performance Separation-ESI Module User Manual 116 / 376...
  • Page 117 (bring the trays into the Home or Load position). Click Next or select to prepare the samples and vials for the selected application, see Samples and Vials. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 117 / 376...

  • Page 118: Samples And Vials

    The tray detail for the method is shown. To set up a sequence, see Sequence Dialog. Figure 7.7 Method Setup Window CESI 8000 Plus High Performance Separation-ESI Module User Manual 118 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 119 A dialog will appear to confirm that the samples are loaded. Verify that they are loaded, and Yes - run now select to start the run, see Acquisition. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 119 / 376...

  • Page 120: Insert Option

    Figure 7.9 Insert Sample ID Dialog Figure 7.10 Insert Data File Dialog Options for the Sample ID (Figure 7.9) or Data File (Figure 7.10) dialogs include: CESI 8000 Plus High Performance Separation-ESI Module User Manual 120 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 121: Sequence Dialog

    Describe Sequence dialog by selecting . If the sequence is modified and saved in the Describe Sequence dialog, select Reload Sequence to reload the described sequence. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 121 / 376...
  • Page 122 Describe Sequence. NOTE When a particular run is selected, the vials used in the run are highlighted in the tray view. CESI 8000 Plus High Performance Separation-ESI Module User Manual 122 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 123: Sequence Table Rows

    — Never hidden and always run, regardless of the number of samples (Figure 7.13). NOTE When the number of samples is set to 0, all rows are hidden except for rows set to Always. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 123 / 376...
  • Page 124 CESI 8000 Software Figure 7.12 Sequence with All 9 Samples Figure 7.13 Sequence with No Samples (All Rows Hidden) CESI 8000 Plus High Performance Separation-ESI Module User Manual 124 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 125 7.14) to four (Figure 7.15). Hidden rows that are not run can be shown by right-clicking the sequence and selecting Show Hidden Rows (Figure 7.16 Figure 7.17). User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 125 / 376...
  • Page 126 Figure 7.17 Sequence with Four Samples and Hidden Rows For more information on setting row types, see Step 6 of Describe Sequence. For more information on the number of samples see Sequence Dialog. CESI 8000 Plus High Performance Separation-ESI Module User Manual 126 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 127: Fill Down Option

    — (Data File only) The current Sample ID for the Data file. Sample ID • — The current user logged into the application. User Name User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 127 / 376...

  • Page 128: Display Options

    Vial Legend. NOTE The vial legend can be shown or hidden from the Display Options menu or by clicking the button highlighted in Figure 7.21. CESI 8000 Plus High Performance Separation-ESI Module User Manual 128 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 129: Vial Legend

    Vial Contents). From this dialog, the user can view, export, or print the current trays. The vials can be viewed as circles or rectangles. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 129 / 376...

  • Page 130: Vial Preview

    Cycle number is the number of times that the specific method has been run. This window is used to show tray collisions (marked in red). Figure 7.23 Sequence Vial Preview CESI 8000 Plus High Performance Separation-ESI Module User Manual 130 / 376...

  • Page 131: Run Acquisition

    The left-hand panel has three tables to show different levels of detail about a method or sequence. The Run Queue table is used to verify that the run initiated in CESI 8000 Plus system is in the 32 Karat software Run Queue. If a sequence is running, the Sequence Run table will show which row of the sequence is currently running.
  • Page 132 Start Now to cancel the waiting and start the run. Click Stop to abort the scheduled run, and the system state will switch to Run Aborted CESI 8000 Plus High Performance Separation-ESI Module User Manual 132 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 133: Sciex Tripletof ® 5600 Mass Spectrometer Using Aao

    Mass spectrometer interface is Offline or Disconnected. Mass spectrometer is on Standby, Stopping, Paused, Unknown or AAO driver connection failed. Mass spectrometer is Ready. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 133 / 376...

  • Page 134: Graph Options

    (select to help distinguish between the traces). • — Changes the line thickness of the trace. Thin Lines CESI 8000 Plus High Performance Separation-ESI Module User Manual 134 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 135: Sequence Transfer Overview

    Passwords to ensure system security. The CESI 8000 software is optimized for use with a user- login enabled system. Sequence Transfer Define an Instrument for the Routine User Start the 32 Karat software and login as an Administrator. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 135 / 376...
  • Page 136 Define the Project for the Instrument Tools > System Administration Wizard Select In the System Administration wizard, select Project and then select Next CESI 8000 Plus High Performance Separation-ESI Module User Manual 136 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 137 Enter the User Name and Password, select Select Select Tools > System Administration Wizard User Next Select and select Select the User Name and select Next User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 137 / 376...
  • Page 138 Select the Domain and then enter the User Name. Select Check Names . Add the name to the Selected Users by selecting Next Select CESI 8000 Plus High Performance Separation-ESI Module User Manual 138 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 139 32 Karat project for routine use on existing systems. As a result, methods may already be in the project folder. Transfer the Sequences Copy the sequences into the project’s Sequence folder. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 139 / 376...
  • Page 140 Ensure that the methods are selected from the corresponding method folder for this project (Figure in the Sequence Run Table 7.29). Verify that any file paths in the Method column are correct. CESI 8000 Plus High Performance Separation-ESI Module User Manual 140 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 141: Describe Sequence

    The sequence will need to be re-described (using Describe Sequence) in order to vary the sample quantity. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 141 / 376...
  • Page 142 This example is for an instrument named QC001 and a 32 Karat project named QC001. Figure 7.31 Describe Sequence Start Dialog Application In the field, select the application. In the Sequence field, select the sequence to describe. CESI 8000 Plus High Performance Separation-ESI Module User Manual 142 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 143 Show hidden rows . For more information on how rows are hidden based upon the number of samples see Sequence Table Rows. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 143 / 376...

  • Page 144: Sequence Verification

    • Program Event — Changes the view of the trays to show the action performed on the vial (for example, separation, rinse, sample inject, etc.). CESI 8000 Plus High Performance Separation-ESI Module User Manual 144 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 145 Show Vial Preview — Opens a table to preview the methods and vials used in the method/ sequence and shows tray collisions, see Vial Preview. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 145 / 376...
  • Page 146 CESI 8000 Software CESI 8000 Plus High Performance Separation-ESI Module User Manual 146 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 147: Using A Sciex Tripletof 5600 Mass Spectrometer With The Cesi 8000 Plus System

    Stock Reagents and Other Consumables Required • Preparation of Reagent Solutions and Test Sample • Procedure for Installation of Adapter and OptiMS Cartridge • Methods for the CESI 8000 Plus System • Capillary Conditioning • Establishing a Stable Spray and Determining Optimum ESI Voltage •...

  • Page 148: Stock Reagents And Other Consumables Required

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System The workflow is as follows: Before you start, ensure you have all the required reagents properly prepared. Description and preparation protocols can be found in the next section.

  • Page 149: Preparation Of Reagent Solutions And Test Sample

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Table 8.2 Materials (Continued) Consumables Vendor Part Number 50 mL volumetric flask 20 mL glass bottle 100 mL glass bottle pH meter Table top mini centrifuge...

  • Page 150: Preparation Of 10% (V/V) Hac-Background Electrolyte (Bge)

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Preparation of 10% (v/v) HAc—Background Electrolyte (BGE) NOTE This solution must be prepared fresh every day. IMPORTANT Sonicate in a water bath for 30 minutes prior to use.

  • Page 151: Reconstitution Of 1 Μm Beta-Galactosidase Digest Solution (Beta-Galactosidase Stock Solution)

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Adjust the pH of the solution to 4.0 by adding aliquots of freshly prepared 20% HAc. Transfer the solution into a clean 100 mL volumetric flask.

  • Page 152: Preparation Of Beta-Galactosidase For Auto-Calibration

    CESI 8000 Plus methods described in this chapter. NOTE Use only CESI-MS vials and CESI-MS caps in the CESI 8000 Plus system buffer and sample trays. Table 8.4 provides the vial content, quantity, and volume for capillary conditioning beta- galactosidase auto-calibration, manual calibration, and system test methods.

