Dionex UltiMate 3000 System Installation And Application
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Dionex UltiMate 3000 System Installation And Application

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UltiMate 3000 Nano and Cap
System Installation and Application
Revision:
1.0
Date:
May 2006
©
2006 Dionex

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Summary of Contents for Dionex UltiMate 3000

  • Page 1 UltiMate 3000 Nano and Cap System Installation and Application Revision: Date: May 2006 © 2006 Dionex...
  • Page 2 UltiMate 3000 Nano and Cap- System Installation and Application...

  • Page 3: Table Of Contents

    UltiMate 3000 Nano and Cap - System Installation and Application Table of Contents Introduction ........................1 General ........................1 Safety Precautions ...................... 2 Unpacking ........................2 Supported System Configurations................3 Intended Use....................... 5 Installation ......................... 7 Facility Requirements ....................7 Rear Panel Connectors ....................
  • Page 4 UltiMate 3000 Nano and Cap- System Installation and Application Preconcentration Kits ....................65 8.3.1 Standard Devices:....................65 8.3.2 Biocompatible Devices ..................65 2D LC Salt Plug Kits....................65 8.4.1 Standard Devices....................65 8.4.2 Biocompatible Devices ..................65 Comprehensive 2D LC Kits ..................65 8.5.1...

  • Page 5: Introduction

    If some detail applies to only one version, the version is identified by name. In order to obtain a full understanding of the system, Dionex recommends that you review this document and the Operating Instructions for the system modules thoroughly before beginning installation and operation of the system.

  • Page 6: Safety Precautions

    UltiMate 3000 Nano and Cap- System Installation and Application 1.2 Safety Precautions To avoid the possibility of personal injury and/or damage to the UltiMate system, observe the safety precautions for the individual system modules (→ Operating Instructions for the instruments).

  • Page 7: Supported System Configurations

    For an overview of the currently available system modules, refer to the table below. If you have any questions, do not hesitate to contact your Dionex sales representative or distributor. Please note: For more information about the configuration of the individual modules, refer to the related Operating Instructions.
  • Page 8 UltiMate 3000 Nano and Cap- System Installation and Application Application UltiMate 3000 System Module Part No. VWD-3100—Variable wavelength detector for one wavelength 5074.0005 VWD-3400—Variable wavelength detector for four wavelengths 5074.0010 Nano HPLC with nano flow cell (must be ordered separately) 6074.0270...

  • Page 9: Intended Use

    Biocompatible autosampler (WPS-3000B) 1.5 Intended Use The UltiMate 3000 system is designed to perform equally well as system for routine analyses or as a sophisticated research instrument for use in capillary, nano, and micro HPLC (high performance liquid chromatography) applications.
  • Page 10 UltiMate 3000 Nano and Cap- System Installation and Application...

  • Page 11: Installation

    2 Installation 2.1 Facility Requirements After unpacking the modules of the UltiMate 3000 system, allow the units to warm up for approximately 4 hours before connecting them to the power supply. This delay allows any condensation that might have occurred during shipping to evaporate. After 4 hours, check the modules;...

  • Page 12: Rear Panel Connectors

    UltiMate 3000 Nano and Cap- System Installation and Application 2.2 Rear Panel Connectors Fig. 2: Rear panel view of an UltiMate 3000 system Please note: Fig. 2 illustrates how the system modules are interconnected. This applies accordingly to for any other system structure.

  • Page 13: Power Connection

    6510.0004) is available as an option. 2.2.2 Interfaces for Device Control Apart from the solvent rack, all modules of an UltiMate 3000 system can be connected to the server PC separately. However, Dionex recommends interconnecting the modules, and then connecting the system to the Chromeleon server PC via only one USB connection, e.g., from the autosampler (→...

  • Page 14: Preparing The System

    Otherwise, use an appropriate intermediate solvent. Important: Les instruments dans un système UltiMate 3000 sont stockés sous 2- propanol ou isopropanol et eau. Lors du démarrage initial des instruments, assurez-vous que les solvants utilisés soient miscibles.
  • Page 15 Connect the drain tubing from the solvent rack to the pump and from the pump to the detector as shown in Fig. 4 a. Dionex recommends connecting the drain tubing from the flow manager as shown in Fig. 4 b. This is to avoid that the gas sensor in the flow manager is influenced by the drain tubing from the other modules.
  • Page 16 UltiMate 3000 Nano and Cap- System Installation and Application • Prepare the individual modules as described in the Operating Instructions for the respective instrument. • Connect the modules on the rear panel as described in Rear Panel Connectors (→ page 8).

