Waters Micromass ZQ 2000 Manual

Waters Micromass
ZQ Detector
Operator’s Guide
34 Maple Street
Milford, MA 01757
71500044702, Revision B

NOTICE
The information in this document is subject to change without notice and should not be
construed as a commitment by Waters Corporation. Waters Corporation assumes no
responsibility for any errors that may appear in this document. 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, the use of this document.
© 2002 WATERS CORPORATION. PRINTED IN THE UNITED STATES OF AMERICA.
ALL RIGHTS RESERVED. THIS DOCUMENT OR PARTS THEREOF MAY NOT BE
REPRODUCED IN ANY FORM WITHOUT THE WRITTEN PERMISSION OF THE
PUBLISHER.
Alliance, Micromass, and Waters are registered trademarks, and Empower, ESCi,
MassLynx, and SAT/IN are trademarks of Waters Corporation.
Microsoft, Windows, and Windows NT are registered trademarks of Microsoft Corporation.
All other trademarks or registered trademarks are the sole property of their respective
owners.

Note: When you use the instrument, follow generally accepted procedures for quality
control and methods development.
If you observe a change in the retention of a particular compound, in the resolution
between two compounds, or in peak shape, immediately determine the reason for the
changes. Until you determine the cause of a change, do not rely on the separation results.
Note: The Installation Category (Overvoltage Category) for this instrument is Level II. The
Level II Category pertains to equipment that receives its electrical power from a local level,
such as an electrical wall outlet.
STOP
Atención: Changes or modifications to this unit not expressly approved by the party
responsible for compliance could void the user’s authority to operate the equipment.
Important : Toute modification sur cette unité n’ayant pas été expressément approuvée
par l’autorité responsable de la conformité à la réglementation peut annuler le droit de
l’utilisateur à exploiter l’équipement.
Achtung: Jedwede Änderungen oder Modifikationen an dem Gerät ohne die
ausdrückliche Genehmigung der für die ordnungsgemäße Funktionstüchtigkeit
verantwortlichen Personen kann zum Entzug der Bedienungsbefugnis des Systems
führen.
Avvertenza: eventuali modifiche o alterazioni apportate a questa unità e non
espressamente approvate da un ente responsabile per la conformità annulleranno
l’autorità dell’utente ad operare l’apparecchiatura.
Atención: cualquier cambio o modificación efectuado en esta unidad que no haya sido
expresamente aprobado por la parte responsable del cumplimiento puede anular la
autorización del usuario para utilizar el equipo.

Caution: Use caution when working with any polymer tubing under pressure:
• Always wear eye protection when near pressurized polymer tubing.
• Extinguish all nearby flames.
• Do not use Tefzel tubing that has been severely stressed or kinked.
• Do not use Tefzel tubing with tetrahydrofuran (THF) or concentrated nitric or
sulfuric acids.
• Be aware that methylene chloride and dimethyl sulfoxide cause Tefzel tubing to
swell, which greatly reduces the rupture pressure of the tubing.
Attention : Soyez très prudent en travaillant avec des tuyaux de polymères sous
pression :
• Portez toujours des lunettes de protection quand vous vous trouvez à proximité de
tuyaux de polymères.
• Eteignez toutes les flammes se trouvant à proximité.
• N'utilisez pas de tuyau de Tefzel fortement abîmé ou déformé.
• N'utilisez pas de tuyau de Tefzel avec de l'acide sulfurique ou nitrique, ou du
tétrahydrofurane (THF).
• Sachez que le chlorure de méthylène et le sulfoxyde de diméthyle peuvent
provoquer le gonflement des tuyaux de Tefzel, diminuant ainsi fortement leur
pression de rupture.
Vorsicht: Bei der Arbeit mit Polymerschläuchen unter Druck ist besondere Vorsicht
angebracht:
• In der Nähe von unter Druck stehenden Polymerschläuchen stets Schutzbrille
tragen.
• Alle offenen Flammen in der Nähe löschen.
• Keine Tefzel-Schläuche verwenden, die stark geknickt oder überbeansprucht sind.
• Tefzel-Schläuche nicht für Tetrahydrofuran (THF) oder konzentrierte Salpeter-
oder Schwefelsäure verwenden.
• Durch Methylenchlorid und Dimethylsulfoxid können Tefzel-Schläuche quellen;
dadurch wird der Berstdruck des Schlauches erheblich reduziert.

Precauzione: prestare attenzione durante le operazioni con i tubi di polimero sotto
pressione:
• Indossare sempre occhiali da lavoro protettivi nei pressi di tubi di polimero
pressurizzati.
• Estinguere ogni fonte di ignizione circostante.
• Non utilizzare tubi Tefzel soggetti a sollecitazioni eccessive o incurvati.
• Non utilizzare tubi Tefzel contenenti tetraidrofurano (THF) o acido solforico o
nitrico concentrato.
• Tenere presente che il cloruro di metilene e il dimetilsolfossido provocano
rigonfiamento nei tubi Tefzel, che riducono notevolmente il limite di pressione di
rottura dei tubi stessi.
Advertencia: manipular con precaución los tubos de polímero bajo presión:
• Protegerse siempre los ojos en las proximidades de tubos de polímero bajo
presión.
• Apagar todas las llamas que estén a proximidad.
• No utilizar tubos Tefzel que hayan sufrido tensiones extremas o hayan sido
doblados.
• No utilizar tubos Tefzel con tetrahidrofurano (THF) o ácidos nítrico o sulfúrico
concentrados.
• No olvidar que el cloruro de metileno y el óxido de azufre dimetilo dilatan los tubos
Tefzel, lo que reduce en gran medida la presión de ruptura de los tubos.

