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Waters Alliance iS HPLC User Manual

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Alliance iS HPLC System
User Guide
715008450
Copyright © Waters Corporation 2023
Version 00
All rights reserved

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Summary of Contents for Waters Alliance iS HPLC

  • Page 1 Alliance iS HPLC System User Guide 715008450 Copyright © Waters Corporation 2023 Version 00 All rights reserved...

  • Page 2: Table Of Contents

    1.4.5 Safety advisories........................11 1.5 Operating the device........................11 1.5.1 Applicable symbols....................... 11 1.5.2 Audience and purpose......................12 1.5.3 Intended use of the Alliance iS HPLC system..............13 1.5.4 Calibrating..........................13 1.5.5 Quality control........................13 1.6 EMC considerations........................13 1.6.1 Canada spectrum management emissions notice..............13 1.6.2 ISM classification: ISM group 1 class B................
  • Page 3 2.6 Warnings that apply to all Waters instruments and devices............19 2.7 Warnings that address the replacement of fuses................23 2.8 Electrical symbols...........................25 2.9 Handling symbols........................... 26 3 System overview......................28 3.1 Features of the system........................28 3.1.1 Flow-through-needle injector....................29 3.2 System components........................29 3.2.1 Detector features........................
  • Page 4 4.7 Choosing extension loops......................68 4.8 Installing and replacing extension loops..................69 4.8.1 Installing an extension loop in a single-valve system............70 4.8.2 Installing an extension loop in a two-valve system............... 71 4.9 Modifying needle and extension loop configuration parameters............ 73 4.10 Choosing a draw rate for the sample syringe................73 4.11 Choosing the needle-placement setting..................
  • Page 5 6.8 Reviewing the results........................91 6.9 Printing the report...........................91 6.10 Putting the Alliance iS system to sleep..................91 6.11 Preparing to shut down the Alliance iS system................92 7 Performance optimization..................94 7.1 General guidelines......................... 94 7.1.1 Carryover..........................95 7.2 Preventing leaks..........................96 7.2.1 Installation recommendations for fittings................96 7.3 Setting up a method........................
  • Page 6 8.8.5 Replacing the vent valve cartridge..................112 8.8.6 Replacing the optional solvent selection valve cartridge.............114 8.8.7 Replacing the in-line filter cartridge on the primary check valve......... 117 8.8.8 Replacing the Check Valve Filter..................123 8.8.9 Replacing the accumulator check valve................124 8.8.10 Replacing the accumulator check valve................127 8.8.11 Replacing the accumulator check valve................129 8.8.12 Replacing the accumulator check valve - video..............131...
  • Page 7 9.6 Responding to a leak sensor alarm....................200 9.7 Diagnostic tests..........................202 9.7.1 Running the system leak test....................203 9.7.2 Running the needle seal readiness test................204 10 System upgrade.....................205 10.1 Empower updates........................205 10.2 Empower ICS updates....................... 205 10.3 Kiosk/console updates....................... 205 10.4 Firmware updates........................205 10.5 System release notes.........................206 11 Disposal protocols....................207...
  • Page 8 12.6.1 Using miscibility numbers (M-numbers)................219 12.7 Solvent stabilizers........................220 12.8 Solvent viscosity.........................220 12.9 Wavelength selection......................... 220 12.9.1 Ultraviolet cutoffs for common solvents................220 12.9.2 Mixed mobile phases......................221 12.9.3 Mobile phase absorbance....................222 13 Specifications......................225 13.1 System specifications.........................225 13.1.1 Instrument control specifications..................226 13.1.2 Environmental specifications....................

  • Page 9: General Information

    This document is believed to be complete and accurate at the time of publication. In no event shall Waters Corporation be liable for incidental or consequential damages in connection with, or arising from, its use. For the most recent revision of this document, consult the Waters website (www.waters.com).

  • Page 10: Trademarks

    All other trademarks are property of their respective owners. 1.4 Safety considerations Some reagents and samples used with Waters instruments and devices can pose chemical, biological, or radiological hazards (or any combination thereof). You must know the potentially hazardous effects of all substances you work with. Always follow good laboratory practices and consult your organization’s standard operating procedures as well as your local requirements for...

  • Page 11: Equipment Misuse Notice

    1.4.4 Equipment misuse notice If equipment is used in a manner not specified by its manufacturer, the protection provided by the equipment may be impaired. 1.4.5 Safety advisories Consult the "Safety advisories" appendix in this publication for a comprehensive list of warning advisories and notices.

  • Page 12: Audience And Purpose

    For compliance with Waste Electrical and Electronic Equipment legislation, contact Waters Corporation for the correct disposal and recycling instructions For indoor use only No pushing Do not connect to an LC system...

  • Page 13: Intended Use Of The Alliance Is Hplc System

    The Alliance iS HPLC system serves QC departments that support the uninterrupted supply of safe and effective products. Specific features of the Alliance iS HPLC system are unlocked within the Empower CDS to help prevent common errors by up to 40% and reduce the associated risks of common and preventable errors associated with HPLC systems.

  • Page 14: Additional Resources

    1.7 Additional resources Waters provides the following additional resources to ensure your continued success with our products. Knowledge base: Obtain quick answers to your troubleshooting questions. Access support articles on Waters instrumentation, informatics, and chemistry. eLearning courses: Learn anytime, anywhere, and at your own pace with eLearning courses.

  • Page 15: Contacting Waters

    1.8 Contacting Waters Contact Waters with technical questions regarding the use, transportation, removal, or disposal of any Waters product. You can reach us through the Internet, telephone, fax, or conventional mail. Contact method Information www.waters.com The Waters website includes contact information for Waters locations worldwide.
  • Page 16 To report any errors that you encounter in this document or to suggest ideas for otherwise improving it, reach us at tech_comm@waters.com. February 20, 2023, 715008450 Ver. 00 Page 16...

  • Page 17: Safety Advisories

    Heed all warnings when you install, repair, or operate any Waters instrument or device. Waters accepts no liability in cases of injury or property damage resulting from the failure of individuals to comply with any safety precaution when installing, repairing, or operating any of its instruments or devices.

  • Page 18: Specific Warnings

    Warning: (Risk of contacting corrosive substances.) Warning: (Risk of exposure to a toxic substance.) Warning: (Risk of personal exposure to laser radiation.) Warning: (Risk of exposure to biological agents that can pose a serious health threat.) Warning: (Risk of tipping.) Warning: (Risk of explosion.) Warning:...

  • Page 19: Required Protection

    Use eye protection when performing this procedure. Requirement: Wear clean, chemical-resistant, powder-free gloves when performing this procedure. 2.6 Warnings that apply to all Waters instruments and devices When operating this device, follow standard quality-control procedures and the equipment guidelines in this section.
  • Page 20 警告： 未经有关法规认证部门明确允许对本设备进行的改变或改装，可能会使使用者 丧失操作该设备的合法性。 警告： 未經有關法規認證部門允許對本設備進行的改變或修改,可能會使使用者喪失操 作該設備的權利。 경고 규정 준수를 책임지는 당사자의 명백한 승인 없이 이 장치를 개조 또는 변경할 경우, 이 장치를 운용할 수 있는 사용자 권한의 효력을 상실할 수 있습니다. 警告 規制機関から明確な承認を受けずに本装置の変更や改造を行うと、本装置のユ ーザーとしての承認が無効になる可能性があります。 Warning: Use caution when working with any polymer tubing under pressure: •...
  • Page 21 Warnung: Bei der Arbeit mit Polymerschläuchen unter Druck ist besondere Vorsicht angebracht: • In der Nähe von unter Druck stehenden Polymerschläuchen stets eine Schutzbrille tragen. • Alle offenen Flammen in der Nähe löschen. • Keine Schläuche verwenden, die stark geknickt oder überbeansprucht sind. •...
  • Page 22 튜브를 부풀려 튜브의 파열 압력을 크게 감소시킬 수 있으므로 유의하십시오. 警告 圧力のかかったポリマーチューブを扱うときは、注意してください。 • 加圧されたポリマーチューブの付近では、必ず保護メガネを着用してください。 • 近くにある火を消してください。 • 著しく変形した、または折れ曲がったチューブは使用しないでください。 • 非金属チューブには、テトラヒドロフラン (THF) や高濃度の硝酸または硫酸など を流さないでください。 • 塩化メチレンやジメチルスルホキシドは、非金属チューブの膨張を引き起こす場合 があり、その場合、チューブは極めて低い圧力で破裂します。 This warning applies to Waters instruments fitted with nonmetallic tubing or operated with flammable solvents. February 20, 2023, 715008450 Ver. 00 Page 22...

  • Page 23: Warnings That Address The Replacement Of Fuses

    Warning: The user shall be made aware that if the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be impaired. Avertissement : L’utilisateur doit être informé que si le matériel est utilisé d’une façon non spécifiée par le fabricant, la protection assurée par le matériel risque d’être défectueuse.
  • Page 24 Avertissement : Pour éviter tout risque d’incendie, remplacez toujours les fusibles par d’autres du type et de la puissance indiqués sur le panneau à proximité du couvercle de la boîte à fusible de l’instrument. Warnung: Zum Schutz gegen Feuer die Sicherungen nur mit Sicherungen ersetzen, deren Typ und Nennwert auf den Tafeln neben den Sicherungsabdeckungen des Geräts gedruckt sind.

