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Dionex MSQ User Manual

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MSQ
™
Hardware
Document No. 031871
Revision 02
October 2003

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  • Page 1 ™ Hardware Document No. 031871 Revision 02 October 2003...
  • Page 2 Dionex Corporation, 1228 Titan Way, Sunnyvale, California 94088-3603 U.S.A.

  • Page 3: Table Of Contents

    Chapter 1 Introducing the MSQ Introducing the MSQ.........................1-i Introduction ............................1-1 System Overview..........................1-2 What Is Mass Detection? ....................1-4 Exterior Features of the MSQ....................1-5 The Source–An Introduction to API Techniques ................1-8 Electrospray ........................1-9 Atmospheric Pressure Chemical Ionization..............1-13 Source Fragmentation......................1-16 Cone Voltage Ramping ....................1-18 Polarity Switching ......................1-19...
  • Page 4 Introducing the MSQ Introduction ____________________________________________________________________________ 1-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 5: Introducing The Msq

    Introducing the MSQ ___________________________________________________________________________ Introduction Introduction The MSQ™ MS detector has been specifically designed and engineered for liquid chromatographic detection using Atmospheric Pressure Ionization (API) and Mass Spectrometry (MS) technology. These technologies can provide sensitive and selective detection of organic molecules.

  • Page 6: System Overview

    Introducing the MSQ System Overview ________________________________________________________________________ System Overview The MSQ MS detector is an integral part of the LC detection system. Key points of the system are: • The sample is introduced into the ion source using an LC system, possibly through a column.
  • Page 7 Entrance cone introduction probe From HPLC Figure 1-2. Schematic diagram of the MSQ API inlet, analyzer, and detector system The LC eluent is ionized at the API probe and the resulting ions are focused into a square quadrupole RF lens. The quadrupole mass analyzer filters the ions before detection.

  • Page 8: What Is Mass Detection

    Most ions encountered in mass detection have just one charge. In this case, the mass- to-charge ratio is often spoken of as the “mass” of the ion. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 9: Exterior Features Of The Msq

    MSQ. Status light Figure 1-3. Front view of the MSQ Figure 1-3 shows the front view of the MSQ. The main feature is the status light. ___________________________MSQ Hardware Manual ____________________________...
  • Page 10 See the chapter Shutting Down and Restarting the System for information on pumping down the MSQ. Figure 1-4 shows the MSQ with the doors open. The source enclosure and reference inlet are now visible. Source...
  • Page 11 Introducing the MSQ _______________________________________________________________________System Overview Figure 1-5 is a schematic of the rear view of the MSQ. PUMP RELAY Rotary pump power To PC SOURCE Contact closure and To rotary pump USER I/O analog inputs Reset communications RESET EXHAUST Exhaust from API...

  • Page 12: The Source-An Introduction To Api Techniques

    The self-cleaning source delivers a constant, low flow of solvent (the cone wash™) to the edge of the inlet orifice, helping to prevent a buildup of involatiles during an LC/MS run. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 13: Electrospray

    Entrance cone introduction probe From HPLC Figure 1-7. Schematic of the MSQ source showing the cone wash Two types of API are commonly encountered. These are Electrospray Ionization (ESI) and Atmospheric Pressure Chemical Ionization (APCI). The following sections discuss the mechanism of ion generation in each.
  • Page 14 Insert capillary +3-5 kV Droplet As the droplet Ions evaporate containing evaporates, the from the surface ions electric field increases and ions move towards the surface Figure 1-9. Positive ion electrospray mechanism 1-10 __________________________ MSQ Hardware Manual ____________________________...
  • Page 15 Entrance cone Cone Wash Probe Atmospheric Pressure Insert capillary Region LC eluent Nebulizing gas, N Insert Sheath gas, N Figure 1-10. Schematic of the ESI source on the MSQ, showing the principal components and pressure regions 1-11 ___________________________MSQ Hardware Manual ___________________________...
  • Page 16 Where, M = actual mass, n = number of charges, and H = mass of a proton. Electrospray allows molecules with molecular weights greater than the mass range of the MS detector to be analyzed. This is a unique feature of electrospray. 1-12 __________________________ MSQ Hardware Manual ____________________________...

  • Page 17: Atmospheric Pressure Chemical Ionization

    Introducing the MSQ _______________________________________________ The Source–An Introduction to API Techniques Flow Rate The electrospray source can be used with flow rates from 5.0 µL/min to 2.0 mL/min. Atmospheric Pressure Chemical Ionization Atmospheric Pressure Chemical Ionization (APCI) is also a very soft ionization technique and has many similarities to electrospray ionization.
  • Page 18 Nebulizing gas, N Corona pin Sheath gas, N Figure 1-13. Schematic of the APCI source on the MSQ, showing the principal components and pressure regions The newly formed ions then enter the focusing region through the entrance orifice and pass into the RF lens region. The RF lens (square quadrupole) helps to focus the ions before they enter the mass analyzer region.
  • Page 19 Introducing the MSQ _______________________________________________ The Source–An Introduction to API Techniques Spectral Characteristics Like electrospray, APCI is a soft ionization technique and forms singly charged ions–either the protonated, [M+H] , or deprotonated, [M-H] molecule–depending on the selected ionization mode. Unlike electrospray,...