  • Page 153: Sample Tray Setup

    The sample tray setup is described in this section. It is important to follow the specific location for each sample as they match the CESI 8000 Plus methods described in this chapter. The beta-galactosidase sample used for the auto-calibration and the beta-galactosidase sample...

  • Page 154: Procedure For Installation Of Adapter And Optims Cartridge

    For installation instructions for the adapter and the OptiMS cartridge, refer to CHAPTER 5, Integrating the CESI 8000 Plus System with a Mass Spectrometer within this manual. Prior to inserting the OptiMS sprayer into the adapter, ensure the positioning stage is aligned as...

  • Page 155: Methods For The Cesi 8000 Plus System

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.4 Pull back Positioning Stage from the SCIEX Mass Spectrometer For additional information, refer to the OptiMS Cartridge Sprayer Tip Installation into the SCIEX Nanospray® III Source...
  • Page 156 The CESI-MS Separation (beta-galactosidase) is a method used to inject and separate a beta- galactosidase control sample by CESI-MS. This method is used to ensure both the CESI 8000 Plus ®...
  • Page 157 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System The time program for all 5 methods differ in a variety of steps; Figure 8.6 through Figure 8.8 show how each time program is set. Figure 8.6 shows the time program settings for the CESI-MS Capillary Conditioning method.
  • Page 158 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.7 shows the time program settings for the CESI-MS Auto-calibration method to be used in a batch run requiring auto-calibration. Figure 8.7 CESI-MS Auto-calibration_ABSciex Method Settings...

  • Page 159: Cesi-Ms Beta-Galactosidase System Performance Test

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System The CESI-MS Cleaning method used at the end of every sequence is shown in Figure 8.10. Refer APPENDIX F for detailed information. Figure 8.10 CESI-MS Cleaning Method Settings...
  • Page 160 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System IMPORTANT If creating a method from scratch, the following applies: 1. Synchronization Mode is set to No Sync. 2. Ensure that the Beckman CE Driver is present on the left pane under Acquisition Method.
  • Page 161 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Go to Advanced MS tab to enter other parameters (Figure 8.14). Figure 8.14 Parameter Settings for Advanced Mass Spectrometer Tab Click Product Ion (+) to enter the mass spectrometer parameters for Product Ion scan (Figure 8.15).

  • Page 162: Capillary Conditioning

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Click Edit Parameters , and a dialog for Source/Gas Compound will appear. Enter parameters in both tabs (Figure 8.16). Figure 8.16 Parameter Settings for Source/Gas and Compound tabs of Product Ion Scan Save the method as CESI_MS_AB_Sciex_Betagal_45min.dam...
  • Page 163 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Capillary conditioning is a procedure that must be performed when using an OptiMS Silica Surface Cartridge for the first time, and when using a cartridge that has been stored for a period longer than 3 days.
  • Page 164 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Click the icon to open 32 Karat software. Direct Control In 32 Karat software, click the icon on the toolbar (Figure 8.19). Figure 8.19 Direct Control Icon on the Toolbar...

  • Page 165: Establishing A Stable Spray And Determining Optimum Esi Voltage

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.21 Single Run Acquisition Dialog The CESI 8000 software will start the series of rinses and at the completion of the initial capillary conditioning method the OptiMS capillary cartridge is ready for the next step, establishing a stable spray.
  • Page 166 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System ® on the SCIEX TripleTOF 5600 mass spectrometer, refer to the Aligning the CESI 8000 Plus System ® with the SCIEX TripleTOF 5600 Mass Spectrometer section within CHAPTER 5 of this manual.
  • Page 167 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.24 Droplet at the Stainless Steel Needle End To fill the separation capillary with background electrolyte (10% Acetic acid) follow these two easy steps: Go to the Direct Control window, click...
  • Page 168 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.26 Droplet at the Tip of the Sprayer WARNING As droplets form at the end of the sprayer tip, ensure that are not aspirated into the mass spectrometer inlet. Do not position the sprayer tip closer than 2 mm from the curtain gas plate.
  • Page 169 However, CE-MS runs use a curtain gas value of 5. It has been set (factory setting) to 5 when the ® TripleTOF 5600 mass spectrometer is interfaced with CESI 8000 Plus mass spectrometer. User Manual CESI 8000 Plus High Performance Separation-ESI Module...
  • Page 170 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System From the Scan type list, select TOF MS , set the Accumulation time to 500 ms , and set the TOF 1500. 5 min Masses (Da) to Min.
  • Page 171 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System ® In the Analyst TF software, go to the Advance MS tab and check the box. Go back to the Accumulation time 1 (sec) Duration 5.00 min...

  • Page 172: Running Cesi-Ms

    Running CESI-MS ® This section provides a tutorial on the use of the CESI 8000 Plus system with the SCIEX TripleTOF 5600 mass spectrometer. The tutorial uses a tryptic digestion of beta-galactoside as the sample. The beta-galactosidase peptide digest is a standard mixture commonly used to evaluate mass spectrometer performance and it will be used here to evaluate the performance of the capillary separation as well.

  • Page 173: Create A Sequence In The Analyst

    This section provides step by step instructions on how to build a sequence of 10 runs of beta- ® galactosidase performance test on the TripleTOF 5600 mass spectrometer with auto-calibration every 5 runs in tandem with the CESI 8000 Plus system. In the navigation bar, under Acquire , double-click...
  • Page 174 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.33 Add Sample Dialog Click to close the Add Sample dialog and the Batch Editor opens again with all the Vial Position information entered. The...
  • Page 175 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.35 Batch Editor Window — Calibrate Tab View Click to ensure that the correct reference table is selected. There are 8 reference ions used for mass spectrometer calibration and the peptide at 729.3 m/z is selected for MS/MS calibration.

  • Page 176: Start A Sequence In The Analyst Tf Software

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System ® Start a Sequence in the Analyst TF Software Click Submit to submit the batch. This will submit the 10 beta-galactosidase separation runs with auto-calibration (Figure 8.37).

  • Page 177: Load Sample And Reagents On The Cesi 8000 Plus System

    The sample tray setup is described in this section. It is important to follow the specific location for each sample as they match the CESI 8000 Plus methods described in this chapter. The beta- galactosidase sample used for the auto-calibration and the beta-galactosidase sample used for...
  • Page 178 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System IMPORTANT Samples are likely to evaporate over time. It is recommended to use a minimum of 50 μL of sample for a sequence with a duration of approximately 24 hours. If the duration of the sequence is over 50 hours, a minimum volume of 80 μL is strongly recommended.

  • Page 179: Create A Sequence In The Cesi 8000 Software

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Create a Sequence in the CESI 8000 Software In the CESI 8000 software, go to Menu > Sequence > Sequence Wizard Sequence Wizard — Method Method...
  • Page 180 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Fill in the fields for the Sample ID Data path , and Data file . By clicking on the blue arrow next to the Data file field, a series of options come up to increment the file name. In this example,...
  • Page 181 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.43 Sequence Table IMPORTANT The autocal mix is always on sample inlet tray position A1, and in this example the sample is on position A2. Ensure that the sample position is designated properly in the sample table before submitting the sequence to run.
  • Page 182 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.45 Sample Sequence Example NOTE Auto-calibration data file names must be different. In the toolbar, go to Sequence > Properties . In the Sequence Properties dialog (Figure 8.46)

  • Page 183: Start A Sequence In The Cesi 8000 Software

    ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Start a Sequence in the CESI 8000 Software To run the sequence, click the Run Sequence icon and the Run Sequence dialog will appear Start (Figure 8.47).

  • Page 184: Automatic Rinse Feature

    20 kV. Automatic Rinse Feature The CESI 8000 Plus system makes use of an “Automatic Rinse” feature. In the event of a hardware failure during the rinse steps as well as the injection step, either during a method run or sequence run, the instrument will (without user intervention) rinse the separation capillary for 3 minutes at 50 psi from the first separation event vial position.