  • Page 25: Electrical Symbols

    Advertencia: Para evitar incendios, sustituir los fusibles por otros del tipo y características indicados en la sección "Sustituir fusibles" del capítulo Procedimientos de mantenimiento. 警告： 为了避免火灾，应更换“维护步骤”一章的“更换保险丝”一节中介绍的相同类型和 规格的保险丝。 警告： 為了避免火災，更換保險絲時，應使用「維護步驟」章節中「更換保險絲」所 指定之相同類型與規格的保險絲。 화재의 위험을 막으려면 유지관리 절차 단원의 “퓨즈 교체” 절에 설명된 것과 동일 경고...

  • Page 26: Handling Symbols

    Symbol Description Indicates that the device or assembly is susceptible to damage from electrostatic discharge (ESD) 2.9 Handling symbols The following handling symbols and their associated statements can appear on labels affixed to the packaging in which instruments, devices, and component parts are shipped. Symbol Description Keep upright!
  • Page 27 Symbol Description Temperature limitation February 20, 2023, 715008450 Ver. 00 Page 27...

  • Page 28: System Overview

    • Plug-and-play method compatibility with HPLC • Direct programming of gradients, in units of pH and ionic strength, using Waters Auto•Blend Plus technology to vary composition, eliminating the need to manually prepare mobile phases • Automatic management of gradient start time and pre-injection steps, in parallel, minimizing cycle time and maximizing sample throughput •...

  • Page 29: Flow-Through-Needle Injector

    3.1.1 Flow-through-needle injector The sample manager's FTN mechanism aspirates a sample and holds it in the sample needle, prepared to inject the sample onto the column. The needle serves as part of the injection flow path when the sample is pushed onto the column. The FTN mechanism facilitates the transfer of LC methods, improves injection accuracy, decreases cycle time for small-volume injections, and does not require learning new injection modes.

  • Page 30: Detector Features

    In addition to the core modules, the system includes a detector (TUV). 3.2.1 Detector features The detector operates as an integral part of a Waters chromatography system. The Alliance iS TUV Detector is an optical, two-channel, ultraviolet/visible (UV/Vis) absorbance detector designed for HPLC applications. For the Alliance iS System, this detector is configured with Empower Chromatography Data Systems (CDS) software.

  • Page 31: Detector Optics

    • Entrance slit • Blazed, plane-holographic, diffraction grating • Beamsplitter • Sample and reference photodiodes • Waters TaperSlit flow cell (its entrance is the exit slit of the monochromator) • Optional cuvette cell February 20, 2023, 715008450 Ver. 00 Page 31...
  • Page 32 Figure 3–2: TUV detector optics assembly 3.2.1.1.1 Optics assembly light path The detector employs an extremely efficient design for exceptionally high-light throughput. The detector employs an extremely efficient design for exceptionally high-light throughput. It operates as follows: 1. The ellipsoidal mirror collects light from the lamp and focuses it through the filter wheel and onto the entrance slit.
  • Page 33 The behavior of the filter depends on the filter time constant you select. You can program a filter time to be Fast, Slow, Normal, or Other. If you select Fast, Slow, or Normal, you do not need to specify a value. The filter constant is determined by the sampling rate. If you select Other, you can specify a value but it will be rounded up or down to a value based on the sampling rate.
  • Page 34 Figure 3–3: Filter time constant comparison 3.2.1.2 Wavelength verification and test The detector’s deuterium arc lamp and integral erbium filter exhibit peaks in the transmission spectrum at known wavelengths. Upon startup, the detector verifies calibration by comparing the locations of these peaks with expected wavelengths based on calibration data stored in the detector’s memory.

  • Page 35: Operational Modes

    • 379.0 nm • 521.5 nm The verification tests for the detector require five minutes of lamp warmup time. If you run the detector continuously, Waters recommends that you perform wavelength verification weekly by cycling power to the detector. 3.2.1.3 Operational modes Detector capabilities include two primary modes of operation.
  • Page 36 Table 3–2: Single-Wavelength mode, primary parameters (continued) Parameter Description Tip: Changing the sensitivity setting affects the 2-V output. Chart polarity (+ or –) Reverses the polarity of the charted chromatogram. Select + for a normal chromatogram, or select – for an inverted chromatogram.
  • Page 37 above 370 nm can contain inaccuracies because of possible UV light interference (second- order effects). 3.2.1.3.2.1 Chart-out function options When operating in Dual-Wavelength mode, the detector offers additional function options for analog outputs to those offered in Single-Wavelength mode. The default operating function for Dual-Wavelength mode is Absorbance.

  • Page 38: Spectrum Scanning

    and plots the resulting ratio on a data system over one output channel (channel A). Use this function when detecting hidden components within individual peaks. The RatioPlot of a spectrally homogeneous peak appears as a rectangular wave. The RatioPlot of an impure peak appears as a distorted wave. To obtain a RatioPlot, you must operate the detector in Dual-Wavelength mode.

  • Page 39: Pump Features

    3.2.1.5 Cuvette operations The detector's cuvette option is used to measure the absorbance spectrum of a sample in a cuvette. Note: This section pertains only to use of the optional cuvette cell. The detector's cuvette option is used to measure the absorbance spectrum of a sample in a cuvette.

  • Page 40: Sample Manager Features

    3.2.2.1 Pressure flow envelope The QSM provides steady (pulse-free) solvent flow at analytical flow rates of up to 5 mL/min at 10,000 psi and linear change to 4000 psi at 10 mL/min. 3.2.2.2 Pressure transducer overview The APT, which measures the pressure on the low-pressure side of the degasser system, is unaffected by altitude or barometric changes.
  • Page 41 Figure 3–4: Needle positioning mechanism’s dual-rotary axes, located below the sample compartment Platter rotary axis Belt Motor axis February 20, 2023, 715008450 Ver. 00 Page 41...

  • Page 42: Injection System

    Figure 3–5: Needle carriage's rotary axis, located inside the sample compartment Needle carriage Needle cartridge Needle carriage rotary axis 3.2.3.2 Injection system The injection flow path includes the assemblies required to aspirate a sample and deliver it to the column. The injection process involves the needle, optional extension loop, sample metering pump, injection valve, and injection/wash port.
  • Page 43 Figure 3–6: SM-FTN flow path for single‐draw aspiration and injection To Process .0625" ID Tygon ¼-28 PEEK Tee Waste ¼-28 Pin Plug .030" ID FEP Sample Metering Check Valve Pump Needle Seal Wash .005" ID PEEK Wash Solvent Solvent .010" ID SS Pressure Sample Manager Inject Valve...
  • Page 44 Figure 3–7: Needle seat assembly, cross view Angled wash manifold Sample needle support sleeve Fitting Seat Seat port assembly Seal cup locking nut Compression spring Needle wash housing The following figure shows standard injection mode cycle time. February 20, 2023, 715008450 Ver. 00 Page 44...
  • Page 45 Figure 3–8: Standard injection mode cycle time definition 3.2.3.3.1 Wash system The wash sequence does not allow wash solvent to enter the sample stream. The wash system cleans the exterior of the sample needle while it is inside the injection/wash port.

  • Page 46: Column Heater/Cooler Features

    8.0 mm ID and 300 mm length, and a single pre-column consumable, with maximum dimensions of 8.0 mm ID and 30 mm length. Note: Columns are not included as part of your system, but are available for purchase on the Waters website (www.waters.com). February 20, 2023, 715008450 Ver. 00 Page 46...

  • Page 47: Touchscreen Features

    3.2.4.3 eConnect technology Waters' new eConnect technology is a standard feature of the CHC that can be utilized by purchasing eConnect-enabled versions of Waters chromatographic columns. These columns are fitted with eConnect tags during manufacture. After you install an eConnect-tagged column in the CHC and shut the component's door, the tag is detected automatically.
  • Page 48 Table 3–6: Additional touchscreen controls Control Description System status One of: IDLE, RUNNING, or ERROR. Preferences Provides access to the following settings: Display and Themes, System Name, Lock Screen, Units and Numbers, Remote Access, and User Note. Volume Indicates whether system volume is on or muted. Camera If present, indicates that the system is controlled remotely by Empower.
  • Page 49 Figure 3–10: Setup view (main) See: • Priming a dry solvent manager via the touchscreen (Page 66) • Equilibrating the Alliance iS system (Page 83) • Preparing to shut down the Alliance iS system (Page 92) 3.2.5.3 Touchscreen Maintain view The following figure shows the actions provided by the Maintain view.
  • Page 50 ˚C and sample pressure in psi or a user-selected unit. Column module Provides the column compartment temperature. Access is limited to Analysts, diagnostic Managers, and Waters engineers. Detector Provides absorbance channels A and B in AU. Access is limited to Analysts, diagnostics Managers, and Waters engineers.
  • Page 51 Figure 3–13: Commands view See: • Equilibrating the Alliance iS system (Page 83) 3.2.5.7 Touchscreen System view The following figure shows the actions provided by the System view. February 20, 2023, 715008450 Ver. 00 Page 51...
  • Page 52 Figure 3–14: System view (main) Note: Scroll down to select any of these options: • Performance counters: Lamp hours, Volume pumped, Injection count • Leak sensors: Configure installed leak sensors • About: SW versions, HW versions, Product information 3.2.5.8 Touchscreen Preferences view The following figure shows the actions provided by the Preferences view.