  • Page 20: Source Fragmentation

    Formation of Diagnostic Fragment Ions The MSQ allows the simultaneous acquisition of MS data at a number of different source voltages. For example, the MSQ can be programmed to acquire data at source voltages of 20, 40, and 60 V on an alternating scan basis within a single acquisition.
  • Page 21 Introducing the MSQ _______________________________________________ The Source–An Introduction to API Techniques Protonated molecule at m/z 240 Source voltage 10V [M+H] Fragment ion at m/z 222 [M+H] Source voltage 25V Fragment ion at m/z 166 Source voltage 35V [M+H] O-tBu 148 166 Figure 1-14.

  • Page 22: Cone Voltage Ramping

    If the source voltage is ramped between 30 and 60 V, the charge distribution envelope is extended and it resembles the lower diagram. 1-18 __________________________ MSQ Hardware Manual ____________________________...

  • Page 23: Polarity Switching

    Polarity Switching Switching between positive and negative ionization modes in a single analytical run is supported by the MSQ. Rapid polarity switching is a technique that is applied to several important areas of MS analysis; for example: •...

  • Page 24: Application Of Api Techniques

    When determining molecular weights, always take account of possible adduct ions. Common adducts are [M+18] (ammonium adducts seen in the presence of buffers such as ammonium acetate), [M+23] (sodium adducts), and [M+39] (potassium adducts). 1-20 __________________________ MSQ Hardware Manual ____________________________...
  • Page 25 Introducing the MSQ _______________________________________________ The Source–An Introduction to API Techniques • Source fragmentation is used in both APCI and electrospray to give structural information. In general, increasing the voltage applied to the source block (the cone voltage) yields increasing amounts of fragmentation, depending on the nature of the compound.
  • Page 26 2.1- to 4.6-mm ID columns Mobile phases O, CH CN, CH OH are most O, CH CN, CH OH are most frequently used. frequently used. Non-polar solvents can be used. Typical mass range <100,000 <1000 1-22 __________________________ MSQ Hardware Manual ____________________________...

  • Page 27: The Self-Cleaning Source: Cone Wash

    LC/MS and the Cone Wash. Introduction The API source on the MSQ includes a self-cleaning solvent delivery system (the cone wash). This makes the source extremely robust and productive and greatly increases the number of samples that can be analyzed before maintenance is required.

  • Page 28: Functional Description

    Note. It is necessary to use the cone wash only for compounds in dirty matrices or when involatile buffers are used. Choose the cone wash solvent to give the most effective solubility for the expected contaminants. 1-24 __________________________ MSQ Hardware Manual ____________________________...

  • Page 29: The Reference Inlet System

    Introducing the MSQ ______________________________________________________________ The Reference Inlet System The Reference Inlet System This section introduces the reference inlet system. Information on how to set up the system is provided in the chapter Reference Inlet System. Introduction The recommended way to introduce a sample for tuning and mass calibration in electrospray is to use the reference inlet system.

  • Page 30: The Mass Analyzer And Detector

    The square quadrupole RF lens helps to focus the ions before they are filtered, according to their mass-to-charge ratio in the mass analyzer. The analyzer in the MSQ is a quadrupole. This is one of the most widely used types of analyzer and can be easily interfaced to various inlet systems.

  • Page 31: The Vacuum System

    It is important to remember that an MS detector must be under high vacuum in order to operate. In the case of the MSQ system, not all of the MS detector is under high vacuum. The ion source is held at atmospheric...

  • Page 32: The Data System

    Introducing the MSQ The Data System ________________________________________________________________________ The Data System The data system has complete control of the MSQ system and runs on a Microsoft® Windows platform. Software Xcalibur™ software controls the MSQ MS detector. When Xcalibur is run, the Home page is displayed (see Figure 1-22). Xcalibur also runs the MSQ server (see Figure 1-23).
  • Page 33 Figure 1-23. The taskbar showing the Xcalibur Home page and server The server is shown as one light. When the light is green, the MSQ is under vacuum with Operate On and the API gas flowing. When the MSQ is pumping down, the light is yellow and flashing.

  • Page 34: Raw Data

    • Choose Tune to display the Tune page. • Choose Pump to pump down the MSQ or Vent to vent the MSQ. • Choose Exit to close the server. If Xcalibur is still running, this will not be allowed and an error message will be displayed.