  • Page 17: Application Examples And Fluid Connections

    • Comprehensive 2D LC (→ page 33) • Parallel LC (→ page 39) When installing the fluid connections in an UltiMate 3000 system, keep the following in mind: Important: Different fitting systems are used in an UltiMate 3000 system. Therefore, install the capillaries and fittings only at the positions for which they are intended.
  • Page 18 (ex. diviseur de débit, vanne de régulation de débit et colonne). Important: Use only the capillaries shipped with the modules and original Dionex spare capillaries. Important: Utilisez uniquement les capillaires fournis avec les unités et les capillaires de rechange d'origine Dionex.
  • Page 19 UltiMate 3000 Nano and Cap - System Installation and Application The following flow splitters and flow cells are available: Description Part No. Splitter cartridge (standard) for nano HPLC applications 6720.3150A (split ratio 1:1000) Splitter cartridge (standard) for nano HPLC applications 6720.3155A...

  • Page 20: Manual Injection (Basic Configuration)

    3.1 Manual Injection (Basic Configuration) For this application, the sample is injected manually and directed to the separation column via the switching valve in the flow manager. Dionex recommends that you stack the system modules as shown below: SR-3000 Solvent Rack LPG-3400 Pump FLM-3300 Flow Manager Fig.
  • Page 21 UltiMate 3000 Nano and Cap - System Installation and Application Fig. 6 and the related table provide an overview of the fluid connections for manual injection. For an example of the fluid connections for nano HPLC, also refer to Fig. 7 (→ page 19).
  • Page 22 6720.9007 standard) or 6721.9007 (biocompatible) The part number refers to the packing unit. For more information, contact your Dionex Sales Representative. These parts are included in the Basic Configuration Kit for the related application (→ section 8.1, page 64).
  • Page 23 UltiMate 3000 Nano and Cap - System Installation and Application The part numbers in Fig. 7 refer to nano HPLC (standard devices): Fig. 7: Fluid connections for manual injection (nano HPLC, standard devices)

  • Page 24: Direct Injection

    The injection valve is switched to Inject position, directing the sample flow from the sample loop through the high-pressure circuit to the separation column. Dionex recommends that you stack the system modules as shown below: SR-3000 Solvent Rack LPG-3400 Pump...
  • Page 25 UltiMate 3000 Nano and Cap - System Installation and Application Fig. 9 and the related table provide an overview of the fluid connections for direct injection. For an example of the fluid connections for nano HPLC, also refer to Fig. 10 (→ page 23).
  • Page 26 6820.0018 6820.0015 Biocompatible 6821.0015 6821.0018 6821.0015 The part number refers to the packing unit. For more information, contact your Dionex Sales Representative. These parts are included in the Direct Injection Kit for the related application (→ section 0, page 64).
  • Page 27 UltiMate 3000 Nano and Cap - System Installation and Application The part numbers in Fig. 10 refer to nano HPLC (standard devices): Fig. 10: Fluid connections for direct injection (nano HPLC, standard devices)

  • Page 28: Preconcentration

    3.7.) The switching valve in the flow manager is switched from 10-1 to 1-2. The micro pump and the flow splitter direct the sample onto the separation column. Dionex recommends that you stack the system modules as shown below: SRD-3600 Solvent Rack...
  • Page 29 UltiMate 3000 Nano and Cap - System Installation and Application Fig. 12 and the related table provide an overview of the fluid connections for preconcentration. For an example of the fluid connections for nano HPLC, also refer to Fig. 13 (→ page 27).
  • Page 30 Standard needle (2.4 µl, fused silica) 6820.3010 (standard) or 6821.3010 (biocompatible) The part number refers to the packing unit. For more information, contact your Dionex Sales Representative. These parts are included in the Preconcentration Kit for the related application (→ section 8.3, page 65).
  • Page 31 UltiMate 3000 Nano and Cap - System Installation and Application The part numbers in Fig. 13 refer to nano HPLC (standard devices): Fig. 13: Fluid connections for preconcentration (nano HPLC, standard devices)