  • Page 185: Beta-Galactosidase Analysis

    (in 100 mM LE separated using 10% HAc as background electrolyte), is shown in Figure 8.49. * Ref. LC/MS Peptide/Protein Mass Standards Kit for Tuning of the AB SCIEX ESI Instrument Protocol. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF...
  • Page 186 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.49 Total Ion Chromatogram (TIC) Create the extracted ion chromatogram (XIC) for peaks 729.3652 m/z and 714.8469, both with a width of 0.05. IMPORTANT The peak range 729.3652 m/z and 714.8469 m/z may need to be adjusted based on the mass spectrometer mass calibration.
  • Page 187 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System Figure 8.50 Extracted Ion Chromatogram (XIC) and Mass Spectra for a Beta-Galactosidase Run User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 187 / 376...
  • Page 188 ® Using a SCIEX TripleTOF 5600 Mass Spectrometer with the CESI 8000 Plus System CESI 8000 Plus High Performance Separation-ESI Module User Manual 188 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 189: Using A Thermo Scientific Mass Spectrometer With The Cesi 8000 Plus System

    Procedure for Installation of Adapter and OptiMS Cartridge • Capillary Conditioning • Establishing a Stable Spray and Determining Optimum ESI Voltage • Tuning • Running CESI-MS The workflow is as follows: User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 189 / 376...

  • Page 190: Required

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Before you start, ensure you have all the required reagents properly prepared. Description and preparation protocols can be found in the next section. Stock Reagents and Other Consumables Required Table 9.1 Stock Reagents...

  • Page 191: Preparation Of 10% (V/V) Acetic Acid (Hac)-Background Electrolyte (Bge)

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Preparation of Reagent Solutions and Test Sample Table 9.3 Required Reagents Reagents Concentration 10% Acetic Acid (v/v) 10% HAc (v/v) Background electrolyte and conductive liquid 20% Acetic Acid (v/v)

  • Page 192: Preparation Of 20% (V/V) Acetic Acid (Hac) - For Le Buffer Ph Adjustment

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Preparation of 20% (v/v) Acetic Acid (HAc) — For LE Buffer pH Adjustment NOTE Prepare fresh and discard after use. Do not stock this solution. Add 80.0 mL of DDI water into a clean 100 mL glass bottle.

  • Page 193: Reconstitution Of 1 Μm Beta-Galactosidase Digest Solution

    A1, as shown Figure 9.1. Samples to be analyzed can be placed in other positions; however, these positions must be specified in the CESI 8000 Plus methods or manually specified in the test sequence. User Manual CESI 8000 Plus High Performance Separation-ESI Module...

  • Page 194: Cartridge

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System IMPORTANT Samples are likely to evaporate over time. It is recommended to use a minimum of 50 μL of sample for a sequence with a duration of approximately 24 hours. If the duration of the sequence is over 50 hours, a minimum volume of 80 μL is strongly recommended.

  • Page 195: Capillary Conditioning

    CESI 8000 Plus methods described in this chapter. NOTE Use only CESI-MS vials and CESI-MS caps in the CESI 8000 Plus system buffer and sample trays. Table 9.4 provides the vial content, quantity and volume needed for capillary conditioning, and system performance test methods.

  • Page 196: Procedure

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Table 9.4 Solution/Reagent Requirements Vial Content Quantity Volume DDI water 2 vials 1.5 mL 0.1 N NaOH 1 vial 1.5 mL 0.1 N HCl 1 vial 1.5 mL...
  • Page 197 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Prepare inlet and outlet buffer trays as shown in Figure 9.1. Then set the trays aside. Open the CESI 8000 software. Click the icon to open the 32 Karat software.

  • Page 198: Voltage

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Figure 9.6 shows the dialog for the single run. Under Run information field, confirm the method path and name are correct for capillary conditioning. It is not necessary to enter the sample ID nor data file name as no data file will be generated.
  • Page 199 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Prior to establishing a stable spray, it is important the sprayer tip position is optimized relative to the mass spectrometer inlet. For detailed information on how to adjust and align the sprayer...
  • Page 200 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System As the conductive liquid capillary fills with background electrolyte, a droplet is observed at the end of the stainless steel needle. After the rinse step completes, proceed to the next step to fill the separation capillary.
  • Page 201 Figure 9.10 Voltage Settings The CESI 8000 software electrical current should be around 2 mA to 3 mA. While the CESI 8000 Plus separation voltage is on, apply ESI voltage in increments of 100 V starting at 500 V. Monitor the Total Ion Count in the mass spectrometer software until ionization is detected.

  • Page 202: Tuning

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Once the OptiMS sprayer position has been optimized based on the stability of the TIC, the minimum ESI voltage is determined. Increase the ESI spray voltage by approximately 200 V. This is your optimal ESI voltage.

  • Page 203: Running Cesi-Ms

    CESI 8000 software. This sequence of events is very important because the mass spectrometer must be set up first so that it is waiting for the CESI 8000 Plus system to send the start signal, which will cause the mass spectrometer to User Manual...

  • Page 204: Software

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System start data acquisition. IMPORTANT Prior to attempting to run the beta-galactosidase sample, make sure the procedures for establishing a stable spray (refer to Establishing a Stable Spray and Determining Optimum ESI Voltage) and tuning (refer to Tuning) have been followed and successfully completed.
  • Page 205 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Figure 9.12 First Segment of a Method Used to Run Beta-Galactosidase Digest Test Sample The tune method for the segment shown in Figure 9.13 is set with optimized ESI voltage for a stable spray.
  • Page 206 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Figure 9.13 Second Segment of a Method Used to Run Beta-Galactosidase Digest Test Sample In the scan event settings, as illustrated in Figure 9.14, set the Data type...

  • Page 207: Software

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Create a Sequence with the Xcalibur Software The newly created beta-galactosidase mass spectrometer method should be programmed into a sequence. The sequence can be queued to start. The mass spectrometer will not begin to run the method until it receives a relay start trigger from the CESI 8000 software.

  • Page 208: Software

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Click , and the sequence table dialog will appear as shown in Figure 9.16. Start a Sequence with the Xcalibur Software Figure 9.16 Sequence Setup-Home Page Highlight row #1 corresponding to the sample to run, and then click the toolbar icon.

  • Page 209: System

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Status tab, which is also on the left pane, will show the status of the sequence. As the sequence is downloaded and queued, the status will change from...
  • Page 210 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Take the two buffer trays and place the vials with the reagents in the location as shown on Figure 9.17. Figure 9.17 Buffer Trays Inlet and Outlet for Beta-Galactosidase Separation Method Dispense the beta-galactosidase test sample into a micro vial, and place it inside of a CESI- MS vial.

  • Page 211: Software

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Create a Sequence in the CESI 8000 Software In the CESI 8000 Plus system, the sequence to run beta-galactosidase will be performed using a method with initial conditions and time program as illustrated in Figure 9.19...

  • Page 212: Automatic Rinse Feature

    20 kV. Automatic Rinse Feature The CESI 8000 Plus system makes use of an “Automatic Rinse” feature. If there is a hardware failure during the rinse steps and also the injection step, either during a method run or sequence run, the instrument will (without user intervention) rinse the separation capillary for 3 minutes at 50 psi from the first separation event vial position.

  • Page 213: Software

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Start a Sequence in the CESI 8000 Software Prior to starting a sequence, make sure that all reagents and sample required to run the experiment are in their appropriate place.

  • Page 214: Beta-Galactosidase Analysis

    Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Click Start Beta-Galactosidase Analysis This section provides an example of beta-galactosidase analysis. From all 150 peptide fragments of beta-galactosidase detected, the 729 and 714 m/z will be used to evaluate the system performance.
  • Page 215 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System Figure 9.24 Example of a Typical Beta-Galactosidase Total Ion Chromatogram Change the view from TIC (total ion chromatogram) to Base Peak Chromatogram. Configure the Base Peak Chromatogram in order to view the following two peaks: 714 and 729.
  • Page 216 Using a Thermo Scientific Mass Spectrometer with the CESI 8000 Plus System IMPORTANT The peak range 714.5 to 714.7 and 729.2 to 729.4 may need to be adjusted based on the mass spectrometer mass calibration. Figure 9.25 Identification and Clear Separation of the Beta-Galactosidase 714 and 729 m/z...