  • Page 35: Raw Data Types

    Introducing the MSQ _______________________________________________________________________ The Data System 1 .09 - 6.1 1 2.66 1 00 2.49E5 TIC carb mix pmix03 2.82 3.59 2.35 3.28 3.72 1 .24 1 .55 2.25 4.75 3.87 4.1 8 5.1 7 5.32 5.42 1 .5...
  • Page 36 (see Figure 1-26) for each ion mass recorded. This has the advantage of reducing the quantity of data recorded to the hard disk and improving processing speeds. Figure 1-26. Full scan centroid spectrum of pentachlorophenol 1-32 __________________________ MSQ Hardware Manual ____________________________...
  • Page 37 Introducing the MSQ _______________________________________________________________________ The Data System Profile With profile acquisition, data is not “centroided” into sticks. Instead, the signal received by the interface electronics is stored to give an analog intensity profile of the data being acquired for every scan (see Figure 1-27).
  • Page 38 MCA is often used to acquire raw data from the infusion of proteins and peptides. 1060 1131 1212 1305 1000 1100 1200 1300 Figure 1-28. Full scan MCA spectrum of horse heart myoglobin 1-34 __________________________ MSQ Hardware Manual ____________________________...
  • Page 39 Introducing the MSQ _______________________________________________________________________ The Data System SIM Mode This acquisition mode is used when only one or a few specific masses are to be monitored during the acquisition. Since most of the acquisition time is spent on these masses, the SIM technique is far more sensitive (typically greater than a factor of ten) than full scan techniques.
  • Page 40 Introducing the MSQ The Data System ________________________________________________________________________ 1-36 __________________________ MSQ Hardware Manual ____________________________...
  • Page 41 Chapter 2 Changing Ionization Modes Changing Ionization Modes ......................2-i Introduction ............................2-1 Switching from ESI to APCI ......................2-2 Switching from APCI to ESI ......................2-4 ____________________________MSQ Hardware Manual _____________________________...
  • Page 42 Changing Ionization Modes Introduction ____________________________________________________________________________ 2-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 43: Changing Ionization Modes

    Changing Ionization Modes ____________________________________________________________________________ Introduction Introduction Use the information in this chapter in conjunction with the animations on the MSQ CD shipped with your system. The chapter is divided into the following sections: • Switching from ESI to APCI •...

  • Page 44: Switching From Esi To Apci

    APCI probe assembly (P/N FM102587), and turn the locking plate counterclockwise into the closed position. Change the APCI blank plug (P/N FM101437) with the APCI corona pin (P/N FM101433), located in the holder in the source enclosure door. ___________________________ MSQ Hardware Manual ____________________________...
  • Page 45 Changing Ionization Modes ________________________________________________________________Switching from ESI to APCI Figure 2-6. APCI corona pin and APCI blank plug 6. Insert the PEEK finger-tight fitting into the APCI probe assembly (P/N FM102587) and screw it into place. ____________________________MSQ Hardware Manual ____________________________...

  • Page 46: Switching From Apci To Esi

    (P/N FM101433), located in the holder in the source enclosure door. Figure 2-7. APCI blank plug and APCI corona pin 3. Turn the locking plate clockwise to the open position, and remove the APCI probe assembly (P/N FM102587). ___________________________ MSQ Hardware Manual ____________________________...
  • Page 47 Changing Ionization Modes ________________________________________________________________Switching from APCI to ESI PEEK fitting Locking plate Figure 2-5. ESI probe assembly Swap the APCI probe assembly (P/N FM102587) with the ESI probe assembly (P/N FM102595), located in the holder in the door. Turn the locking plate on the ESI probe assembly clockwise into the open position, insert the ESI probe assembly (P/N FM102595), and turn the locking plate counterclockwise into the closed position.
  • Page 48 Changing Ionization Modes Switching from APCI to ESI ________________________________________________________________ ___________________________ MSQ Hardware Manual ____________________________...
  • Page 49 Chapter 3 LC/MS and the Cone Wash LC/MS and the Cone Wash ......................3-i Introduction ............................3-1 LC/MS Considerations ........................3-2 Flow Rates .........................3-2 HPLC Solvents and Mobile Phase Additives ..............3-3 Setting Up the Cone Wash......................3-7 Flow Splitting ..........................3-9 ___________________________MSQ Hardware Manual _____________________________...
  • Page 50 LC/MS and the Cone Wash Introduction ____________________________________________________________________________ 3-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 51: Lc/Ms And The Cone Wash

    This chapter contains the following information: • Details of HPLC solvents and mobile phase additives that focus on LC/MS applications using the MSQ. • Instructions on how to set up the cone wash and information on when to use it.

  • Page 52: Lc/Ms Considerations

    This section discusses the considerations to be taken into account when choosing solvents and additives. It also provides guidance on how to optimize LC/MS analyses to produce high quality data using the MSQ. Flow Rates In general, the column in use determines the flow rate. Each column has an optimum flow rate.