  • Page 32: Lc Salt Plug

    The process is iterated with increasing concentrations of salt injected until all the peptides from the ion exchange column are eluted and separated on the reverse phase column. Dionex recommends that you stack the system modules as shown below: SRD-3600 Solvent Rack...
  • Page 33 UltiMate 3000 Nano and Cap - System Installation and Application The system includes the modules listed in the table below. In addition, the 2D LC Salt Plug Kit (→ section 8.4, page 65) is required: System Module Part No. Nano HPLC SRD-3600 5035.9230...
  • Page 34 UltiMate 3000 Nano and Cap- System Installation and Application Fig. 15 and the related table provide an overview of the fluid connections for 2D LC salt plug. Also, refer to Fig. 16 (→ page 32). Fig. 15: Fluid connections for 2D LC salt plug (overview)
  • Page 35 Standard needle (2.4 µl, fused silica) 6820.3010 (standard) or 6821.3010 (biocompatible) The part number refers to the packing unit. For more information, contact your Dionex Sales Representative. These parts are included in the 2D LC Salt Plug Kit (→ section 8.4, page 65).
  • Page 36 UltiMate 3000 Nano and Cap- System Installation and Application Fig. 16, too, illustrates the fluid connections for 2D LC salt plug. The part numbers in the picture refer to the standard devices. Fig. 16: Fluid connections for 2D LC salt plug (nano HPLC, standard devices)

  • Page 37: Comprehensive 2D Lc

    UltiMate 3000 - System Installation and Application 3.5 Comprehensive 2D LC This application supports online comprehensive two-dimensional separation of peptides: While the autosampler's injection valve is in Load position, sample is drawn by the syringe through the needle and placed in the sample loop. The needle pair withdraws liquid from the well or vial and then descends into the wash port.
  • Page 38 UltiMate 3000 Nano and Cap- System Installation and Application Dionex recommends that you arrange the system modules as shown below: SRD-3600 Solvent Rack DGP-3600 Pump SR-3000 Solvent Rack VWD-3x00 Detector LPG-3400 Pump FLM-3300 Flow Manager WPS-3000 or WPS-3000 T Autosampler...
  • Page 39 UltiMate 3000 - System Installation and Application Fig. 18 and the related table provide an overview of the fluid connections for 2D LC comprehensive for capillary (1 dimension) nano (2 dimension) HPLC. Also, refer to Fig. 19 (→ page 38).
  • Page 40 UltiMate 3000 Nano and Cap- System Installation and Application Description Part No. Capillary/Nano HPLC Solvent lines (analytical) 6030.2548 Solvent lines from degasser to proportioning valve 6035.2540 (set of 3 including the appropriate fittings) Connection proportioning valve to working pump head (including fittings) 6035.2514...
  • Page 41 Standard needle (2.4 µl, fused silica) 6820.3010 (standard) or 6821.3010 (biocompatible) The part number refers to the packing unit. For more information, contact your Dionex Sales Representative. These parts are included in the Comprehensive 2D LC Kit (→ section 8.5, page 65).
  • Page 42 UltiMate 3000 Nano and Cap- System Installation and Application Fig. 19, too, illustrates the fluid connections for comprehensive 2D LC for capillary (1 dimension) and nano (2 dimension) HLPC. The part numbers in the picture refer to the standard devices.