  • Page 53: Empower Features

    • Waters: Alliance HPLC, Arc HPLC, and ACQUITY Arc • Agilent: Agilent1100 and Agilent1260 Waters' instrument modules whose parameters are mapped include Pump, Autosampler, Column Compartment, and Detector. Third-party mappings are specific to their instrument modules. Translated projects are viewable in Empower's Method Editor, which is opened through the iMTA.

  • Page 54: Auto Additions

    3.3 Auto Additions The Auto Additions feature is designed to save time by setting up an injection with as many as up to ten different samples. If you use Empower 3 to control the autosampler, you can use the Auto Additions function to make an injection composed of sample from as many as 10 vials, one of which is the sample vial.

  • Page 55: Installation And Configuration

    4 Installation and configuration This section helps you set up and configure your Waters system for use. Proper setup is critical to successful operation of the system. 4.1 Setting up the system Proper setup is critical to correct operation and performance of the system.

  • Page 56: Network Connections

    4.2.1 Network connections A network cable must be connected to an external workstation in order to communicate with Empower. Connect the network cable from the rear of the system to the acquisition client. Figure 4–1: Connecting network cable 4.2.2 Power connections A single cable provides power to the whole system.

  • Page 57: Making Solvent Bottle Connections

    Figure 4–2: Connecting power cable Note: The power cables connecting the CHC and the detector to the rear of the Integrated Fluidics Module (IFM) assembly will be in place at the time the system is installed and must not be replaced. 4.2.3 Making solvent bottle connections You will need to connect solvent bottles before the system can be used.

  • Page 58: Making Waste Connections

    4.2.4 Making waste connections Proper waste connections ensure that drips and system waste are routed to approved waste collection containers. To avoid solvent and sample spills, make waste connections from the appropriate system outlets to an approved waste container. Figure 4–3: Connecting the system to a waste container 4.2.5 Installing the column Install the column in the CHC prior to running samples.
  • Page 59 2. Move the lower column clip as necessary to match the size of the column. 3. Remove the plugs from the inlet and outlet ends of the column. 4. Orient the column so that the outlet faces up and the inlet faces down. 5.

  • Page 60: Powering-On The System

    4.3 Powering-on the system The Alliance iS system power button is located on the front door of the sample manager. After the system is plugged in, the power button LED will blink. To power-on the system: Push the power button located on the front door of the sample manager. The power button LED will light up solid and the system will power-on.

  • Page 61: Opening The Console From Empower Software

    Figure 4–6: Alliance iS power button 4.5 Opening the console from Empower software After powering-on the system, open the console from Empower. You can access the console from the Empower system status panel. 1. From Empower, click the arrow on the upper right-hand side of the system status panel. February 20, 2023, 715008450 Ver.
  • Page 62 Figure 4–7: Launching the system console 2. From the console, you can access configuration, diagnostics, and detailed statuses of all parts of the system. February 20, 2023, 715008450 Ver. 00 Page 62...

  • Page 63: Priming The System

    Figure 4–8: System console 4.6 Priming the system After powering-on the system, you must prime it before the system is ready for use. Requirement: You must prime the system after starting it, as well as after changing the mobile phase, after changing the sample needle, and after the system is idle for four hours or more. Recommendation: If you are introducing new solvents, prime them at 4 mL/min for seven minutes.

  • Page 64: Priming The Seal-Wash System

    sample temperatures, and needle characterization for your next system startup. For details, see the touchscreen. 4.6.1 Priming the seal-wash system Priming the seal wash system is part of the system startup workflow on the touchscreen. Prime the seal wash in the Alliance iS QSM to fill the tubing paths with solvent. Tip: When primed, the seal-wash system is used to lubricate the plungers and flush away solvent and any precipitated salts that were dragged past the plunger seals from the high-...

  • Page 65: Required Tools And Materials

    • Use seal wash that is fully soluble with all chromatographic solvents and that contains at least 10% organic solvent. This concentration prevents microbial growth and ensures that the seal wash can solubilize the mobile phase. • Before priming the seal-wash system, ensure that the volume of seal wash is adequate for priming.

  • Page 66: Priming The Pump

    4.6.2 Priming the pump After powering-on the system, prime the pump. Priming prepares a new system for use and for a change in reservoirs or solvents. It also prepares a system for restarting after it is idle for more than four hours. During priming, the vent valve moves to the vent position, allowing flow without disturbing the column or sample manager with minimum back pressure, and directing flow to waste.

  • Page 67: Priming The Sample Manager

    Figure 4–9: Location of solvent vent tubing Solvent vent tubing 3. On the touchscreen, tap Setup > Startup > NEXT. 4. From the Prime Solvents screen, select solvent line A, B, C, or D. 5. In the Priming Duration box, specify the number of minutes. Default: 2.0 minutes Recommendation:...

  • Page 68: Choosing Extension Loops

    • Preparing a new sample manager for operation. • Preparing a sample manager for operation after it has been idle for more than 24 hours. • Changing the wash solvent. • Removing bubbles from the lines. Ensure that the wash solvent is correctly composed, that it is of LC-MS grade, and that it is miscible with other solvents used in the system.

  • Page 69: Installing And Replacing Extension Loops

    Table 4–2: The following extension loops are available to use in the sample manager Loop size 50 µL 100 µL - Standard 250 µL 1000 µL 2000 µL Recommendations: • The recommended maximum injection volume is 75% of the total volume of needle and sample loop.

  • Page 70: Installing An Extension Loop In A Single-Valve System

    4.8.1 Installing an extension loop in a single-valve system In a single-valve system, the extension loop is installed between the pressure transducer and the sample needle. 1. If system flow is running, stop the flow. On the touchscreen, tap COMMANDS, and then tap the pause button next to Flow is On.

  • Page 71: Installing An Extension Loop In A Two-Valve System

    Figure 4–11: Single-valve system Extension loop with holder Sample needle tool-free fitting Pressure transducer 4. Install a different sized extension loop between the TFF adapter fitting and the sample needle. 5. See Modifying needle and extension loop configuration parameters (Page 73), for reporting the correct extension loop volume configuration in the touchscreen.
  • Page 72 Figure 4–12: COMMANDS screen 2. Open the sample manager fluidics door. 3. Disconnect the tool-free fitting that is attached to extension loop and to sample needle. Figure 4–13: Multidraw valve system Multidraw valve February 20, 2023, 715008450 Ver. 00 Page 72...

  • Page 73: Modifying Needle And Extension Loop Configuration Parameters

    Extension loop with holder Sample needle tool-free fitting 4. Using the tool-free fittings, install the extension loop between the multidraw valve and the sample needle. 5. See Modifying needle and extension loop configuration parameters (Page 73), for reporting the correct extension loop volume configuration in the touchscreen. 6.

  • Page 74: Choosing The Needle-Placement Setting

    Table 4–3: Maximum syringe draw rates (continued) Solvent type 48-µL needle 100% dimethyl sulfoxide (DMSO) TBD µL/min Increasing the syringe draw rate reduces the time required to aspirate sample. Note that increasing the draw rate too much results in poor area and height reproducibility. When increasing the draw rate, be sure to confirm the continued acceptability of the method.

  • Page 75: Recovering Maximum Sample From Vials

    (Page 103). See also: Waters Sample Vials and Accessories brochure on www.waters.com. 4.13 Creating a new plate type If the plate type is not set correctly in Empower, bent needles can result. 1. In Empower software, open the Configure System window.

  • Page 76: Creating A New Plate Type Using An Existing Plate Type As A Template

    5. Type the dimensions of the new plate type. 6. Click OK. See also: The console online Help for additional information about plate type properties and dimensions. 4.13.1 Creating a new plate type using an existing plate type as a template Starting with an existing plate type as a template can save time compared to creating an all new plate type.

  • Page 77: Determining When To Take The Needle And Extension Loop Offline

    • The Automatic setting causes the Sample Manager to wait for three times the volume of the needle and loop combined to flow before the injection valve position is changed to Load, to ensure that the sample has flowed completely out of the needle and loop. •...

  • Page 78: Choosing The Loop-Offline Option

    Tip: A programmed gradient typically flows through all parts of the instrument that contact the sample. If you initiate the needle and extension-loop offline option before the gradient reaches its final conditions, the highly organic portion of the gradient does not pass through the needle. As a result, the gradient can fail to remove all sample from the needle, resulting in low sample recovery and an increased risk of carryover.

  • Page 79: Method Management

    Extra-column effects can also be modified. See the Dwell Volume and Extra-Column Volume: What Are They and How Do They Impact Method Transfer white paper ( 720005723EN) on www.waters.com. Intelligent Method Translator (iMTA) (Page 53).

  • Page 80: Daily Routine Analysis

    6 Daily routine analysis 6.1 Starting the hardware and software After waking up the Alliance iS system, start the Empower control panel and Alliance iS console if Empower is not already running. Note: The Alliance iS system is assumed to be powered-up and asleep. System state is IDLE. If the system is powered-down, see Powering-on the system (Page 60).