  • Page 217: Shutdown And Decoupling Overview

    Cartridge Removal and Instrument Shutdown To remove the OptiMS cartridge from the CESI 8000 Plus system, make sure that the MS ESI voltage is off and then perform the following steps: If the cartridge is not going to be used for a short period of time (up to three days), then run the capillary cleaning method for short term storage.
  • Page 218 Figure 10.1 Load Button on Direct Control Window Open the cartridge cover (Figure 4.7). The CESI 8000 Plus coolant pump will start up and expel the coolant from the cartridge coolant lines (Figure 10.2). This will take about 30 seconds. Wait for the pump to turn off before removing the cartridge.
  • Page 219 To retract the stage for a Thermo Scientific mass spectrometer, refer to Aligning the CESI 8000 Plus System with a Thermo Scientific Mass Spectrometer CHAPTER To retract the stage for a SCIEX mass spectrometer, refer to Aligning the CESI 8000 Plus System with the ® SCIEX TripleTOF...
  • Page 220 Figure 10.5 OptiMS Capillary Sprayer Removal Insert the protective sleeve onto the OptiMS sprayer to protect it from breakage (Figure 10.6). Figure 10.6 Placing OptiMS Plastic Sleeve on Sprayer Tip CESI 8000 Plus High Performance Separation-ESI Module User Manual 220 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 221 Pass the tubing with sprayer end through the access panel, and then remove coolant tubing from the notched arm (Figure 10.7 Figure 10.8). Figure 10.7 Putting Tubing/Sprayer through Access Panel Figure 10.8 Removing Coolant Tubing from Notch User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 221 / 376...

  • Page 222: Decoupling The Cesi 8000 Plus System

    Decoupling the CESI 8000 Plus System If the mass spectrometer is to be used for a period of time without the CESI 8000 Plus system, or if one or both instruments are to be moved, then it is best to decouple the CESI 8000 Plus system from the mass spectrometer.
  • Page 223 Shutdown Procedures and Decoupling Instruments Shut down the CESI 8000 Plus system, and then unplug the power cord for the CESI 8000 Plus system and CESI 8000 Plus cart. Decouple both the mass spectrometer adapter’s high-voltage cables from the output and input...
  • Page 224 Shutdown Procedures and Decoupling Instruments IMPORTANT Always lower the CESI 8000 Plus cart to its lowest setting before moving the CESI 8000 Plus system. Figure 10.11 Unlocking CESI 8000 Plus Mobile Cart Wheels Use the thumbscrew on the Thermo Scientific mass spectrometer to loosen the adapter. Then remove the...

  • Page 225: Decoupling From The Sciex Mass

    Cartridge Removal and Instrument Shutdown section earlier in this chapter. Shut down the CESI 8000 Plus system, and then unplug the power cord for the CESI 8000 Plus system and CESI 8000 Plus cart. User Manual...
  • Page 226 Disconnect the black and red ground banana plugs from the CESI 8000 Plus system panel. Unlock the CESI 8000 Plus cart wheels by lifting the lever at each caster upwards with your foot (Figure 10.15). Lower the cart to its lowest setting. Then slowly move the CE instrument away from the mass spectrometer.
  • Page 227 Shutdown Procedures and Decoupling Instruments Figure 10.15 Unlocking CESI 8000 Plus Mobile Cart Wheels Loosen the mass spectrometer adapter locking screw and then slide the adapter all the way off of the stage (Figure 10.16). Put the mass spectrometer adapter in a safe place.
  • Page 228 Shutdown Procedures and Decoupling Instruments CESI 8000 Plus High Performance Separation-ESI Module User Manual 228 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 229: Appendix A: Specifications

    Temperature: 15 °C to 40 °C (15 °C to 30° C recommended) Maximum Heat Dissipation 400 W (1024 BTU/hour) Pollution Degree TTL: 2 Contact closures: 2 User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 229 / 376...

  • Page 230: Validated Controller Configuration

    • 2 serial ports • 2 Ethernet ports • 8 USB ports NOTE SCIEX fully validates and supports the controllers supplied with the system. Only limited support is available for customer-supplied computers. NOTE Specifications are subject to change without notice.

  • Page 231: Sample Temperature Control

    ±0.3 psi at 25 psi ±1.0 psi at 100 psi Pressure Direction Applied at inlet or outlet for all pressure functions, rinses, and injections User-settable in software User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 231 / 376...

  • Page 232: Detector Specifications

    Output 2 not used Output 3 depends on what is programmed: Current signal when voltage is programmed Voltage signal when current or power is programmed CESI 8000 Plus High Performance Separation-ESI Module User Manual 232 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 233: Laser Induced Fluorescence (Lif) Detector (Optional)

    UV Source 30 W pre-aligned deuterium lamp Scan Collection Frequency 0.5 Hz to 32 Hz Detector 256 element diode array Bandwith 6 nm minimum (absorbance averaging) User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 233 / 376...
  • Page 234 AU/V values can be set in the software. Output 3 depends on what is programmed: Current signal when voltage is programmed Voltage signal when current or power is programmed CESI 8000 Plus High Performance Separation-ESI Module User Manual 234 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 235: Appendix B: Nominal Network Configuration

    5600 mass spectrometer acquisition computer. One port can be used for another system (such as a SCIEX LC system), and one port can be dedicated to a CESI 8000 Plus system, and the third port is connected to the Internet.

  • Page 236: Systems

    (PC) used by the CESI 8000 Plus system. When reconnecting back to the CESI 8000 Plus system, you will want to reconnect to exactly the same network connector on the mass spectrometer acquisition computer that was used before switching.

  • Page 237: Switching From A Sciex Mass Spectrometer To Another Mass

    Spectrometer Close the 32 Karat software on the CESI 8000 Plus controller. Disconnect the crossover network cable connecting the CESI 8000 Plus system to the mass spectrometer acquisition computer. Connect the relay/trigger cable from the CESI 8000 Plus system to the target mass spectrometer.
  • Page 238 B.4). Figure B.4 Change MS Type Dialog Click Change The CESI 8000 Plus system and the 32 Karat software are now properly configured for a non- SCIEX mass spectrometer. CESI 8000 Plus High Performance Separation-ESI Module User Manual 238 / 376...

  • Page 239: Switching To A Sciex Mass Spectrometer From Another Mass

    Close the 32 Karat software on the CESI 8000 Plus controller. Disconnect the relay/trigger cable from the CESI 8000 Plus system. Reconnect the crossover network cable from the CESI 8000 Plus system to the SCIEX mass spectrometer acquisition computer. Verify the correct network settings by performing the steps in the...
  • Page 240 Switching to the CESI 8000 Plus System from Different Mass Spectrometer Systems section above within this appendix. Click Change The CESI 8000 Plus system and the 32 Karat software are now properly configured for a SCIEX mass spectrometer. CESI 8000 Plus High Performance Separation-ESI Module User Manual...