  • Page 53: Hplc Solvents And Mobile Phase Additives

    LC/MS and the Cone Wash ____________________________________________________________________LC/MS Considerations HPLC Solvents and Mobile Phase Additives The following section is a guide for the choice of solvent and mobile phase additives to use. The choice of solvents for LC will be dictated primarily by the separation requirements, but there are some guidelines that need to be followed.
  • Page 54 Propan-2-ol (IPA), 2-methoxyethanol, ethanol, and so on These have all been used with LC/MS, but their use tends to be application- specific. • Dimethyl sulfoxide (DMSO) This solvent is commonly used by synthetic chemists for primary dilution. ___________________________ MSQ Hardware Manual ____________________________...
  • Page 55 LC/MS and the Cone Wash ____________________________________________________________________LC/MS Considerations Other Additives • Trifluoroacetic acid (TFA) This is frequently used for peptide and protein analysis. High levels, >0.1% v/v, can cause suppression of sensitivity in positive ion mode. TFA may completely suppress ionization in negative ion mode. •...
  • Page 56 Negative ion Surfactants, organic acids; for example, acetic acid, formic acid, trifluoroacetic acid (TFA). Positive ion Acetic acid, formic acid, ammonium acetate (<0.1M). Negative ion Triethylamine (TEA), ammonium hydroxide (ammonia solution), ammonium acetate (<0.1M). ___________________________ MSQ Hardware Manual ____________________________...

  • Page 57: Setting Up The Cone Wash

    Setting Up the Cone Wash Use the following information in conjunction with the setup and maintenance animations on the MSQ CD shipped with the instrument. Note. It is necessary to use the cone wash only for dirty matrices or with involatile buffers.
  • Page 58 Figure 3-2. Cone wash nozzle in the on position Caution. Do not leave the cone wash running when the source heater is turned off; this could lead to cone wash solvents condensing on the RF lens. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 59: Flow Splitting

    LC/MS and the Cone Wash ___________________________________________________________________________ Flow Splitting Flow Splitting Due to the MSQ’s source design, flow splitting of the LC eluent is not usually required. However, if hyphenated detection is required, flow splitting can be achieved in the following way.
  • Page 60 For example, if 200 mg emerges from the insert and 800 mg from the waste stream in one minute, then the split ratio is 4:1 and the flow rate into the source can be calculated as 0.2 mL/min. 3-10 __________________________ MSQ Hardware Manual ____________________________...
  • Page 61 Chapter 4 Reference Inlet System Reference Inlet System ......................4-i Introduction ............................4-1 Overview ............................4-2 Setting Up the Reference Inlet System...................4-3 ____________________________MSQ Hardware Manual _____________________________...
  • Page 62 Reference Inlet System Introduction ____________________________________________________________________________ 4-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 63: Reference Inlet System

    Reference Inlet System ____________________________________________________________________________ Introduction Introduction The MSQ’s built-in reference inlet system allows easy calibration and tuning. This chapter provides instructions on how to set up the reference inlet system. ____________________________MSQ Hardware Manual ____________________________...

  • Page 64: Overview

    This method provides a steady flow of sample directly into the source (typically at flow rates of <50 µL/min). Note. Calibration should be performed in positive electrospray mode. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 65: Setting Up The Reference Inlet System

    Setting Up the Reference Inlet System Use the following information in conjunction with the setup and maintenance animations on the MSQ CD shipped with the instrument. These instructions show how to configure the reference inlet system to introduce tuning and mass calibration samples into the source. They assume that the source is set up for electrospray ionization.
  • Page 66 To print a report, click the Print Report button. Note. Allow time for the probe heater to warm up and stabilize at the required temperature before beginning autotune and calibration. ___________________________ MSQ Hardware Manual ____________________________...
  • Page 67 Reference Inlet System ___________________________________________________________ Standard Mass Scale Calibration Standard Mass Scale Calibration If there is a significant change in the observed masses, you may wish to perform a standard mass scale calibration. 1. Ensure that there is calibrant in the calibration reference bottle. If not, unscrew the calibration reference bottle (P/N FM102771), fill it with calibrant, and screw it back into place.
  • Page 68 To print a report, click the Print Report button. Note. Allow time for the probe heater to warm up and stabilize at the required temperature before beginning autotune and calibration. ___________________________ MSQ Hardware Manual ____________________________...
  • Page 69 The Heater............................ 5-21 Heater Removal ......................5-21 Cleaning the Heater......................5-21 Heater Replacement ......................5-22 The Rotary Pump ......................... 5-23 Checking the Rotary Pump Oil Level and Color ............5-23 Changing the Rotary Pump Oil..................5-25 ___________________________ MSQ Hardware Manual_____________________________...
  • Page 70 Routine and Preventive Maintenance Introduction ____________________________________________________________________________ 5-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 71: Routine And Preventive Maintenance

    “loss of performance” basis. This chapter contains details of how to perform all the user maintenance tasks on the MSQ, both routine and as required. Use this information in conjunction with the setup and maintenance animations on the MSQ CD shipped with the instrument.