  • Page 81: Setting Up Solvents

    Figure 6–2: Alliance iS console (to be updated) From the console, you can access configuration, diagnostics, and detailed statuses of all parts of the system. 7. Open the Empower project for the analysis. 6.2 Setting up solvents Mobile phase solvents and the seal wash, needle wash, and purge solvents are set up before running equilibration.
  • Page 82 Note: There can be up to four mobile phase solvent lines, identified by the system as A, B, C, and D. Pay particular attention to how the solvents are lettered in the project because their identifiers determine which solvent line to connect to each bottle. The seal wash, needle wash, and purge solvents have dedicated lines but it is possible for a method to specify filling a bottle with the same preparation as a mobile phase bottle.

  • Page 83: Installing The Column

    • Priming the seal-wash system (Page 64) • Priming the QSM (Page 66) • Solvent considerations (Page 208) • Replacing the solvent bottle filters (Page 156) • Replacing the optional solvent selection valve cartridge (Page 114) 6.3 Installing the column Install the column after loading the solvent bottles so that old mobile phase cannot pass through the new column.
  • Page 84 Figure 6–4: Prime Solvents screen 5. Select the solvent lines to be primed. 6. Increment or decrement Priming Duration in units of 30 seconds and tap Next. Note: You can also edit the minute or seconds fields manually. 7. If needed for the analysis, toggle-on Prime Seal Wash, enter Seal Wash Prime Duration in units of minutes and seconds, and tap Next.
  • Page 85 Figure 6–6: Equilibration Final Conditions and Flow Rate screen 14. Toggle-on Set Final Conditions. 15. Set Flow Rate using the keypad and tap Next to advance. Note: A minimum of five column volumes is recommended. Figure 6–7: Equilibration Composition screen 16.

  • Page 86: Preparing And Loading Samples

    Figure 6–9: Summary screen 19. Review the settings on the Summary screen and tap Start. The message System Startup In progress displays on the Status screen while equilibration is running. 20. When equilibration ends, examine the results to ensure that the system is ready for routine work.
  • Page 87 Sample preparation equipment Cleaning test sample glassware. 2. Fill the sample plates or trays as specified for the method. Waters vials are preferred. Observing vial and plate recommendations (Page 104). Tip: Vial positions V1 through V4, located on the right-hand and left-hand sides of the sample tray, accommodate 4-mL vials.

  • Page 88: Checking System Status And Health

    Figure 6–11: Loading a tray onto the sample platter Figure 6–12: Sample plate vial positions 7. Slide the plate or tray backwards until it clicks into place. Notice: To avoid damaging the sample needle, the sample plates must be positioned correctly, and the sample tray must be fully engaged. 8.

  • Page 89: Data Acquisition Checks

    • System is qualified: Checks the date set by Administration > System Qualification > Set the System Qualification. This date must be supported by valid documentation and test results, and is typically updated when a Waters engineer re-qualifies the system. Data acquisition cannot proceed if qualification is expired.

  • Page 90: Monitoring From The Empower Control Panel

    6.6.3 Monitoring from the Empower control panel You can monitor the Alliance iS HPLC system from the control panel of the Empower CDS, which appears at the bottom of the Run Samples window and can also launch through QuickStart menu. The control panel displays the current (or most recent) values of several parameters as follows: Figure 6–13: Empower control panel...

  • Page 91: Acquiring Data

    6.7 Acquiring data To acquire chromatographic data from the Alliance iS system, prepare and run the sample set in Empower. See the Data Acquisition, Acquiring Data section in the Empower online documentation. 6.8 Reviewing the results Review sample set results in Empower. See the Data Analysis section in the Empower online documentation.

  • Page 92: Preparing To Shut Down The Alliance Is System

    Figure 6–15: Sleep mode notification 6.11 Preparing to shut down the Alliance iS system Note: Powering-down the system (Page 60) for more information relating to shutdown. 1. On the touchscreen, tap Setup to see the Setup view (Page 48). 2. Tap Shutdown, read the guidance on the Welcome screen, and then tap Next to advance to the Sample Temperature screen.
  • Page 93 12. Tap Done. Shutdown continues to run in the background unless an error occurs. February 20, 2023, 715008450 Ver. 00 Page 93...

  • Page 94: Performance Optimization

    7 Performance optimization Review the following subjects related to your Alliance iS HPLC System: • General performance optimization guidelines (Page 94) • Preventing leaks (Page 96) • Setting up a method (Page 103) • Sample chamber considerations (Page 104) •...

  • Page 95: Carryover

    You can measure carryover by observing analyte peaks that appear when you run a blank sample immediately after an analytical sample. Waters specifies sample carryover on the Alliance iS System at 0.002% maximum. A common cause of carryover is inadequate washing of the system. Choosing an appropriate wash solvent can minimize carryover for a particular analysis.

  • Page 96: Preventing Leaks

    (downstream of the check valves) can leak solvent, but do not introduce air. To prevent leaks, follow Waters’ recommendations for the proper tightening of system fittings. Note that different techniques apply to re-tightening fittings versus installing them for the first time.
  • Page 97 Warning: To avoid personal contamination with biologically hazardous materials, wear clean, chemical-resistant, powder-free gloves when performing this procedure. Recommendations: • To prevent band spreading, ensure that the tubing is fully bottomed in its connection port before tightening the compression screw. •...
  • Page 98 Lock ring Ferrule End of lock ring with larger inside diameter (ID) Figure 7–2: Long 1/4-28 fitting with flangeless ferrule and stainless steel lock ring, first- use or reinstall Compression screw Lock ring Ferrule End of lock ring with larger inside diameter (ID) 7.2.1.2 High-pressure pin plug Tighten the pin plug finger-tight, plus approximately a 1/6-turn using a wrench.
  • Page 99 7.2.1.3 Metallic fitting with short or long flats and two-piece metallic ferrule (V-detail) The procedure for tightening metallic fittings differs for new versus reused fittings. First-use Tighten the fitting finger-tight plus an additional 3/4-turn using a 1/4-inch open-end wrench. For detailed instructions about assembling new fittings, see the Assembling new fittings section of the Alliance iS System Guide.
  • Page 100 Figure 7–7: Metallic fitting with short or long flats and two-piece metallic ferrule, first-use tightening Reinstall Tighten the fitting finger-tight plus as much as an additional 1/6-turn using a 1/4-inch open-end wrench. Figure 7–8: Metallic fitting with short flats and two-piece metallic ferrule, reinstall Short flats Compression screw Two-piece metallic ferrule...

  • Page 101: Required Tools And Materials

    Figure 7–10: Metallic fitting with short or long flats and two-piece metallic ferrule, reinstall tightening 7.2.1.3.1 Assembling new metallic fittings You must mark new metallic fittings before tightening them to ensure proper assembly. You must mark new metallic fitting and tubing assemblies with ferrules and ensure that the two marks are aligned when you tighten them.
  • Page 102 Figure 7–11: New fitting, first-use tightening 7.2.1.4 One-piece PEEK fitting Tighten the fitting finger-tight. Tips: • Before tightening this fitting, ensure that the tubing is fully bottomed in the connection port. • Using the aluminum flangeless nut extender (included in the system startup kit) will help achieve proper tightness of this fitting.

  • Page 103: Setting Up A Method

    Ferrule 7.2.1.6 Tool-free fitting Tighten the fitting finger-tight. Figure 7–14: TFF, first-use or reinstallation Retainer cap Compression screw Fitting collar Protective cap Face seal gasket Welded tubing assembly 7.3 Setting up a method You create a new method using the system's Empower software. (See Method management (Page 79) for information on measuring dwell volume and transferring...

  • Page 104: Sample Chamber Considerations

    7.5 Observing vial and plate recommendations Incorrect selection of sample vials and plates can lead to issues with system function and performance. Waters recommends that you observe these usage guidelines for sample vials and plates in the sample manager: • Vials •...

  • Page 105: Cycle Time Between Injections

    For maximum column lifetime, follow the manufacturer's recommendations at all times. To greatly improve column lifetime and performance, Waters recommends that you obtain and follow the manufacturer’s guidelines for operational ranges for column temperature, mobile phase pH, and buffer additives.

  • Page 106: Preventive Maintenance

    8 Preventive Maintenance 8.1 Maintenance This is the start of your concept. 8.2 Maintenance safety guidelines When performing maintenance procedures, adhere to the following safety guidelines. Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials. Consult the Safety Data Sheets regarding the solvents you use.

  • Page 107: Safety And Handling

    Wait 10 seconds before disconnecting an assembly. 8.5 Spare parts To ensure that your system operates as designed, use only Waters Quality Parts. Visit www.waters.com/wqp for information about Waters Quality Parts, including how to order them.

  • Page 108: Pump Maintenance

    Required tools and materials • Chemical-resistant, powder-free gloves • Protective eyewear To clean the exterior of the equipment: • Clean surfaces of the equipment using only a clean, soft, lint-free paper towel or clean cloth dampened with water. 8.8 Pump maintenance The customer can perform the following pump maintenance tasks: •...

  • Page 109: Servicing The Air Filter In The Door

    Maintenance procedure Frequency Replace the pump head and seal-wash As necessary housing Clean the device's exterior with a soft, lint-free As necessary cloth, or paper dampened with water 8.8.2 Servicing the air filter in the door Required tools and materials •...