  • Page 241: Advanced Networking And Computer Configuration For The Analyst ® Tf

    One port should be dedicated to another system (such as a SCIEX LC system), and one port should be dedicated to CESI 8000 Plus system. The third port connection is dedicated to the Internet. In the CESI 8000 Plus controller (PC), there are one (or more) network connections available.
  • Page 242 Nominal Network Configuration acquisition computer, and this connection will not change. That is, once connected, the network cable need never be removed from the CESI 8000 Plus controller. • The mass spectrometer acquisition computer has three network ports. • The CESI 8000 Plus controller has two available network ports.
  • Page 243 Leave the Internet Protocol TCP/IP Properties as shown (default) for normal Internet connection. Different IT environment can have different settings. Work with the local IT group to define those settings. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 243 / 376...
  • Page 244 Interface metric check box and enter (Figure B.13). Figure B.13 Advanced TCP/IP Settings 8. Close all windows and go back to the Network Connections page. CESI 8000 Plus High Performance Separation-ESI Module User Manual 244 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 245 Figure B.14 Local Area Connection 2 10. Right-click the renamed network connection ( CESI 8000 ) and select Properties (Figure B.15). Figure B.15 CESI 8000 Plus Network Connection Properties 11. Highlight the Internet Protocol (TCP/IP) Properties and click (Figure B.16).
  • Page 246 Default gateway : Leave it blank. • Preferred DNS server : Do not change; leave it blank. Figure B.17 Internet Protocol (TCP/IP) Properties 14. Select Advanced CESI 8000 Plus High Performance Separation-ESI Module User Manual 246 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 247 16. Click Network Connections and exit to the window. 17. Right-click the CESI 8000 network connection again and select Properties (Figure B.19). Figure B.19 Network Connections User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 247 / 376...
  • Page 248 20. Change Value from Auto Negotiation 100Mbps/Full Duplex (Figure B.21). Figure B.21 Link Speed and Duplex Settings 21. Click and exit all windows. CESI 8000 Plus High Performance Separation-ESI Module User Manual 248 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 249 B.22). Figure B.22 Control Panel 2. Switch the Windows view to Classic View , if not already set (Figure B.23). Figure B.23 Selecting Classic View User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 249 / 376...
  • Page 250 8. Following the steps above, modify the network interface metric to Network Connection (or rename to other device interface name). CESI 8000 Plus High Performance Separation-ESI Module User Manual 250 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 251 Figure B.26 Network and Sharing Center NOTE There will be more than one connection on the above window if the system has more than one network port installed. Locate an available network connection to set up the CESI 8000 Plus connection. 2. Click...
  • Page 252 Turn off file and printer sharing (Figure B.28). Figure B.28 Update Advanced Sharing Settings 4. Click Change adapter settings in the left pane (Figure B.29). Figure B.29 Change Adapter Settings CESI 8000 Plus High Performance Separation-ESI Module User Manual 252 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 253 B.30). Figure B.30 Ethernet Properties 6. Highlight Internet Protocol Version 4 (TCP/IPv4) Properties and click (Figure B.31). Figure B.31 Internet Protocol Version 4 (TCP/IPv4) Properties User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 253 / 376...
  • Page 254 : Do not change; leave it blank. • Preferred DNS server : Do not change; leave it blank. Figure B.33 DNS Server Address 9. Click Advanced CESI 8000 Plus High Performance Separation-ESI Module User Manual 254 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 255 13. Click Configure , which is located just below and to the right of Connect using (Figure B.35). Figure B.35 Configuring the Network User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 255 / 376...
  • Page 256 Panel Control Items > Windows Firewall > Customize Settings (Figure B.37). Select Turn off Windows Firewall in both Private and Public network settings. Click Figure B.37 Firewall Settings CESI 8000 Plus High Performance Separation-ESI Module User Manual 256 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 257 Figure B.39 Network and Sharing Center NOTE There will be more than one connection at the above window if the system has more than one network port installed. Locate an available network connection to set up the CESI 8000 Plus connection. User Manual...
  • Page 258 Local Area Connection and select Properties (Figure B.41). Figure B.41 Local Area Connection Properties 7. Highlight Internet Protocol Version 4 (TCP/IPv4) and click Properties (Figure B.42). CESI 8000 Plus High Performance Separation-ESI Module User Manual 258 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 259 Figure B.42 CESI 8000 (Local Area Connection) Properties Dialog 8. Click Use the following IP address (Figure B.43). Figure B.43 Internet Protocol Version 4 (TCP/IPv4) Properties User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 259 / 376...
  • Page 260 13. Right-click CESI 8000 and select Properties 14. Click Configure , which is located just below and to the right of Connect using (Figure B.45). CESI 8000 Plus High Performance Separation-ESI Module User Manual 260 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 261 B.46). Figure B.46 Value List 16. Exit all network configuration windows. 17. Perform the steps in the “Network Sharing Setting for the Crossover Connection” section. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 261 / 376...

  • Page 262: Network Sharing Setting For The Crossover Connection

    Navigate to the Network and Sharing Center and select options (Figure B.47). Figure B.47 Network and Sharing Center Select Change advanced sharing settings (Figure B.48). Figure B.48 Homegroup Options CESI 8000 Plus High Performance Separation-ESI Module User Manual 262 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 263 B.49). Leave everything else as the default selection. Figure B.49 Advanced Sharing Settings Save changes Select to save all changes (Figure B.50). Figure B.50 Saving Changes User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 263 / 376...

  • Page 264: Setting The Mass Spectrometer Type

    Select the Connect to AB SCIEX MS check box, and verify/set the IP address 192.168.1.1 Select Change (Figure B.52). Figure B.52 Changing the MS Type CESI 8000 Plus High Performance Separation-ESI Module User Manual 264 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 265: Curtain Gas Patch Installation

    Before installing the patch, open the hardware manager and deactivate all profiles. Make sure the ® Analyst TF software is closed before installing the patch. Locate the patch download file on the CESI 8000 Plus Sharepoint site. Unzip the file onto the desktop. .msi Double-click the...
  • Page 266 Nominal Network Configuration Figure B.55 License Agreement Figure B.56 Program Installation Figure B.57 Completion Wizard CESI 8000 Plus High Performance Separation-ESI Module User Manual 266 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 267: Ce-Ms Driver Installation

    B.60, waiting for the wizard shown in Figure B.62 to complete, Finish and then selecting Figure B.64. Figure B.59 BCI CE-MS Driver — InstallShield Wizard User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 267 / 376...
  • Page 268 Nominal Network Configuration Figure B.60 Install Folder Figure B.61 BCI CE-MS Driver Setup Figure B.62 Completion Wizard CESI 8000 Plus High Performance Separation-ESI Module User Manual 268 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 269: Saving Network Configurations

    — File location: C:\Program Files\BCI CE-MS Driver NOTE Refer to Figure B.63 for an example of a network configuration file. Figure B.63 Network Configuration File — Example User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 269 / 376...

  • Page 270: Analyst Hardware Profile Configuration

    To configure the Mass Spectrometer Hardware Profile ® Open the Hardware Configuration editor in the Analyst TF software (Figure B.64). Figure B.64 Hardware Configuration Editor CESI 8000 Plus High Performance Separation-ESI Module User Manual 270 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 271 New Profile (Figure B.65). Figure B.65 Creating a New Profile Profile Name Name the profile by entering a name, such as “CESI 8000 Plus profile”, into the field (Figure B.66), and then selecting Figure B.66 Naming the Profile Add Device...
  • Page 272 Click Add Device Click again. Select Software Application from the Device Type menu (Figure B.68). Figure B.68 Device Type Menu in the Available Devices Dialog CESI 8000 Plus High Performance Separation-ESI Module User Manual 272 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 273 Set up the device: a. From the Create New Hardware Profile window, click the mass spectrometer and select Setup Device (Figure B.70). Figure B.70 Added Devices User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 273 / 376...
  • Page 274 Figure B.72 Software Application Settings Make sure the BCI CE Driver is selected, and click Create New Hardware Profile From the window, click the Autosampler. a. Select Setup Device CESI 8000 Plus High Performance Separation-ESI Module User Manual 274 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 275 Close all settings windows and navigate back to the dialog. Verify that the final hardware configuration profile appears (Figure B.74). Figure B.74 Final Hardware Configuration Profile User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 275 / 376...

  • Page 276: Curtain Gas Setting And Verification

    (Figure B.75). Figure B.75 Hardware Configuration Editor Dialog Restart the SCIEX acquisition computer. Once the profile has been activated, the right corner of the Analyst window should appear as shown in Figure B.76.
  • Page 277 Figure B.78 Enter Password Dialog Adjust Curtain Gas Settings Set the curtain gas to in the window and click (Figure B.79). Figure B.79 Adjust Curtain Gas Setting Window User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 277 / 376...

  • Page 278: Curtain Gas Verification

    Repeat the process until the read back value (see Curtain Gas Verification) is between Curtain Gas Verification To verify and adjust the curtain gas: Power on the CESI 8000 Plus system. ® In the Analyst TF software, double-click Manual Tuning...
  • Page 279 (Figure B.82). NOTE The Curtain Gas CUR field cannot be changed while the CESI 8000 Plus hardware profile is active. Figure B.82 Checking the Curtain Gas Readback Value User Manual CESI 8000 Plus High Performance Separation-ESI Module...
  • Page 280 Nominal Network Configuration NOTE As long as the user is running the CESI 8000 Plus hardware profile, the instrument pulls its curtain gas value from the curtain gas patch, rather than the SW input. Therefore, the Curtain ® TF software will not reflect the curtain gas setting of 5, nor can it...