  • Page 43: Parallel Lc

    UltiMate 3000 Nano and Cap - System Installation and Application 3.6 Parallel LC This application allows you to increase the throughput for peptide separations. While the autosampler's injection valve is in Load position, sample is drawn by the syringe through the needle and placed in the sample loop.
  • Page 44 UltiMate 3000 Nano and Cap- System Installation and Application Dionex recommends that you arrange the system modules as shown below: SRD-3600 Solvent Rack DGP-3600 Pump SR-3000 Solvent Rack VWD-3x00 Detector LPG-3400 Pump FLM-3200 Flow Manager WPS-3000 or WPS-3000 T Autosampler...
  • Page 45 UltiMate 3000 Nano and Cap - System Installation and Application Fig. 21 and the related table provide an overview of the fluid connections for parallel LC. For an example of the fluid connections for nano HPLC, also refer to Fig. 22 (→ page 44).
  • Page 46 UltiMate 3000 Nano and Cap- System Installation and Application Description Part No. Nano/Nano Capillary/Capillary Monolith./Monolith. HPLC HPLC HPLC Solvent lines (analytical) 6030.2548 Solvent lines from degasser to proportioning valve 6035.2540 (set of 3 including the appropriate fittings) Connection proportioning valve to working pump head (including fittings) 6035.2514...
  • Page 47 Standard needle (2.4 µl, fused silica) 6820.3010 (standard) or 6821.3010 (biocompatible) The part number refers to the packing unit. For more information, contact your Dionex Sales Representative. These parts are included in the Parallel LC Kit for the related application (→ section 8.6, page 66).
  • Page 48 UltiMate 3000 Nano and Cap- System Installation and Application The part numbers in Fig. 22 refer to nano HPLC (standard devices): Fig. 22: Fluid connections for parallel LC (nano HPLC; standard devices)

  • Page 49: Installing A Trap Column

    • The retention times (with known sample) shift to later elution • The column pressure drop is larger than 10 bar Please note: The pressure stability option of the UltiMate 3000 system ("Hold pressure" mode) maintains a constant pressure during valve switching, however, it is not designed to compensate for dead volumes.
  • Page 50 UltiMate 3000 Nano and Cap- System Installation and Application To establish a zero dead volume fitting connection when installing the trap column, follow the steps below. Both connecting tubings use a PEEK nut and ferrule at the trap column side, and a one-piece PEEK fingertight is required to connect the trap column to the valve (see Fig.

  • Page 51: Automated Control By Chromeleon

    Please note: The descriptions below refer to Chromeleon 6.80. 4.1 General The modules of the UltiMate 3000 system can be controlled by the Chromeleon Chromatography Management System. To control the modules, a suitable Chromeleon version (e.g., 6.50 Service Pack 10, 6.60 Service Pack 6, 6.70 Service Pack 3, or 6.80) and a Timebase Class 1 Chromeleon license are required.
  • Page 52 If you install the modules in a different order, reopen the pump’s and autosampler’s Properties pages and make the necessary configuration changes. Fig. 25: Installation of an UltiMate 3000 system in the Server Configuration program (here: for Preconcentration, or 2D LC Salt Plug)

  • Page 53: Assigning A Flow Splitter To A Pump

    Please note: For the standard configuration of the UltiMate 3000 system with a DGP-3600M pump, Dionex recommends assigning the flow splitter to the right pump (MicroPump).
  • Page 54 UltiMate 3000 Nano and Cap- System Installation and Application Flow splitter assignment also affects the properties that are available for the pump in the Commands dialog box: Chromeleon Description Flow and/or Flow rate in µl/min MasterFlow Pumps without flow splitter assignment: Flow indicates the total flow through the pump.

  • Page 55: Recording The Pump Pressure As A Separate Channel

    Accept this setting if you want to record the column pressure as a separate channel. Fig. 27: Configuration tab page Please note: When your UltiMate 3000 system includes one flow manager: Accept the default name (ColumnPressure), under which the column pressure signal is identified in the installation environment.
  • Page 56 UltiMate 3000 Nano and Cap- System Installation and Application If the column pressure is recorded as a separate channel, ColumnPressure appears in the Commands dialog box, also. Chromeleon Description ColumnPressure Click the "+"sign beside the name to display the items underneath: Delta−reports the signal's slope, i.e., the difference between the...

  • Page 57: Synchronizing The Autosampler With A Pump

    UltiMate 3000 Nano and Cap - System Installation and Application 4.4 Synchronizing the Autosampler with a Pump If your system includes a WPS-3000 or WPS-3000T autosampler, you can synchronize the injection command of the autosampler with the strokes of a DGP-3600 or LPG-3400 pump.

  • Page 58: Displaying The Degasser-Related Parameters

    UltiMate 3000 Nano and Cap- System Installation and Application • Select None to disable synchronization. • When the UltiMate 3000 system includes a DGP-3600 pump: Select UM3PUMP _L_STRK to enable synchronization with the left pump. To enable synchronization with the right pump, select UM3PUMP _R_STRK.