  • Page 72: Maintenance Schedule

    Maintenance Schedule Table 5-1 is a list of routine maintenance procedures that should be carried out on the MSQ at the intervals specified. The maintenance schedule provides only a rough guide to the frequency of maintenance tasks. The appropriate frequency depends on instrument usage and the level of system-induced contamination from samples and matrices.

  • Page 73: The Electrospray And Apci Probes

    Routine and Preventive Maintenance __________________________________________________________The Electrospray and APCI Probes The Electrospray and APCI Probes To extend their lifetime, regularly flush both the ESI and APCI probes with solvent, especially after prolonged use with buffers. The probes can also be stripped down and cleaned. Replace the capillaries if they become blocked. Flushing the Capillaries To prevent blockage, flush the capillaries with [50:50] acetonitrile:water or methanol:water after use with phosphates, ion-pairing agents, acids, or other...

  • Page 74: Esi Probe Removal

    Unscrew and remove the PEEK finger-tight fitting from the ESI probe assembly (P/N FM102595). Turn the locking plate clockwise to the open position and remove the ESI probe assembly (P/N FM102595). PEEK fitting Locking plate Figure 5-5. ESI probe assembly ___________________________ MSQ Hardware Manual ____________________________...

  • Page 75: Esi Probe Disassembly

    Routine and Preventive Maintenance __________________________________________________________The Electrospray and APCI Probes ESI Probe Disassembly The starting point for this procedure is the ESI probe removed from the instrument. Using the 2.5 mm Allen key, unscrew the M3 x 10 cap head stainless steel screw (P/N FM103046).

  • Page 76: Cleaning The Esi Probe

    A significant increase in LC pump backpressure (that is, up to 300 psig at 1 mL/min added to the total LC system backpressure) or instability in the signal could be symptoms of a partially blocked capillary. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 77: Esi Probe Assembly

    Routine and Preventive Maintenance __________________________________________________________The Electrospray and APCI Probes ESI Probe Assembly The starting point for this procedure is a disassembled ESI probe. Insert the ESI ceramic sleeve (P/N FM103394) into the ESI ceramic probe assembly. Place the O-rings in position and insert the ESI probe mount. Screw in the two M3 x 8 cap head stainless steel screws (P/N 5313020) and tighten, using the 2.5 mm Allen key.

  • Page 78: Apci Probe Removal

    Unscrew and remove the PEEK finger-tight fitting from the APCI probe assembly (P/N FM102587). Turn the locking plate clockwise to the open position and remove the APCI probe assembly (P/N FM102587). PEEK fitting Locking plate Figure 5-5. APCI probe assembly ___________________________ MSQ Hardware Manual ____________________________...

  • Page 79: Apci Probe Disassembly

    Routine and Preventive Maintenance __________________________________________________________The Electrospray and APCI Probes APCI Probe Disassembly The starting point for this procedure is the APCI probe removed from the instrument. Using the 2.5 mm Allen key, unscrew the M3 x 10 cap head stainless steel screw (P/N FM103046).

  • Page 80: Replacing The Capillary

    10 mm spanner. Place the locking plate and probe clamp in position. Screw in the M3 x 10 cap head stainless steel screw (P/N FM103046) and tighten, using the 2.5 mm Allen key. 5-10 __________________________ MSQ Hardware Manual ____________________________...

  • Page 81: The Source Block Assembly

    Routine and Preventive Maintenance _______________________________________________________________ The Source Block Assembly The Source Block Assembly The source block assembly can be removed from the instrument (see page 5- 12) and disassembled into its component parts for cleaning. Typically, the entrance cone needs to be cleaned most frequently because it becomes dirty with use over a long period.
  • Page 82 Rub the outside of the cone with the lapping paper until the buildup has been removed. Replace the entrance cone assembly and turn counterclockwise until locked in place. Reinsert the probe and PEEK fitting. 5-12 __________________________ MSQ Hardware Manual ____________________________...