  • Page 110: Replacing The Leak Sensor

    8.8.3 Replacing the leak sensor Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials. Consult the Safety Data Sheets regarding the solvents you use. Additionally, consult the safety representative for your organization regarding its protocols for handling such materials. Warning: To avoid personal contamination with biologically hazardous or toxic compounds, wear clean, chemical-resistant, powder-free gloves when performing this procedure.

  • Page 111: Replacing The Mixer

    Leak sensor connector 4. Grasp the leak sensor by its serrations and pull upward on it to remove it from its reservoir. Figure 8–3: Leak sensor serrations Serrations 5. Unpack the new leak sensor. 6. Align the leak sensor’s T-bar with the slot in the side of the leak sensor reservoir, and then slide the leak sensor into place.

  • Page 112: Replacing The Vent Valve Cartridge

    Required tools and materials • • • To replace the mixer: Enter your first step here. 8.8.5 Replacing the vent valve cartridge Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials. Consult the Safety Data Sheets regarding the solvents you use.
  • Page 113 Figure 8–6: Location of construction material indicator Valve cartridge construction material indicator 5. Use the 1/4-inch open-end wrench to remove the fittings attached to the vent-valve cartridge. 6. Use the 2-mm hex wrench to remove the hex screw at the 10-o’clock position on the vent-valve cartridge.

  • Page 114: Replacing The Optional Solvent Selection Valve Cartridge

    • Orient the new cartridge exactly as the old one was oriented. • The vent-valve cartridge must slide fully into the vent-valve cartridge chamber. If it does not, report the problem to Waters Technical Service. 11. Insert the 2-mm hex screw at the 10-o’clock position on the vent-valve cartridge.
  • Page 115 Required tools and materials • Chemical-resistant, powder-free gloves • Protective eyewear • 2-mm hex wrench (startup kit) • Solvent selection valve cartridge To replace the optional solvent selection valve cartridge: 1. Open the solvent manager’s door. 2. Ensure that the solvent-selection valve is set to D Warning: To avoid injuries arising from contact with spilled solvent (the result of unintentional siphoning), move the solvent bottles to a location below the solvent...
  • Page 116 Figure 8–10: Location of construction material indicator Valve cartridge construction material indicator. 5. Remove the finger-tight fittings attached to the solvent selection valve cartridge. 6. Use the 2-mm hex wrench to remove the hex screw at the 10 o’clock position on the cartridge.

  • Page 117: Replacing The In-Line Filter Cartridge On The Primary Check Valve

    • Orient the new cartridge exactly as the old one was oriented. • The cartridge must slide fully into the solvent selection valve assembly. If it does not, report the problem to Waters Technical Service. 11. Insert the 2-mm hex screw at the 10 o’clock position on the solvent selection valve cartridge, and then use the 2-mm hex wrench to tighten it.
  • Page 118 Required tools and materials • Chemical-resistant, powder-free gloves • In-line filter cartridge To replace the in-line filter cartridge on the primary check valve: Requirement: Wear clean, chemical-resistant, powder-free gloves when replacing the in-line filter cartridge on the primary check valve. Flush the solvent manager with nonhazardous solvent.
  • Page 119 Figure 8–14: Removing cap nut from ferrule holder fitting Ferrule holder fitting Cap nut 5. Pull the cap nut off the tube to remove the in-line filter cartridge. Figure 8–15: Pulling cap nut from tube In-line filter cartridge Cap nut Tube February 20, 2023, 715008450 Ver.
  • Page 120 Figure 8–16: In-line filter cartridge, locking ring, and cap nut In-line filter cartridge Metal locking ring Cap nut Tube 6. Inspect the filter cartridge to determine whether it is constructed of stainless steel or titanium, and ensure that you have the correct replacement cartridge. No marking indicates a filter cartridge constructed of stainless steel, and "Ti"...
  • Page 121 Figure 8–17: Sliding cap nut on tube Cap nut Tube 8. Slide the metal locking ring onto the tube, ensuring that the thicker end of the metal locking ring is facing toward the cap nut. Figure 8–18: Sliding metal locking ring on tube Metal locking ring Thicker end of metal locking ring facing toward cap nut Tube...
  • Page 122 Cap nut 9. Unpack the new inline filter cartridge. 10. Place the new in-line filter cartridge onto the end of the tube. Figure 8–19: Placing in-line filter cartridge onto end of tube In-line filter cartridge Tube Cap nut 11. Insert the in-line filter cartridge with tubing into the ferrule holder fitting and finger-tighten the cap nut to the extent possible.

  • Page 123: Replacing The Check Valve Filter

    Figure 8–20: Installing cap nut on ferrule holder fitting Ferrule holder fitting Cap nut 12. Power-on the solvent manager. 13. Prime the solvent manager (see Priming the solvent manager). 8.8.8 Replacing the Check Valve Filter Provide context for your task here (optional). Required tools and materials •...

  • Page 124: Replacing The Accumulator Check Valve

    8.8.9 Replacing the accumulator check valve Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials. Consult the Safety Data Sheets regarding the solvents you use. Additionally, consult the safety representative for your organization regarding its protocols for handling such materials. Warning: To avoid eye injury, use eye protection when performing this procedure.
  • Page 125 Figure 8–21: Compression fitting on the check valve Place the 5/16-inch open-end wrench here Compression fitting Notice: When you remove the valve assembly, ensure that the PEEK washer, which is normally on the top face of the check valve, does not remain in the pump head.
  • Page 126 Figure 8–23: Accumulator check valve Chamfered edge PEEK washer Check valve Check valve housing 1/2-inch hex nut 5/16-inch open-end wrench flat 8. Insert the check valve assembly into the pump head, tighten the check valve nut with your fingers to the extent possible, and then use the 1/2-inch wrench to tighten the nut an additional 1/8-turn.

  • Page 127: Replacing The Accumulator Check Valve

    8.8.10 Replacing the accumulator check valve A blocked or faulty check valve can cause the system pressure to drop to near zero during operation. The check valve allows system fluid to flow in one direction, from the inlet to the outlet, and prevents fluid backflow.
  • Page 128 3. Insert the new check-valve 1/8 turn past finger tight. 4. Reattach the inlet tubbing fitting 1/4 past finger tight. 5. Prime the quaternary pump. February 20, 2023, 715008450 Ver. 00 Page 128...

  • Page 129: Replacing The Accumulator Check Valve

    8.8.11 Replacing the accumulator check valve A blocked or faulty check valve can cause the system pressure to drop to near zero during operation. The check valve allows system fluid to flow in one direction, from the inlet to the outlet, and prevents fluid backflow.
  • Page 130 2. Remove the inlet tubbing. 3. Remove the check valve. 4. Insert the new check-valve 1/4 turn past finger tight. February 20, 2023, 715008450 Ver. 00 Page 130...

  • Page 131: Replacing The Accumulator Check Valve - Video

    5. Reattach the inlet tubbing fitting 1/8 past finger tight. 6. Prime the quaternary pump. 8.8.12 Replacing the accumulator check valve - video A blocked or faulty check valve can cause the system pressure to drop to near zero during operation.
  • Page 132 • 1/2-inch open-end wrench • Accumulator check-valve assembly (70001064) Before you begin, be sure to flush the system with nonhazardous solvent. To replace the accumulator check valve: 1. Open the bottom door and locate the check valve. 2. Remove the inlet tubbing. 3.

  • Page 133: Replacing The Pump Plungers And Seals

    5. Reattach the inlet tubbing fitting 1/8 past finger tight. 6. Prime the quaternary pump. 8.8.13 Replacing the pump plungers and seals The primary and actuator pump plungers and seals should be replaced annually to ensure reliable system performance, or when issues related to worn or damaged seals and plungers arise, such as: leak test failures, unstable pressure, and shifting retention times.

  • Page 134: Replacing The Primary Pump Head And Accumulator Pump Head Plunger And Seals

    8.8.14 Replacing the primary pump head and accumulator pump head plunger and seals Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow. Use these procedures to replace the following: •...