  • Page 281: Tripletof ® 5600 Mass Spectrometer Manual And Auto-Calibration Methods

    TripleTOF 5600 Mass Spectrometer Manual and Auto-Calibration Methods Overview This appendix outlines the methods for manual and automatic calibration of the SCIEX ® TripleTOF 5600 mass spectrometer while performing CE-MS runs. When performing CESI-MS runs, the mass spectrometer can be calibrated periodically by infusing a calibrant solution through the OptiMS capillary and using it to automatically calibrate the mass spectrometer.

  • Page 282: Manual Calibration Before Auto-Calibration

    > > (Figure C.1). The Tuning Options dialog will open (Figure C.2). Figure C.1 Create Reference File Figure C.2 Tuning Options Dialog 1. Reference Button CESI 8000 Plus High Performance Separation-ESI Module User Manual 282 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 283 C.5. Ensure that the radio button for Positive (“Positive Ion” mode) is checked and the Retention time tolerance +/- is set to 30 000 seconds. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 283 / 376...
  • Page 284 +/- 30 seconds. to open the Tuning Options window containing the newly created reference table Click (Figure C.6). Figure C.6 Tuning Options Dialog CESI 8000 Plus High Performance Separation-ESI Module User Manual 284 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 285: Manual Calibration Of The Mass Spectrometer

    20 minutes by clicking Voltage . Ensure that the capillary inlet is in the BI:A1 position and the outlet is in the BO:A1 position (Figure C.8). User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 285 / 376...

  • Page 286: Manual Calibration In Tof Mass Spectrometer Mode

    Under Period , set the Duration minute. Figure C.9 shows the MS tab in the Tune Method Editor dialog after setting up all the parameters. CESI 8000 Plus High Performance Separation-ESI Module User Manual 286 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 287 (spray voltage) and adjust the sprayer position until the spray is stable. Start Mass Click , a TIC window will be acquired in approximately 1 minute. The Spectrum windows are shown in Figure C.11. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 287 / 376...
  • Page 288 C.12. Figure C.12 Opening a File from the TIC Window Pane of the data file that was acquired will open as shown in Figure C.13. CESI 8000 Plus High Performance Separation-ESI Module User Manual 288 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 289 (Figure C.14). Figure C.14 Deleting MS Data Pane After deleting the pane, the will look as shown in Figure C.15. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 289 / 376...
  • Page 290 If the reference file B-Gal CE-MS Calibration Ref is not found, then refer to Create a Reference Table for CE-MS Calibration for the procedure on how to create this file. CESI 8000 Plus High Performance Separation-ESI Module User Manual 290 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 291 Entire file In the area, click the icon to apply this calibration to all samples in the file. Click Save Figure C.18 TOC Calibration Toolbar User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 291 / 376...

  • Page 292: Manual Calibration In Product Ion Mode

    Collision Energy Spread High Sensitivity tab, set . Ensure that Tune mode is selected. Figure C.20 shows the window after setting up all the parameters. CESI 8000 Plus High Performance Separation-ESI Module User Manual 292 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 293 Product Ion calibration are shown in the window (Figure C.21). Figure C.21 TIC and Mass Spectrum Windows Open File Right-click the pane and click (Figure C.22). User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 293 / 376...
  • Page 294 To open the average MS, click and drag to highlight the pane. Double-click it to obtain an average mass spectrum. Right-click the mass spectrum and click Re-calibrate TOF (Figure C.24). CESI 8000 Plus High Performance Separation-ESI Module User Manual 294 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 295 , which is the same as the one used before for TOF Tolerance mass spectrometer calibration. Set the Da. The Product ion masses will appear in the table (Figure C.25). Figure C.25 TOF Calibration Window User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 295 / 376...

  • Page 296: Methods For Auto-Calibration

    This method uses BGE vials that are to be placed in the A4 position of both the inlet and the outlet buffer trays. Figure C.26 Time Program CESI 8000 Plus High Performance Separation-ESI Module User Manual 296 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 297: Ms Method For Auto-Calibration

    In the pane, click In the tab, click Edit Parameters (Figure C.28). This will open a new window (Figure C.29) containing 2 tabs: Source/Gas Compound User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 297 / 376...
  • Page 298 Product Ion (+) 729.4 . In the tab, click Edit Parameters Source/Gas Compound to set up the parameters under for the MS/MS experiment (Figure C.31). CESI 8000 Plus High Performance Separation-ESI Module User Manual 298 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 299 1. Product Ion (+) 729.4 Figure C.32 MS Tab and Parameters Settings Dialog Figure C.33 Acquisition Method and the Beckman CE Driver 1. Beckman CE Driver User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 299 / 376...

  • Page 300: Executing Auto-Calibration

    This section provides step-by-step instructions on how to build a sequence of 10 runs of beta- ® galactosidase performance test on theTripleTOF 5600 mass spectrometer with auto-calibration every 5 runs in tandem using the CESI 8000 Plus system. In the navigation bar, under Acquire, double-click Build Acquisition batch CESI 8000 Plus High Performance Separation-ESI Module...
  • Page 301 , browse to the applicable method. In this example choose . Refer to CESI_MS_AB_Sciex_Beta-Gal_45min CHAPTER Methods for the CESI 8000 Plus System for steps to create this method. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 301 / 376...
  • Page 302 “CE infusion” mode, all the reference ions are present at the same time. The tolerance is set to +/- 30 seconds. Reference tables are shown in Figure C.38. CESI 8000 Plus High Performance Separation-ESI Module User Manual 302 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 303: Start A Sequence In The Analyst

    Start a Sequence in the Analyst TF Software Submit Click on the right to submit the batch. This will submit the 10 beta-galactosidase separation runs with auto-calibration (Figure C.39). User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 303 / 376...
  • Page 304 At this point the TripleTOF 5600 mass spectrometer is waiting for the trigger signal from the CESI 8000 software to start data acquisition. CESI 8000 Plus High Performance Separation-ESI Module User Manual 304 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 305: System

    A1 and A2 respectively. Samples to be analyzed can be placed in other positions; however, these positions must be specified in the CESI 8000 Plus methods or manually specified in the sequence table.

  • Page 306: Software

    In the Method field, click the yellow folder to browse to the CESI method for the separation of beta-galactosidase (Figure 8.8), as shown in Figure C.43. CESI 8000 Plus High Performance Separation-ESI Module User Manual 306 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 307 Data file name (Figure C.44). Figure C.44 Setting up the Sequence Wizard — Unknowns Page User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 307 / 376...
  • Page 308 To edit the sequence table in the CESI 8000 Insert Line software: highlight the first run, right-click the highlighted run, and click (Figure C.46). CESI 8000 Plus High Performance Separation-ESI Module User Manual 308 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 309 . In the Sequence Properties dialog (Figure C.48), ensure that under File paths, the data is being saved on a desired folder. A folder can also be created. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 309 / 376...

  • Page 310: Software

    Start a Sequence in the CESI 8000 Software To run this sequence, click the Run Sequence icon and the Run Sequence dialog opens. Click Start to initiate the sequence. CESI 8000 Plus High Performance Separation-ESI Module User Manual 310 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 311 Once the CE method starts, the status in the MS Queue Server will change from PreRun NOTE ® When the trigger signal is sent from the CESI 8000 Plus system to the TripleTOF 5600 mass spectrometer, the Queue Server will change from PreRun to Acquiring. User Manual...