  • Page 83: Cleaning The Cone Wash Nozzle

    Routine and Preventive Maintenance _______________________________________________________________ The Source Block Assembly Cleaning the Cone Wash Nozzle The cone wash nozzle (P/N FM102521) should require cleaning only if it becomes blocked. When the pump supplying the cone wash with solvent is switched on, check the backpressure; if it rises, this could indicate a blockage in the nozzle.
  • Page 84 Remove the cone wash nozzle (P/N FM102521). Loosen the thumbscrews on the source block and pull out the source block assembly (P/N FM102573). Thumbscrews Source block Figure 5-5. Removing the source block assembly 5-14 __________________________ MSQ Hardware Manual ____________________________...
  • Page 85 _______________________________________________________________ The Source Block Assembly Disassembling the Source Block Assembly The starting point for this procedure is the source block assembly removed from the MSQ. WARNING. Allow the source block and probe heater assembly to cool before carrying out any maintenance.
  • Page 86 Schedule topic on page 5-2. WARNING. Allow the source block and probe heater assembly to cool before carrying out any maintenance. 1. Totally immerse the RF lens in a measuring cylinder or beaker of [50:50] methanol:water and sonicate. 5-16 __________________________ MSQ Hardware Manual ____________________________...
  • Page 87 Routine and Preventive Maintenance _______________________________________________________________ The Source Block Assembly Figure 5-7. Cleaning the RF Lens Caution. To prevent the RF lens from touching the bottom of the vessel and hence becoming damaged, either suspend it on a wire or place a tissue at the bottom of the vessel.
  • Page 88 Replace the extraction cone insulator (P/N FM102264), extraction cone (P/N FM102263), and hexapole screw insulator (P/N FM102248). Replace the RF lens and screw in the three spring screws at the base of the RF lens. 5-18 __________________________ MSQ Hardware Manual ____________________________...
  • Page 89 Routine and Preventive Maintenance _______________________________________________________________ The Source Block Assembly Replacing the Source Block Assembly The starting point for this procedure is the source block assembly removed from the MSQ. Thumbscrews Source block Figure 5-5. Replacing the source block assembly Push the source block assembly (P/N FM102573) into place in the source block enclosure and tighten the thumbscrews on the source block.
  • Page 90 Figure 5-5. ESI probe assembly and source block enclosure Cleaning the Extraction Cone The starting point for this procedure is the source block assembly removed from the MSQ and disassembled. Caution. Exercise great care when handling the extraction cone. Always store with the cone facing upward.

  • Page 91: The Heater

    Routine and Preventive Maintenance _____________________________________________________________________________The Heater The Heater If the instrument is used primarily in APCI mode, it is recommended that the heater be cleaned on a monthly basis. If used in ESI mode, the heater will need cleaning less frequently. Heater Removal The starting point for this procedure is the source setup for ESI or APCI operation, with the LC and gas flows off, and the probe cooled.

  • Page 92: Heater Replacement

    Insert the screw insulators and the two M3 x 10 cap head stainless steel screws (P/N FM103046). Tighten, using the 2.5 mm Allen key. Push in the heater connectors. Replace the source block cove. Insert the ESI or APCI probe. 5-22 __________________________ MSQ Hardware Manual ____________________________...

  • Page 93: Checking The Rotary Pump Oil Level And Color

    Maintaining the Fore Pump The fore pump (the rotary or backing pump) is external to the MSQ and requires routine maintenance to keep it running at its optimum performance level. The pumps used for this purpose come from two manufacturers–...
  • Page 94 4. Remove the oil filler plug located above the oil sight glass, marked , from the pump. 5. Pour the oil into the pump until the oil level in the oil sight glass is close to, but not above, the upper mark. 5-24 __________________________ MSQ Hardware Manual ____________________________...

  • Page 95: Changing The Rotary Pump Oil

    Routine and Preventive Maintenance _____________________________________________________________________ The Vacuum System oil filter oil filler plug oil sight glass oil drain plug Figure 5-6. Busch Rotary pump 6. Replace the oil filler plug. Changing the Rotary Pump Oil The oil in the rotary pump should be replaced at least once every six months.
  • Page 96 Fill the pump reservoir up to, but not above, the upper mark. Replace the filler plug. Pump down the instrument to prepare for operation. Note: Leave the system pumping for at least half an hour before beginning operation. 5-26 __________________________ MSQ Hardware Manual ____________________________...
  • Page 97 Chapter 6 Troubleshooting Troubleshooting .........................6-i Introduction ............................6-1 Troubleshooting Help ........................6-2 Resolving Common Problems ......................6-3 Checking the MSQ Power Supply Requirements..............6-3 Restarting the PC .......................6-3 HPLC System Troubleshooting......................6-4 Buffers and Additives......................6-4 Mobile Phase Reservoir.....................6-4 Bubble Problems and Degassing ..................6-4 Contamination in the LC System..................6-5 Tubing and Fittings......................6-5...

  • Page 98: Troubleshooting

    Troubleshooting Introduction ____________________________________________________________________________ 6-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 99: Introduction

    MSQ LC/MS system. If you encounter a problem that is not described here, or have a problem that is not resolved by the remedy suggested, contact your local Dionex Service Representative for assistance. This chapter is divided into the following sections: •...

  • Page 100: Troubleshooting Help

    Problems relating to MS resolution. The troubleshooting help system describes the visible symptoms, the probable cause of the problem, and suggestions on how to remedy it. To open the troubleshooting help, double-click on the troubleshooting help desktop icon. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 101: Resolving Common Problems

    Checking the MSQ Power Supply Requirements The MSQ should be connected to a suitable power supply. Full details of the power requirements for your detector can be found in the MSQ Pre- Installation Requirements Guide. Note. For details of the power requirements of other system peripherals, refer to the appropriate manufacturer’s specifications.