  • Page 135: Required Materials

    Replace the pump head components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged. Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials. Consult the Safety Data Sheets regarding the solvents you use.
  • Page 136 6. Tap Move Backward, and then wait for the plunger to stop. 8.8.14.2 Removing the primary pump head or accumulator pump head Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow.
  • Page 137 To remove the primary pump head or accumulator pump head: Requirement: Wear clean, chemical-resistant, powder-free gloves when removing the primary pump head or accumulator pump head. Locate the seal wash tubing secured to the seal wash housing with barbed fittings. Use needle-nose pliers to remove the seal wash tubing.
  • Page 138 Figure 8–25: Loosening cap nut on inlet filter fitting Inlet filter fitting Cap nut b. Unscrew and remove the inlet filter fitting and cap nut from the primary check valve. Figure 8–26: Unscrewing inlet filter fitting and cap nut from primary check valve Primary check valve Inlet filter fitting...
  • Page 139 3. Follow these steps if replacing the accumulator pump head only. Proceed to step 4 to resume procedures for replacing the primary pump head. a. Using the 5/16-inch open-end wrench to hold the check valve cartridge in place, disconnect the tubing connection from the check valve using the 1/4-inch open-end wrench.
  • Page 140 6. Stand the pump head upright on a clean surface. 8.8.14.3 Removing the pump head plunger Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow.
  • Page 141 Notice: To avoid contaminating system components, wear clean, chemical-resistant, powder-free gloves when performing this procedure. Recommendation: Replace the plunger seals when you replace the plunger. Required tools and materials • Chemical-resistant, powder-free gloves • Protective eyewear • Plunger removal tool (recommended) To remove the pump head plunger: 1.
  • Page 142 Plunger Plunger removal tool 8.8.14.4 Removing the pump head seals Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow. Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials.
  • Page 143 Figure 8–33: Releasing support plate from pump head (this image does not show the transducer) Head bolts Support plate 3. Lift the pump head from the support plate. Figure 8–34: Lifting pump head from support plate Pump head Seal wash housing Support plate 4.
  • Page 144 Figure 8–35: Lifting seal wash housing from support plate Seal wash housing Support plate 5. Remove the old seal wash seal from the seal wash housing and discard the old seal. Figure 8–36: Seal wash seal Seal wash seal Seal wash housing Notice: To avoid scratching any metal surfaces, use care when screwing the threaded end of the seal removal tool into the plunger seal.
  • Page 145 Figure 8–38: O-ring location in pump head O-ring 8.8.14.5 Installing the new pump head seals Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow. Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials.
  • Page 146 Note: If necessary, you can also replace the seal wash housing during this procedure. Required tools and materials • Chemical-resistant, powder-free gloves • T27 TORX driver • Seal-extraction tool • Methanol • Fluoropolymer O-ring • Plunger seal and plunger seal back-up ring •...
  • Page 147 Figure 8–40: Plunger seal location in seal wash housing Plunger seal and back-up ring Insert threaded end of seal extraction tool here 4. With the seal wash seal cavity facing upward, orient the seal wash housing so that the holes on its side align with the holes on the side of the pump head, and then guide it into place.
  • Page 148 5. Press the seal wash seal into the cavity gently with the soft side of your thumb. Figure 8–42: Installing seal wash seal in seal wash housing Seal wash seal Seal wash housing 6. Place the support plate on top of the pump head, ensuring that the support plate's smaller boss is facing toward the pump head and the round side of the plate is oriented toward the bottom side of the pump head.
  • Page 149 Figure 8–44: Round side of support plate oriented toward bottom side of pump head Round side of support plate Bottom side of pump head 7. Holding the assembly together, use a T27 TORX driver to fully tighten the pump head screws, and then loosen 1/2 turn.
  • Page 150 8.8.14.6 Installing the new pump head plunger Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow. Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials.
  • Page 151 Plunger (sapphire part) Support plate 8.8.14.7 Reinstalling the primary pump head or accumulator pump head Replace pump components annually in accordance with the Waters preventive maintenance (PM) schedule, or any time they appear damaged to prevent a disruption in your workflow. Warning: Observe Good Laboratory Practice (GLP) at all times, particularly when working with hazardous materials.
  • Page 152 To reinstall the pump head: Notice: To avoid damaging the plunger, ensure that the pump head assembly is not tilted relative to the actuator housing when you position it on the mechanism. 1. Verify that the actuator piston is moved backward. If not, complete Moving the pump plunger backward (Page 136), and then continue to the next step.
  • Page 153 a. Finger-tighten as tight as possible. b. Use the 1/4-inch open-end wrench to tighten the fitting an additional 1/6-turn for existing fittings or 3/4-turn for new fittings. Figure 8–50: Outlet tubing fitting on pump head Outlet tubing Outlet tubing fitting Primary pump head 5.
  • Page 154 Figure 8–52: Inserting inlet filter fitting and cap nut into primary check valve Primary check valve Inlet filter fitting Cap nut Figure 8–53: Tightening inlet filter fitting and cap nut on primary check valve Primary check valve Inlet filter fitting February 20, 2023, 715008450 Ver.
  • Page 155 Cap nut 7. Finger-tighten the cap nut as tight as possible. Figure 8–54: Tightening cap nut on inlet filter fitting Primary check valve Inlet filter fitting Cap nut 8. Reinstall the seal wash tubing on the barbed fittings on the seal wash housing. Figure 8–55: Location of seal wash tubing Location of seal wash tubing Location of seal wash tubing...

  • Page 156: Replacing The Solvent Bottle Filters

    8.8.15 Replacing the solvent bottle filters A clogged solvent bottle filter can cause weak or intermittent loss of prime, a bad gradient profile, retention time shifts, and broad peaks. A contaminated solvent bottle filter can cause a contamination peak to be observed. Solvent bottle filters are critical clean parts made of stainless steel to protect your system from contamination.

  • Page 157: Washing The Needle's Exterior

    Maintenance procedure Frequency Replace the sample needle and needle guide When its capacity or material compatibility doesn’t suit your chromatographic needs, or as needed Replace the sample syringe During scheduled, routine maintenance, when its capacity doesn’t suit your chromatographic needs, or as needed Replace the wash syringe During scheduled routine maintenance or as needed...

  • Page 158: Calibrating The Needle Z Axis

    8.9.2.1 Stopping a needle wash routine before it finishes You can interrupt an active needle wash routine through the console. To stop a needle wash routine before it finishes: In the sample manager information window, click Control > Reset SM. Alternative: In the sample manager control panel of the data application, right-click, and then click Reset SM.

  • Page 159: Replacing The Needle

    Replace the needle annually during the prescribed preventive maintenance (PM) schedule or any time the needle appears damaged or bent. Recommendation: Waters Technical Service recommends that you replace the needle seal each time you replace the needle. See Replacing the needle seal and return line > not return line (Page 169) after you complete this procedure.
  • Page 160 Figure 8–56: Captive screw on access panel Captive screw 7. Unscrew the needle from the finger-tight fitting, and then release it from the clip. Figure 8–57: Sample needle location Image will show the following: Sample needle Finger-tight fitting Clip 8. Locate the two needle latches (one on the needle carriage and one on the right side of the compartment).
  • Page 161 Figure 8–58: Two needle latches in closed position Needle tubing Needle latches Notice: Subsequent drafts will show the system with only the top notch as described in the caption. Figure 8–59: Image to be updated (Needle latches/grooves are different) >>Needle latches in open position Notch Needle tubing...
  • Page 162 Latches Ferrule Warning: To avoid puncture injuries, handle sample needles, syringes, fused silica lines, and borosilicate tips with extreme care. Notice: To avoid damage to the end of the needle, do not touch or press the end of the sample needle. 9.
  • Page 163 Figure 8–61: Need new pic >> Sample needle assembly Fitting ID sleeve HPS identifier Mounting sleeve Needle mounting cylinder Needle tip Protective sleeve Warning: To avoid puncture injuries, handle sample needles, syringes, fused silica lines, and borosilicate tips with extreme care. Notice: To avoid damage to the end of the needle, do not touch or press the end of the sample needle.
  • Page 164 Figure 8–62: ***Once available, will replace with a new image and step for updated system >>Installing needle assembly in sample compartment Needle tip Piercing needle Needle tubing loop at the back of the sample compartment 13. Insert the ferrule into the mounting cavity. Figure 8–63: ***Once available, will replace with a new image and step for the updated system >>Ferrule in mounting cavity Ferrule...
  • Page 165 14. Route the needle tubing through the two notches below the Z-flag. Figure 8–64: ******Once available, will replace with a new image and step for the updated system Notches Needle tubing Z-flag 15. Close the needle latch, as shown here, to secure the needle assembly. Notice: Subsequent drafts will show the system with one needle latch as described in the caption.
  • Page 166 Figure 8–65: Needle latch in closed position Needle tubing Needle latch 16. ***Once available, will replace with a new image and step for the updated system >> Ensure that the needle tubing is routed to the left-hand side of the needle carriage’s rails and that it is secured in the guide channel on the roof of the compartment.
  • Page 167 Note: You might need to slightly rotate or twist the needle to ensure that it routes straight down the channel before tightening the screw on the needle tubing clamp. 19. ***Need new image and step for the updated system >> At the needle tubing clamp, bend the needle to the right toward port 4 on the injection valve.
  • Page 168 Follow the steps outlined in Running the needle seal readiness test (Page 204). 27. Waters recommends that you replace the needle seal each time you replace the sample needle (see Replacing the needle seal and return line > not return line (Page 169).