  • Page 312: Auto-Calibration Data Analysis

    20 kV. Automatic Rinse Feature The CESI 8000 Plus system makes use of an “Automatic Rinse” feature. If there is a hardware failure during the rinse steps and also the injection step, either during a method run or sequence run, the instrument will (without user intervention) rinse the separation capillary for 3 minutes at 50 psi from the first separation event vial position.
  • Page 313 To get the list of ions present in the mass spectrum, right-click the mass spectrum and select List data MS before calibration . This is shown for the Figure C.52. Figure C.52 Obtaining List Data User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 313 / 376...
  • Page 314 Use as reference . This is the same reference table previously used for auto-calibration. This is shown in Figure C.54 for the MS before calibration CESI 8000 Plus High Performance Separation-ESI Module User Manual 314 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 315 1. Mass Spectrometer Before Calibration 2. Data Table From Mass Spectrometer Before Calibration 3. Mass Spectrometer After Calibration 4. Data Table From Mass Spectrometer After Calibration User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 315 / 376...
  • Page 316 For evaluating the MS/MS mass accuracy, repeat steps MS/MS before calibration MS/MS after calibration For the MS/MS experiment, the mass shift after calibration is lower than it was before calibration (Figure C.57). CESI 8000 Plus High Performance Separation-ESI Module User Manual 316 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 317: Failure

    Refer to the AB SCIEX Mass Calibration Tutorial found under Start Menu > All Programs > AB SCIEX > Analyst TF 1.7 > Hardware and Software Guides for more information. Successful auto-calibration runs have a green check mark. An open red circle with a diagonal line through it indicates that the sample was acquired but the calibration failed due to one or more of the reference ions failing to meet the calibration criteria.

  • Page 318: Auto-Calibration Troubleshooting

    If the mass shift is greater than or equal to 80% of the reference ions is over 100 ppm, manual calibration has to be performed. Additional troubleshooting can be found in Auto-calibration Troubleshooting Table. CESI 8000 Plus High Performance Separation-ESI Module User Manual 318 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 319: Table

    2. If manual calibration doesn’t help, instrument optimization has experiment. the MS/MS is less than to be performed. 100 ppm for ≥ 80% of the reference ions. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 319 / 376...
  • Page 320 ® TripleTOF 5600 Mass Spectrometer Manual and Auto-Calibration Methods CESI 8000 Plus High Performance Separation-ESI Module User Manual 320 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 321: Overview

    • Check both Inlet Outlet to increment the rinse vials at inlet and outlet buffer trays. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 321 / 376...

  • Page 322: Injection

    To set an injection step with auto vial increment, open the method on 32 Karat software and then open the injection step. The auto vial increment section is indicated on the figure below by a red square. CESI 8000 Plus High Performance Separation-ESI Module User Manual 322 / 376...
  • Page 323 12 repetitions of the same method. The table below summarizes which vial position will be used at each cycle during the above injection step. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 323 / 376...

  • Page 324: Step

    To set a separation step with use auto vial increment, open the method on 32 Karat software and then open the separation step. The auto vial increment section is indicated on the figure below by a red square. CESI 8000 Plus High Performance Separation-ESI Module User Manual 324 / 376...
  • Page 325 12 cycles, which is equivalent to 12 repetitions of the same method. The table below summarizes which buffer vial positions will be used at each cycle during the above separation step. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 325 / 376...

  • Page 326: Method

    6 Out vial inc 3 means that only the outlet vial will be incremented cycles. In another example, after 3 cycles. Figure D.8 Time Program CESI 8000 Plus High Performance Separation-ESI Module User Manual 326 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 327: Sequence

    In other words, the cycle count will re-start at 1. • If the sequence has different methods, the CESI 8000 Plus system will revert to the initial set of specified at the start of each method. Therefore, do not combine different methods if the auto vial increment feature is been used.
  • Page 328 Auto Vial Increment Feature CESI 8000 Plus High Performance Separation-ESI Module User Manual 328 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 329: Conductive Liquid Capillary

    Figure E.1 Profile of Phosphate Contamination NOTE During this method, the sprayer must rest in the holster and remain immersed in no more than 10 mL of DDI water. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 329 / 376...
  • Page 330 Conductive Liquid Capillary Conditioning To clean up phosphate contamination, set up the CESI 8000 Plus method (Figure E.2). Figure E.2 CLC Conditioning Method IMPORTANT This method uses reverse rinses. Only one vial is required in the buffer inlet tray, at position A1.

  • Page 331: Overview

    Replacing Fuses IMPORTANT To achieve optimal instrument performance, consistent user maintenance must be performed regularly on the CESI 8000 Plus system. A yearly planned maintenance by a SCIEX FSE is recommended. User Manual CESI 8000 Plus High Performance Separation-ESI Module...

  • Page 332: Using Cesi-Ms Vials And Caps

    Figure F.1 CESI-MS Vials 1. CESI-MS Vial Cap 2. Maximum Fill Level 3. CESI-MS Vials Put the cap on the vial and press it into position. CESI 8000 Plus High Performance Separation-ESI Module User Manual 332 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 333: Vials

    4. Micro Vial inside CESI-MS Vial Place the micro vial in the CESI-MS vial. Put the cap on the CESI-MS vial. Put the capped vial in the tray. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 333 / 376...

  • Page 334: Capillary Cleaning Procedure

    CESI 8000 Plus system. WARNING Maintenance or repair procedures not specifically described in this manual present a risk of electrical shock or injury. Refer additional servicing to SCIEX Technical Support. WARNING Do not attempt to defeat any of the instrument interlocks or safety mechanisms.

  • Page 335: Procedure

    Prepare the reagents listed above for the capillary shutdown by placing the reagent vials on the inlet and outlet buffer trays as indicated in Figure F.5. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 335 / 376...

  • Page 336: Plate

    If there is a spill, then it may become necessay to remove the OptiMS interface plate to clean the CESI 8000 Plus system. To remove and then re-install the OptiMS interface plate into a CESI 8000 Plus system, perform the following steps: Removing OptiMS Interface Plate Remove the OptiMS cartridge.
  • Page 337 Re-installing OptiMS Interface Plate Hold the handle of the OptiMS interface plate and insert it as shown in Figure F.8. Figure F.8 OptiMS Interface Plate Insertion User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 337 / 376...

  • Page 338: Block

    Loosen the two thumbscrews and lift the cartridge lock down bar. Remove the OptiMS cartridge from the interface block. If the trays are still in the way, remove them for access to both opening levers. CESI 8000 Plus High Performance Separation-ESI Module User Manual 338 / 376...
  • Page 339 With your fingers on the sides of the lever, press the lever up into the interface block until it snaps into place. Repeat for the second lever. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 339 / 376...
  • Page 340 Pry gently with the electrode tool to remove the electrode from the interface block. e. Remove the electrode from the electrode tool. Repeat for second electrode. Install an electrode into the interface block. CESI 8000 Plus High Performance Separation-ESI Module User Manual 340 / 376...

  • Page 341: Block

    Perform steps under Remove the electrodes one at a time as shown in Figure F.11. Immerse both electrodes in the DDI water with the opening levers. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 341 / 376...
  • Page 342 Lower the clamp bar and tighten the two thumbscrews. Close the cartridge cover. IMPORTANT To avoid corrosion of the ion source, frequently clean the dry chemical waste that accumulates beneath the sprayer. CESI 8000 Plus High Performance Separation-ESI Module User Manual 342 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 343: Refilling Coolant

    The instrument power should be on with the OptiMS cartridge installed. Slowly fill the coolant supply until the fill indicator is within the yellow lines in the coolant sight glass (Figure F.15). User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 343 / 376...

  • Page 344: Rings

    Using Vials and Hardware Maintenance Figure F.15 Coolant Sight Glass Location on the CESI 8000 Plus System Remove the coolant fill adapter and close the sample cover. The coolant fill adapter comes with a plunger. When adding coolant, the plunger should not be used.
  • Page 345 F.16). Use the tweezers that were supplied with the instrument (or your thumbnail and forefinger) to remove the quad rings. Figure F.16 Location of the Quad Rings on the CESI 8000 Plus System Install the new quad ring in the quad ring recess of the interface block.

  • Page 346: Replacing Fuses

    Make sure to replace the fuses with the correct type and rating for continued protection against risk of fire and/or improper instrument operation. CAUTION If the fuses continue to blow after being replaced, contact a SCIEX FSE for additional assistance. Items required: •...
  • Page 347 8.0 A Slow Blow; ¼ inch (2 ea.) 6.3 A Time Delay; 20 mm (2 ea.) Reinstall the fuse block and reconnect the power cable. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 347 / 376...
  • Page 348 Using Vials and Hardware Maintenance CESI 8000 Plus High Performance Separation-ESI Module User Manual 348 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 349: Troubleshooting

    IMPORTANT For any maintenance not covered in this manual, contact SCIEX Technical Support. Troubleshooting and Flow Diagrams The following is a list of possible problems when using the CESI 8000 Plus system with a mass spectrometer: NOTE Whenever the problem involves positioning the sprayer tip, make certain that the droplets fall freely from the tip and the sprayer tip does not touch the mass spectrometer inlet.