  • Page 102: Hplc System Troubleshooting

    Degassing in an ultrasonic bath is a poor technique for removal of gas from solvents. Normal-phase solvents do not need to be degassed. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 103: Contamination In The Lc System

    Troubleshooting _____________________________________________________________ HPLC System Troubleshooting Bubbles trapped in the pump head are also a problem and can be removed • Flushing the pump with degassed mobile phase (try increasing the flow rate to 5 mL/min). • Opening the purge valve and increasing the flow. •...
  • Page 104 Never over-tighten PEEK fittings, as this can cause leaks. Stainless steel fittings can also be used, but exercise care not to over-tighten, as the tubing can become crushed and the flow restricted. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 105: Injection Valves

    Troubleshooting _____________________________________________________________ HPLC System Troubleshooting Injection Valves Rheodyne and Valco manufacture the most commonly used injection valves. They can be used manually or as part of an autosampler system. The injectors can be fitted with various injection loop volumes, although they are most suitable for volumes up to 100 µL.
  • Page 106 Test a UV detector by monitoring the output either via the analog inputs (check output voltage) or by viewing the UV detector display. Injecting a solution of erythromycin, for example, should give a good response at a wavelength setting of 280 nm. ___________________________ MSQ Hardware Manual ____________________________...

  • Page 107: Preventive Maintenance And Spares

    Filtering If possible, filter solvents (especially if buffers are being used) and samples to prevent unwanted particulate matter from entering the pump and subsequently the MSQ. • Degassing Thoroughly degas all solvents to prevent air from entering the pump, to minimize problems associated with bubbles, and to improve check valve operation.
  • Page 108 Troubleshooting HPLC System Troubleshooting _____________________________________________________________ 6-10 __________________________ MSQ Hardware Manual ____________________________...
  • Page 109 Instrument Standby and Shutdown....................7-2 In Between Analytical Runs ....................7-2 Up to Two Weeks ......................7-3 Two Weeks or More ......................7-4 Restarting the System ........................7-6 Pre-Switch on Checklist ....................7-6 System Start-up Procedure ....................7-7 Pumping Down the MSQ ....................7-7 ___________________________MSQ Hardware Manual _____________________________...
  • Page 110 Shutting Down and Restarting the System Introduction ____________________________________________________________________________ 7-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 111: Shutting Down And Restarting The System

    _____________________________________________________________________________ Introduction Introduction This chapter provides details of how to shut down the MSQ system for a short period (up to 2 weeks) or for a longer period. It also describes how to restart your system following a long-term shutdown.

  • Page 112: Instrument Standby And Shutdown

    In Between Analytical Runs If the MSQ is to be left for more than 15 minutes between analytical runs, the API gas flow can be turned off to conserve the supply. Follow the steps described below: Ensure that the LC flow has been turned off.
  • Page 113 Take the instrument out of operate. • In the MSQ Tune window, click on the Toggle Operate button. The button will turn from green to gray and the text will change from “On” to “Off.”...
  • Page 114 Shutting Down and Restarting the System Instrument Standby and Shutdown __________________________________________________________ One Month or More If the MSQ system is unlikely to be used for more than one month, perform the following: Note. Leave the MSQ under vacuum. It is good working practice not to vent the instrument unless non-routine maintenance is being carried out.
  • Page 115 (see Figure 7-1). Figure 7-1. The taskbar showing the server icon Refer to the topic The Server, in the chapter Introducing the MSQ, for more information on the server. Exit from Xcalibur and shut down the PC in the usual way. Ensure that you have switched off the PC monitor, printer, and any other associated hardware.

  • Page 116: Restarting The System

    Pump down the MSQ Once you have completed these procedures, the system is ready for tuning and calibration; see the MSQ Getting Started manual for details. Pre-Switch on Checklist Before you switch on the system after an extended shutdown period, a major overhaul, or instrument relocation, perform a number of visual checks on the system.

  • Page 117: System Start-Up Procedure

    Plug in the MSQ and switch it on at the mains. Press the ON switch located at the rear of the instrument. Note. The MSQ vacuum pumps will not start immediately. Refer to the topic Pumping Down the MSQ for information on starting the vacuum pumps.

  • Page 118: Pumping Down The Msq

    You can also monitor the vacuum status of the instrument by observing the status light on the front of the instrument. For more information about the status light, refer to the topic Exterior Features of the MSQ in the chapter Introducing the MSQ.
  • Page 119 Chapter 8 Consumables and Spares Consumables and Spares......................8-i Introduction ............................8-1 Consumables............................8-2 General Consumables Kit (P/N 060046) ................8-2 Probe Maintenance Kit (P/N 061495) ................8-4 Source Maintenance Kit (P/N 061494)................8-5 Spares ..............................8-6 ____________________________MSQ Hardware Manual _____________________________...
  • Page 120 Consumables and Spares Introduction ____________________________________________________________________________ 8-ii ____________________________ MSQ Hardware Manual ____________________________...