  • Page 59: Soft Key Menus

    UltiMate 3000 Nano and Cap - System Installation and Application 5 Soft Key Menus For all UltiMate 3000 Nano and Cap system modules except the solvent rack, four soft keys under the front panel display provide access to various menus, allowing you to change certain settings and/or perform certain commands.
  • Page 60 UltiMate 3000 Nano and Cap- System Installation and Application...

  • Page 61: Troubleshooting

    UltiMate 3000 Nano and Cap - System Installation and Application 6 Troubleshooting The following table provides a summary of possible operating problems, lists probable causes, and suggests remedial actions: Problem Probable Cause Remedial Action No display on the LCD. The instrument is not connected Connect the power cord.
  • Page 62 UltiMate 3000 Nano and Cap- System Installation and Application Problem Probable Cause Remedial Action High noise level, pulsation There are pressure fluctuations Prime the pump; check general from the pump. function (→ Pump manual). There are gas bubbles in the Prime the system system.
  • Page 63 UltiMate 3000 Nano and Cap - System Installation and Application Problem Probable Cause Remedial Action Poor reproducibility (cont'd) Carry-over occurs in the system. Flush the needle using an appropriate solvent. The capillary connections are not Check and tighten the capillary installed properly or they are not connections.
  • Page 64 UltiMate 3000 Nano and Cap- System Installation and Application Problem Probable Cause Remedial Action After switching from the There is dead volume in the → section 3.7 loading pump flow to the connection to the trap column. nano flow, there is a drop in...

  • Page 65: Routine Maintenance

    UltiMate 3000 Nano and Cap - System Installation and Application 7 Routine Maintenance The system modules of the UltiMate 3000 system are made of high-quality components and materials to minimize maintenance requirements. The painted surfaces, as well as the display, are relatively resistant to weak acids, alkali, and organic solvents.
  • Page 66 UltiMate 3000 Nano and Cap- System Installation and Application...

  • Page 67: Accessories And Spare Parts

    UltiMate 3000 Nano and Cap - System Installation and Application 8 Accessories and Spare Parts Dionex accessories and spare parts are always maintained at the latest technical standard. Therefore, part numbers are subject to alteration. However, updated parts will always be compatible with the parts they replace.

  • Page 68: Basic Configuration Kits

    UltiMate 3000 Nano and Cap- System Installation and Application 8.1 Basic Configuration Kits The kits include all parts that are necessary for the configuration! 8.1.1 Standard Devices Description Part No. Basic Configuration Kit for Nano HPLC 6720.0065 Basic Configuration Kit for Capillary HPLC 6720.0082...

  • Page 69: Preconcentration Kits

    UltiMate 3000 Nano and Cap - System Installation and Application 8.3 Preconcentration Kits The kits include all parts that are necessary for the configuration! 8.3.1 Standard Devices: Description Part No. Preconcentration Kit for Nano HPLC 6720.0047 Preconcentration Kit for Capillary HPLC 6720.0048...

  • Page 70: Parallel Lc Kits

    UltiMate 3000 Nano and Cap- System Installation and Application 8.6 Parallel LC Kits The kits include all parts that are necessary for the configuration! 8.6.1 Standard Devices Description Part No. Parallel LC Kit, Nano/Nano 6720.0054 Parallel LC Kit, Cap/Cap 6720.0055 Parallel LC Kit, 2x Monolithic 6720.0056...

  • Page 71: Technical Information

    UltiMate 3000 Nano and Cap - System Installation and Application 9 Technical Information Column flow range: 50 nl/min to 2.5 ml/min using predefined splitter cartridges and active flow control Electronically controlled and actively balanced flow Flow control: splitter, independent from solvent composition and...
  • Page 72 UltiMate 3000 Nano and Cap- System Installation and Application...

  • Page 73: Index

    UltiMate 3000 Nano and Cap - System Installation and Application 10 Index 2D LC Salt Plug ..........28, 65 Injection Command..........53 Installation ............. 7 Intended Use ............5 Accessories ............63 Applications ............13 2D LC Salt Plug............28 Leak ..............54 Comprehensive 2D LC.........33...

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