  • Page 350: Sample Preparation Considerations For Analysis With Cesi-Ms

    Instead of using the 32 Karat software button in this instance, use the Show 32 Karat button at the center bottom of the user interface dialog. CESI 8000 Plus High Performance Separation-ESI Module User Manual 350 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 351: Tip

    Very gently submerge the sprayer end of the cartridge in the 50 mL tube (Figure G.2). NOTE When inserting sprayer end into tube, try to not touch the sides of the tube. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 351 / 376...
  • Page 352 Figure G.3 Wipe Clean Sprayer End with Dry Paper Wipe Reinsert the sprayer back into the mass spectrometer adapter. Remove the 50 mL tube from holster and empty contents. CESI 8000 Plus High Performance Separation-ESI Module User Manual 352 / 376...

  • Page 353: Electrospray Cannot Be Established Between The Cesi 8000 Plus System And Mass Spectrometer

    Troubleshooting and Mobile Cart Homing Procedure Electrospray Cannot Be Established Between the CESI 8000 Plus System and Mass Spectrometer User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 353 / 376...

  • Page 354: Electrospray Is Detected At Zero Ion Spray (Is) Voltage While Applying Ce Voltage

    Troubleshooting and Mobile Cart Homing Procedure Electrospray is Detected at Zero Ion Spray (IS) Voltage while Applying CE Voltage CESI 8000 Plus High Performance Separation-ESI Module User Manual 354 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 355: Unstable Electrospray While Applying Ce Voltage And Is Voltage

    Troubleshooting and Mobile Cart Homing Procedure Unstable Electrospray while Applying CE Voltage and IS Voltage User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 355 / 376...

  • Page 356: Droplet At Capillary Tip Disappeared Indicating That Electrospray Has Started, But No Mass Spectrometer Signal Is Detected

    Troubleshooting and Mobile Cart Homing Procedure Droplet at Capillary Tip Disappeared Indicating that Electrospray has Started, but No Mass Spectrometer Signal is Detected CESI 8000 Plus High Performance Separation-ESI Module User Manual 356 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 357: Signal Of Total Ion Current (Tic) Is Lower Than Usual And/Or Background Signal Intensity Fluctuates More Than 40

    Troubleshooting and Mobile Cart Homing Procedure Signal of Total Ion Current (TIC) is Lower Than Usual and/or Background Signal Intensity Fluctuates More Than 40% User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 357 / 376...

  • Page 358: Unstable Ce Current

    Troubleshooting and Mobile Cart Homing Procedure Unstable CE Current CESI 8000 Plus High Performance Separation-ESI Module User Manual 358 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 359: No Analyte Signals Detected By Mass Spectrometer During A Ce-Ms Separation

    Troubleshooting and Mobile Cart Homing Procedure No Analyte Signals Detected by Mass Spectrometer During a CE-MS Separation User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 359 / 376...

  • Page 360: Some Analyte Peaks Are Missing Or Smaller Than Expected

    Troubleshooting and Mobile Cart Homing Procedure Some Analyte Peaks are Missing or Smaller Than Expected CESI 8000 Plus High Performance Separation-ESI Module User Manual 360 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 361: Ce Current Gradually Decreases During Ce-Ms Separation

    Troubleshooting and Mobile Cart Homing Procedure CE Current Gradually Decreases During CE-MS Separation User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 361 / 376...

  • Page 362: The Iron-Acetate Cluster M/Z 537 Is Suppressing The Sample Signals

    Troubleshooting and Mobile Cart Homing Procedure The Iron-Acetate Cluster m/z 537 is Suppressing the Sample Signals CESI 8000 Plus High Performance Separation-ESI Module User Manual 362 / 376 RUO-IDV-05-3897-B | B11949AF...

  • Page 363: High Voltage System Unable To Deliver The Required Current

    Troubleshooting and Mobile Cart Homing Procedure High Voltage System Unable to Deliver the Required Current User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 363 / 376...

  • Page 364: Fine Tuning Sprayer Tip Position For Thermo Scientific Mass Spectrometer

    Figure G.4 Thermo Scientific Mass Spectrometer Sprayer Tip Distance and ESI Voltage Correlation Perform the following steps to optimize the sprayer tip position after placing OptiMS cartridge on CESI 8000 Plus system, the OptiMS sprayer on mass spectrometer adapter, and before performing a CESI-MS separation: Fill both OptiMS separation capillary and CLC with background electrolyte.
  • Page 365 Repeat this procedure: • After installing an OptiMS cartridge. • If signal CESI separation voltage is changed. • If a different background electrolyte is used. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 365 / 376...

  • Page 366: Fine Tuning Sprayer Tip Position For Sciex Mass Spectrometer

    Figure G.5 SCIEX Mass Spectrometer Sprayer Tip Distance and ESI Voltage Correlation Perform the following steps to optimize the sprayer tip position after placing OptiMS cartridge on the CESI 8000 Plus system, the OptiMS sprayer on mass spectrometer adapter, and before performing a CESI-MS separation: Repeat this procedure: Fill both OptiMS separation capillary and CLC with background electrolyte.
  • Page 367 Repeat this procedure: • After installing an OptiMS cartridge. • If signal CESI separation voltage is changed. • If a different background electrolyte is used. User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 367 / 376...

  • Page 368: Cesi 8000 Plus Mobile Cart Homing Procedure

    If the legs fail to function properly, unplug the power, wait 10 seconds, plug the power back in and repeat the above step. The above procedure must be performed anytime the power module is replaced. If this does not resolve the problem, then contact SCIEX Technical Support. CESI 8000 Plus High Performance Separation-ESI Module User Manual...

  • Page 369: Contact Us

    SCIEXUniversity SCIEX Support SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout the world. They can answer questions about the system or any technical issues that might arise. For more information, visit the SCIEX website at sciex.com...

  • Page 370: Documentation

    Documentation for the hardware products can be found on the Customer Reference DVD that comes with the system or component. For the latest versions of the documentation, visit the SCIEX website at sciex.com. NOTE To request a free, printed version of this document, contact sciex.com/contact-us.

  • Page 371: Index

    Conductive Liquid Capillary Conditioning, Beta-Galactosidase Stock Solution, 151, Configure Beta-Galactosidase Test Sample, 151, Application, Blocked Sprayer Tip, Configure Instrument, Buffer Tray Setup, 152, Consignes de sécurité avertissement, User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 371 / 376...
  • Page 372 Loading the Cartridge and Samples, Étiquette de mise en garde chariot mobile, Lock, Étiquette de mise en garde RoHS (Chine), Login, Étiquette de recyclage (WEEE), Logout, Étiquette marque CE, CESI 8000 Plus High Performance Separation-ESI Module User Manual 372 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 373 Optional, Run Acquisition, Options Run Acquisition window, Graph, Run Application, Output Data File Name, 118, Run Complete, Output Data Path, 118, Run Number, Run Queue, User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 373 / 376...
  • Page 374 Troubleshooting Flow Diagrams, Security, 113, Tuning, Select Method, Sequence, Unlock, Select Application, Users, Sequence Describe, 141, Properties, Select, Verification, 143, Transfer, Version, Verification, Vial Actions Sequence Dialog, CESI 8000 Plus High Performance Separation-ESI Module User Manual 374 / 376 RUO-IDV-05-3897-B | B11949AF...
  • Page 375 仪器安全防护措施 , Describe Sequence, 小心 , Run Application, 尖锐物 , Vials, 注释 , Vials and Caps, 活动部件 , Voltage, 电气安全 , 警告 , 电气安全 , Xcalibur User Manual CESI 8000 Plus High Performance Separation-ESI Module RUO-IDV-05-3897-B | B11949AF 375 / 376...
  • Page 376 Index CESI 8000 Plus High Performance Separation-ESI Module User Manual 376 / 376 RUO-IDV-05-3897-B | B11949AF...

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