  • Page 121: Consumables And Spares

    ____________________________________________________________________________ Introduction Introduction This chapter lists the parts most commonly used in the course of working with and maintaining your MSQ. The parts are categorized as follows: • Consumable Parts. Keep a stock of each of these parts, as they may need to be replaced frequently.

  • Page 122: Consumables

    Consumables and Spares Consumables ___________________________________________________________________________ Consumables All the consumables required for the upkeep of your MSQ are contained in a General Consumables Kit (P/N 060046). In addition to the individual parts, this kit contains the MSQ O-Ring and Screw Kit (P/N 060777).
  • Page 123 Consumables and Spares ___________________________________________________________________________Consumables MSQ O-Ring and Screw Kit (P/N 060777) Part Description Dionex Quantity Part Number Part Number in Kit M3 × 6 cap head stainless steel screw 060818 5313041 O-ring BS010 Viton degas 060804 5711000 O-ring BS009 Viton degas...

  • Page 124: Probe Maintenance Kit (P/N 061495)

    PIN, CORONA, APCI, MSQ 060781 FM101433 PLUG, BLANK, APCI, MSQ 060783 FM101437 SLEEVE, CERAMIC, ESI PROBE, MSQ 060790 FM103394 SCREW, ST STL, CAP HD, M3X10, MSQ 060803 FM103046 O-RING, VITON, BS010, MSQ 060804 FM5711000 O-RING, VITON, BS009, MSQ 060805 FM5711020...

  • Page 125: Source Maintenance Kit (P/N 061494)

    KIT, O-RING AND SCREW, MSQ 060777 FM104674 PLUG, SEALING, MSQ 060785 FM102277 SEAL, VACUUM HOUSING, MSQ 060789 FM101633 O-RING, VITON, 3 X 1, MSQ 060807 FM5711933 O-RING, VITON, BS207, MSQ 060809 FM101417 O-RING, VITON, BS007, MSQ 060810 FM101464 O-RING, VITON, BS014, MSQ...
  • Page 126 Dionex Quantity Part Part Number Number CONNECTOR, BULKHEAD, LEGRIS, MSQ 060762 902810 SCREW, ST STL, CAP HD, M3X8, MSQ 060817 5313020 SCREW, ST STL, CAP HD, M3X6, MSQ 060818 5313041 O-RING, VITON, BS010, MSQ 060804 5711000 O-RING, VITON, BS009, MSQ...
  • Page 127 ASSY, BOTTLE, WASTE, MSQ 060745 FM102770 ASSY, BOTTLE, REFERENCE, MSQ 060744 FM102771 O-RING, VITON, 2.4 X 3.3, MSQ 060814 FM103016 SCREW, ST STL, CAP HD M3X10, MSQ 060803 FM103046 O-RING, VITON, BS225, MSQ 060815 FM103048 SLEEVE, CERAMIC, ESI PROBE, MSQ 060790 FM103394...
  • Page 128 _________________________________________________________________________________ Index Index flushing (Note), 5-3 capillary ESI insert capillary, 1-11 replacing, 5-6, 5-10 acetic acid, 1-1, 3-3 carboxylic acid, 1-19 acetonitrile, 3-3 Cautions acidic compounds, 1-12 cleaning RF lens, 5-17 acquisition modes cleaning the source block, 5-16 Full Scan, 1-32 phosphoric acid, 3-5 raw data types, 1-31 tetrahydrofuran, THF, 3-5...
  • Page 129 6-4 preventative maintenance and spares, 6-9 troubleshooting, 6-4 electrospray. See ESI tubing and fittings, 6-5 entrance cone use of solvents and additives with MSQ, 3-3 cleaning, 5-11 UV detectors, 6-7 applications, 1-21 comparison with APCI (table), 1-22 introduction, 1-9...
  • Page 130 PC, 6-3 sample infusion probe temperature, 4-4, 4-6 reference inlet system starting vacuum pumps, 7-7 functional description, 1-25 MSQ under vacuum, 7-3 introduction, 1-25 reference inlet system (figure), 1-25 restarting the system, 7-6 reverse phase solvents, 3-3 RF lens...
  • Page 131 Index__________________________________________________________________________________ sample infusion system system overwiew, 1-2 flow rate (Note), 4-2 MSQ Instrument Tuning and Calibration Wizard introduction, 4-i figure, 1-30 probe temperature (Note), 4-4, 4-6 setup, 4-3 schedule, maintenance, 5-2 self cleaning source, 1-3, 1-23 tetrahydrofuran, THF Sequence Setup, 1-29...
  • Page 132 _________________________________________________________________________________ Index Home Page (figure), 1-28 server, 1-29 introduction, 1-28 server (figure), 1-29 rebooting the PC, 6-3 ____________________________MSQ Hardware Manual ______________________________...

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