  • Page 169: Replacing The Needle Seal And Return Line > Not Return Line

    8.9.5 Replacing the needle seal and return line > not return line To prevent a disruption in your workflow, replace the needle seal and return line annually during the prescribed preventive maintenance (PM) schedule or any time the seal appears dirty, contaminated, or clogged.
  • Page 170 Result: The needle carriage moves toward the back of the sample compartment. 5. Open the sample compartment door and the fluidics compartment door. 6. Using the T20 TORX driver, loosen the captive screw that secures the access panel, and then remove the panel. Notice: Image to be updated when showing the one screw (see caption).
  • Page 171 Figure 8–71: Location of tubing on the wash station Wash station assembly Wash station tubing Injector 8. To remove the wash station assembly, push down on it, and then rotate and lift up to release. Remove the wash station. Notice: Image to be added showing the wash station and holder.
  • Page 172 Figure 8–73: Sliding support sleeve out of the housing Support sleeve Seal port tube Slot Spring cup Load cell cable (Not in Beta system) Spring Housing Locking nut 10. Locate the locking nut attached to the bottom of the wash station that houses the needle seal.
  • Page 173 Seal Locking nut Seal port 12. Waters recommends replacing the return line when you replace the needle seal. To remove the return line: a. Remove one end of the return line from the inject valve. b. Unscrew the finger-tight fitting.
  • Page 174 Figure 8–76: Return line location in the locking nut >> insert image from Arc Return line Locking nut Notice: To prevent contaminating system components, wear clean, chemical- resistant, powder-free gloves, and work on a clean surface when replacing the seal. 13.
  • Page 175 Figure 8–78: Seal notch Seal Notch Seal cup Pin (Subsequent drafts will not include this pin) 14. Finger-tighten the locking nut into the bottom of the wash station. Notice: Image to be added showing an updated locking nut and seal port. Figure 8–79: Locking nut on the washing station Washing station support sleeve Locking nut...
  • Page 176 Figure 8–80: Wrench placement locations Place one 7/16-inch open-end wrench here Place the other 7/16-inch open-end wrench here 16. Ensure that the seal port tube remains in line with the threaded hole in the support sleeve. Notice: Image to be updated showing an updated seal port tube, locking nut and seal port.
  • Page 177 17. Slide the seal port tube into the slot on the side of the housing. Notice: This image shows a load cell cable. Image to be updated showing no load cell cable and an updated locking nut and seal port. The seal port now has a groove cut into it for the tubing and also has the prongs on it.
  • Page 178 Figure 8–83: Support sleeve in housing Fitting hole Slot 19. Ensure that the seal port tube is bent upward at a 90-degree angle, and that it is approximately 2.5 cm (1.0 inch) from the housing. Note: To avoid binding the seal port tube, ensure that the tube does not contact either side of the inject/wash station assembly.
  • Page 179 Notice: Image to be added showing an updated clip. Figure 8–85: Wash tubing secured by clip on sample compartment wall Wash tubing Clip 22. Using your fingers, tighten the PEEK fitting that secures the wash station to the sample compartment floor. Figure 8–86: Wash station assembly Wash station PEEK fitting...
  • Page 180 Figure 8–87: Tubing and cable locations Wash tubing Seal port tube Load cell cable (Not in Beta system) 24. Screw the seal port’s fitting into port 1 of the injection valve, and then use the 1/4-inch open-end wrench to tighten the fitting 1/4-turn beyond finger-tight. February 20, 2023, 715008450 Ver.
  • Page 181 Figure 8–88: Seal port tube location on injection valve Seal port tube 25. Reinstall the access panel, and then use the T20 TORX driver to tighten the one screw to secure the panel to the front of the unit. Requirement: Ensure that the seal port tube and sample needle tubing are routed through the gap in the access panel and that they do not cross each other.

  • Page 182: Replacing The Inject Valve

    Figure 8–89: Tubing routed through access panel gap Seal port tube Access panel gap Needle tubing 26. Close the sample compartment door and the fluidics compartment door. 27. You must complete the needle seal readiness test to verify that the needle seal works properly.

  • Page 183: Detector Maintenance

    Enter your first step here. 8.10 Detector maintenance The customer can perform the following detector maintenance tasks: • 8.10.1 Replacing the detector's leak sensor The detector has a leak sensor in the drip tray that monitors the detector for leaks. The sensor stops system flow when it detects accumulated, leaked liquid in its reservoir.
  • Page 184 3. Remove the leak sensor from its reservoir by grasping it by its serrations and pulling upward on it. Figure 8–91: Removing the leak sensor Serrations 4. Unpack the new leak sensor. 5. Align the leak sensor’s T-bar with the slot in the side of the leak sensor reservoir. Figure 8–92: Align the leak sensor T-bar with the slot on the leak sensor reservoir T-bar Slot on the leak sensor reservoir...

  • Page 185: Replacing The Flow Cell

    Figure 8–93: Leak sensor installed in leak sensor reservoir Leak sensor installed 7. Plug the leak sensor connector into the front of the instrument. 8. In the console, select your detector from the system tree. 9. In the detector information window, click Control > Reset to reset the detector. 8.10.2 Replacing the flow cell To prevent system errors, replace the flow cell annually during the prescribed preventive maintenance (PM) schedule or any time it appears dirty, contaminated, or clogged.
  • Page 186 1. Use the touchscreen to set the following preconditions: • Power-off the lamp. • Stop the solvent flow. • Place the detector in low-power state. From the touchscreen tap Maintain > Replace Components > Replace Flow Cell. 2. Tap NEXT until you view the Preconditions option, and then tap START to set the preconditions.
  • Page 187 Note: To avoid damaging the capillary tubing, do not touch it. 6. Unpack and inspect the new flow cell, ensuring that the flow cell type is correct for your application. Note: When replacing the flow cell, replace the flow cell inlet tubing with the tubing included with the new flow cell.

  • Page 188: Replacing The Lamp

    Lamp Change Record table. Note: Waters warrants 2000 hours of lamp life, or one year since date of purchase, whichever comes first. Warning: To prevent burn injuries, allow the lamp to cool for 30 minutes before removing it.
  • Page 189 Figure 8–96: Lamp assembly cover Lamp assembly cover Phillips head screw 8. Disconnect power to the lamp, and then disconnect the cord. 9. Loosen the two captive screws in the lamp base. Figure 8–97: Lamp assembly base captive screws 10. Lift out the lamp assembly from the lamp housing. Notice: To prevent shattering the glass, use care when disposing of the lamp because the lamp gas is under slight negative pressure.
  • Page 190 Figure 8–98: Removing the lamp assembly 11. Position the new lamp so the cut-out located on the lamp base is at the 1 o’clock position, in line with the alignment pin on the lamp housing. Figure 8–99: Aligning the lamp Cut-out on lamp base at 1 o’clock position Alignment pin on lamp housing 12.

  • Page 191: Column Heater Maintenance

    8.11 Column heater maintenance The customer can perform the following column heater maintenance tasks: • 8.11.1 Recommended maintenance schedule for the column heater Maintenance procedure Frequency Replace solvent filters During scheduled routine maintenance or as necessary Clean the air filter in the door As necessary Replace the air filter in the door During scheduled routine maintenance or as...

  • Page 192: Replacing The Column

    (PM) schedule or any time that you notice peak shape problems or loss of resolution. If installing a Waters-branded column, this procedure requires no tools. You can easily replace it using the column clips and tool-free fittings. Replacing the column involves removing the following: •...
  • Page 193 Figure 8–100: Removing the column from the black clips Top black clip Bottom black clip c. Locate the fasteners that secure the tubing at the top of the column compartment, and then remove the tubing from fasteners 2 through 4 only. Tip: You will not remove the tubing from fastener 1 because it secures the tubing to another module (and should remain connected).
  • Page 194 Figure 8–101: Four fasteners that secure the tubing d. Unscrew the fitting located on the bottom of the column, and set aside to install the new column. e. Unscrew the fitting located on the top of the column, and set aside to install the new column.
  • Page 195 10. Insert the column into the upper and lower black clips, ensuring that each black clip grasps the exposed threads on the tool-free fitting. Figure 8–102: Installing the replacement column 11. Close the column compartment door. Note: Verify that the tubing is situated inside the compartment before you close the column compartment door.

  • Page 196: Servicing The Air Filter

    8.11.3 Servicing the air filter Required tools and materials • Mild detergent and water • Air filter (if replacing) To service the air filter: 1. Open the bottom door. 2. Slide the air filter up and out of the frame inside the door. Figure 8–103: Door air filter Air filter Air filter frame...

  • Page 197: Troubleshooting

    9 Troubleshooting 9.1 Symptoms Use this list of symptoms to get more information about unexpected or undesirable behaviors and how to fix them. Symptom Description Possible Cause Slow baseline drift The baseline slowly drifts • Ambient temperature upward. • Contaminated solvent •...

  • Page 198: Resolving Solvent Issues

    9.3 Resolving solvent issues This section explains how to resolve problems caused by incorrect or contaminated solvents. This is the start of your concept. 9.4 Resolving sample issues This section explains how to resolve problems caused by incorrect or contaminated samples. This is the start of your concept.
  • Page 199 How to perform a dynamic leak test (Page 200) Describes how to test the system for leaks. Replacing the leak sensor (Page 110) Describes how to replace a faulty leak sensor. 9.5.2.1 Overview Leak sensors in the drip trays continuously monitor the system for leaks. A leak sensor stops system flow when its optical sensor detects about 1.5 mL of accumulated, leaked liquid in its surrounding reservoir.

  • Page 200: Responding To A Leak Sensor Alarm

    9.5.2.3 Drying the leak sensor Provide context for your task here (optional). Enter your first step here. 9.5.2.4 How to perform a dynamic leak test Performing a dynamic leak test: 1. Ensure that the solvent line is fully submerged in solvent in the solvent reservoir. 2.
  • Page 201 Notice: To avoid scratching or otherwise damaging the leak sensor: • Do not allow buffered solvents to accumulate and dry on it. • Do not submerge it in a cleaning bath. Required tools and materials • Chemical-resistant, powder-free gloves • Cotton swabs •...

  • Page 202: Diagnostic Tests

    Prism Tip: If you cannot easily manipulate the leak sensor after removing it from its reservoir, detach the connector from the front of the device (see Replacing the leak sensor (Page 110)). 6. Use a nonabrasive, lint-free wipe to dry the leak-sensor prism. 7.

  • Page 203: Running The System Leak Test

    tubing. It indirectly confirms that there is no drop in system pressure when it registers a positive rise in pressure. The Maintain menu also lists these functions: • Replace components, which enables you to replace the sample syringe, needle, and needle seal.

  • Page 204: Running The Needle Seal Readiness Test

    5. From Setup, specify the flow rate, and then tap NEXT. Recommendation: Waters recommends that you specify a flow rate of 1.000 mL/min. 6. Review the Summary page, and then tap START to run the test. The test completes in approximately two minutes.

  • Page 205: System Upgrade

    4. Install the new version by running the following command: OrionSystemSetup.exe Note: If during the ICS installation an error indicates that the WatersNGINXInstrumentService service cannot start, refer to the work-around on https://code.waters.com/confluence/x/hQNHTQ. 10.3 Kiosk/console updates Note: Under construction. 10.4 Firmware updates Note: Under construction.

  • Page 206: System Release Notes

    10.5 System release notes Note: Under construction. February 20, 2023, 715008450 Ver. 00 Page 206...

  • Page 207: Disposal Protocols

    11 Disposal protocols Disposal of system components is performed either by Waters personnel or by the customer per local jurisdiction. 11.1 Description of constituent materials For detailed descriptions of Waters materials, see Safety Data Sheets on waters.com. 11.2 Disposal of system components Disposal of system components is performed either by Waters personnel or by the customer per local jurisdiction.

  • Page 208: Solvent Considerations

    Explore the Waters website for resources on controlling contamination. For information about preventing and eliminating contamination, refer to Controlling Contamination in LC/MS Systems (715001307) on the Waters website (www.waters.com). 12.1.1 Clean solvents Clean solvents ensure reproducible results and permit operation with minimal instrument maintenance.

  • Page 209: Water

    12.2 Solvent recommendations This section provides information on wash and purge solvents and lists the solvents recommended for your system. Contact Waters Customer Service or Marketing to determine whether you can use solvents not addressed by the these lists without adversely affecting component or system performance.
  • Page 210 You can use the solvents listed below in your system. Note: Without the appropriate compatibility kit, these solvents can shorten equipment life. If you routinely use the solvents on this list, Waters recommends that you install a hexane/THF compatibility kit. See: Hexane/THF compatibility kit (Page 210) •...

  • Page 211: Cleaning Agents

    Cleaning agents require short (less than 30 minutes) contact time when flushing instruments. • Formic acid (≤30%) • Phosphoric acid (≤30%) • Sodium hydroxide (≤1M) See also: The cleaning procedures in Controlling Contamination in LC/MS Systems (715001307) on the Waters website (www.waters.com). February 20, 2023, 715008450 Ver. 00 Page 211...

  • Page 212: Wash Solvent Guidelines

    Notice: To avoid damaging and clogging components in the wash and purge flow path, Waters recommends not using nonvolatile buffers or additives as wash solvents. See also: Wash solvent recommendation (Page 212) for details on the Waters recommendation regarding nonvolatile buffer solutions.

  • Page 213: Solvents To Avoid

    12.2.2.2 Optional uses for wash solvents You have the option to utilize wash solvents for these additional purposes. • By default, the system washes the exterior of the sample needle after an injection, but you can choose to also utilize wash solvents in an optional procedure that cleans the exterior of the needle before or after an injection.

  • Page 214: Material Limitations For Strong Acids And Bases

    Additionally, consult the safety representative for your organization regarding its protocols for handling such materials and follow good laboratory practices. For recommended system cleaning and flushing procedures, contact Waters. See also: The cleaning procedures in Controlling Contamination in LC/MS Systems (715001307) on the Waters website (www.waters.com).

  • Page 215: Integrated Fluidics Module Solvent Recommendations

    10% of an organic solvent, such as ACN or MeOH. • To determine whether a specific method is suitable for use with your systems’ components, contact your Waters sales representative or local technical support organization. 12.4.1 Integrated Fluidics Module solvent recommendations To optimize overall performance without adversely affecting the sample manager and pump hardware, follow certain solvent recommendations.

  • Page 216: Detector Solvent Recommendation

    • Notice: To avoid damaging and clogging components in the wash and purge flow path, Waters recommends not using nonvolatile buffers or additives as wash solvents. IPA or organic solvents are effective seal wash solvents for normal-phase separations that employ mobile phases of intermediate polarity (such as hexane or THF). When you...
  • Page 217 Table 12–1: Properties of common solvents (continued) Solvent Vapor pressure mm Boiling point (°C) Flash point (°C) Hg (Torr) Cyclopentane 400 at 20 °C 49.26 o-Dichlorobenzene 1.2 at 20 °C 180.48 Dichloromethane 350 at 20 °C 39.75 –– Dimethyl acetamide 1.3 at 25 °C 166.1 Dimethyl sulfoxide...

  • Page 218: Solvent Miscibility

    Table 12–1: Properties of common solvents (continued) Solvent Vapor pressure mm Boiling point (°C) Flash point (°C) Hg (Torr) Trifluoroacetic acid 97.5 at 20 °C 71.8 Water 17.54 at 20 °C 100.0 –– o-xylene 6 at 20 °C 144.41 12.6 Solvent miscibility Before you change solvents, refer to the following table to determine solvent miscibility.

  • Page 219: Using Miscibility Numbers (M-Numbers)

    Table 12–2: Solvent miscibility (continued) Polarity Solvent Viscosity cP, Boiling point Miscibility λ cutoff (nm) index 20 °C (at 1 °C (at 1 atm) number (M) atm) Methoxyethan 1.72 124.6 — Dimaethylform 0.90 153.0 — amide DMSO 2.24 189.0 — Methanol 0.60 64.7...

  • Page 220: Solvent Stabilizers

    12.7 Solvent stabilizers Warning: Certain solvents degrade, or become unstable, over time. Highly unstable solvents present a potential explosion hazard. Notice: Do not leave solvents containing stabilizers, such as THF with BHT, to dry in the system’s flow path. A dry flow path, including the detector flow cell, becomes contaminated with residual stabilizer, and a substantial cleaning effort is needed to restore the flow path to its initial condition.

  • Page 221: Mixed Mobile Phases

    Table 12–3: UV cutoff wavelengths for common chromatographic solvents (continued) Solvent UV cutoff (nm) Isopropanol Isopropyl ether Methanol n-Propanol 12.9.2 Mixed mobile phases The following table provides approximate wavelength cutoffs for solvents, buffers, detergents, and mobile phases. The solvent concentrations represented are those most commonly used. If you want to use a different concentration, you can determine approximate absorbance using Beer’s law, because absorbance is proportional to concentration.

  • Page 222: Mobile Phase Absorbance

    Triton X-100, 0.1% Waters PIC Reagent A, 1 vial/liter Waters PIC Reagent B-6, 1 vial/liter Waters PIC Reagent B-6, low UV, 1 vial/liter Waters PIC Reagent D-4, 1 vial/liter 12.9.3 Mobile phase absorbance This following table lists the absorbances at several wavelengths for frequently used mobile phases.
  • Page 223 Table 12–5: Mobile phase absorbance measured against air or water (continued) Mobile phase Absorbance (AU) at specified wavelength (nm) 200 205 210 215 220 230 240 250 260 280 Unstablized THF (old) >2.5 >2.5 >2.5 >2.5 >2.5 >2.5 >2.5 >2.5 2.5 1.45 Acids and bases Acetic acid, 1%...
  • Page 224 — Tris HCl, 20 mM, pH 8.0 1.80 1.90 1.11 0.43 0.13 <0.0 — — — — Waters PIC reagents BRI J 35, 1% 0.06 0.03 0.02 0.02 0.02 0.01 <0.0 — — — CHAPS, 0.1% 2.40 2.32 1.48 0.80 0.40 0.08 0.04 0.02 0.02 0.01 PIC A, 1 vial/L 0.67 0.29 0.13 0.05 0.03 0.02 0.02 0.02 0.02 <0.0...

  • Page 225: Specifications

    13 Specifications The operating and performance specifications presented here depend on the conditions in individual laboratories. Refer to the Alliance iS Site Preparation Guide, or contact the Waters Technical Service organization for additional information about specifications. Notes: • If your system includes a TUV detector, consult the TUV Overview and Maintenance Guide for specifications.

  • Page 226: Instrument Control Specifications

    Table 13–1: Alliance iS System general specifications (continued) Item Specification Cycle time ≤30 seconds inject-to-inject a. The standard pH operating range for the system is between 1 and 13. Operating the system at pH 1 or above pH 13 for more than brief periods can result in increased wear on system components not included in preventive maintenance kits and require more frequent routine preventive maintenance intervals.

  • Page 227: Electrical Specifications

    Table 13–3: Alliance iS environmental specifications (continued) Attribute Specification Ambient transportation and storage humidity 20% to 85%, non-condensing 13.1.3 Electrical specifications Note: The total system power is a function of the devices, modules, and instruments that it comprises. For further information on an individual component, refer to its specific operator's guide.

  • Page 228: Performance Specifications

    13.2 Performance specifications The tables in this section list the performance specifications for the Alliance iS System modules. February 20, 2023, 715008450 Ver. 00 Page 228...