Caution: 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.
Attention : 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
défectueuses.
Vorsicht: Der Benutzer wird darauf aufmerksam gemacht, dass bei unsachgemäßer
Verwenddung des Gerätes unter Umständen nicht ordnungsgemäß funktionieren.
Precauzione: l’utente deve essere al corrente del fatto che, se l’apparecchiatura viene
usta in un modo specificato dal produttore, la protezione fornita dall’apparecchiatura
potrà essere invalidata.
Advertencia: el usuario deberá saber que si el equipo se utiliza de forma distinta a la
especificada por el fabricante, las medidas de protección del equipo podrían ser
insuficientes.

Caution: To protect against fire hazard, replace fuses with those of the same type and
rating.
Attention : Remplacez toujours les fusibles par d’autres du même type et de la même
puissance afin d’éviter tout risque d’incendie.
Vorsicht: Zum Schutz gegen Feuergefahr die Sicherungen nur mit Sicherungen des
gleichen Typs und Nennwertes ersetzen.
Precauzione: per una buona protezione contro i rischi di incendio, sostituire i fusibili con
altri dello stesso tipo e amperaggio.
Advertencia: sustituya los fusibles por otros del mismo tipo y características para evitar
el riesgo de incendio.

Caution: To avoid possible electrical shock, disconnect the power cord before servicing
the instrument.
Attention : Afin d’éviter toute possibilité de commotion électrique, débranchez le cordon
d’alimentation de la prise avant d’effectuer la maintenance de l’instrument.
Vorsicht: Zur Vermeidung von Stromschlägen sollte das Gerät vor der Wartung vom
Netz getrennt werden.
Precauzione: per evitare il rischio di scossa elettrica, scollegare il cavo di alimentazione
prima di svolgere la manutenzione dello strumento.
Precaución: para evitar descargas eléctricas, desenchufe el cable de alimentación del
instrumento antes de realizar cualquier reparación.

Commonly Used Symbols
Direct current
Courant continu
Gleichstrom
Corrente continua
Corriente continua
Alternating current
Courant alternatif
Wechselstrom
Corrente alternata
Corriente alterna
Protective conductor terminal
Borne du conducteur de protection
Schutzleiteranschluss
Terminale di conduttore con protezione
Borne del conductor de tierra

Frame or chassis terminal
Borne du cadre ou du châssis
Rahmen- oder Chassisanschluss
Terminale di struttura o telaio
Borne de la estructura o del chasis
Caution or refer to manual
Attention ou reportez-vous au guide
Vorsicht, oder lesen Sie das Handbuch
Prestare attenzione o fare riferimento alla guida
Actúe con precaución o consulte la guía
Caution, hot surface or high temperature
Attention, surface chaude ou température élevée
Vorsicht, heiße Oberfläche oder hohe Temperatur
Precauzione, superficie calda o elevata temperatura
Precaución, superficie caliente o temperatura elevada
Commonly Used Symbols (Continued)

Caution, risk of electric shock (high voltage)
Attention, risque de commotion électrique (haute tension)
Vorsicht, Elektroschockgefahr (Hochspannung)
Precauzione, rischio di scossa elettrica (alta tensione)
Precaución, peligro de descarga eléctrica (alta tensión)
Caution, risk of needle-stick puncture
Attention, risques de perforation de la taille d’une aiguille
Vorsicht, Gefahr einer Spritzenpunktierung
Precauzione, rischio di puntura con ago
Precaución, riesgo de punción con aguja
Caution, ultraviolet light
Attention, rayonnement ultrviolet
Vorsicht, Ultraviolettes Licht
Precauzione, luce ultravioletta
Precaución, emisiones de luz ultravioleta
Commonly Used Symbols (Continued)
UV

Fuse
Fusible
Sicherung
Fusibile
Fusible
Electrical power on
Sous tension
Netzschalter ein
Alimentazione elettrica attivata
Alimentación eléctrica conectada
Electrical power off
Hors tension
Netzschalter aus
Alimentazione elettrica disattivata
Alimentación eléctrica desconectada
Commonly Used Symbols (Continued)
1
0

Waters Micromass ZQ Detector Information
Intended Use
Waters designed the Waters®Micromass®ZQ™ Detector to with an HPLC system to
determine mass-to-charge ratio (m/z) for a wide range of analytes.
Biological Hazard
When you analyze physiological fluids, take all necessary precautions and treat all
specimens as potentially infectious. Precautions are outlined in “CDC Guidelines on
Specimen Handling,” CDC – NIH Manual, 1984.
Calibration
Follow the calibration methods set forth in this guide, using pure standards. The
concentration range should cover the entire range of quality-control samples, typical and
atypical specimens.
Quality Control
Routinely run three quality-control samples. Quality-control samples should represent
subnormal, normal, and above-normal levels of a compound. Ensure that quality-control
sample results are within an acceptable range, and evaluate precision from day to day and
run to run. Data collected when quality-control samples are out of range may not be valid.

Table of Contents 15
Preface ....................................................................................... 23
Chapter 1
Overview .......................................................................................... 27
1.1 About the Micromass ZQ Detector........................................ 27
1.2 Theory and Principles of Operation ...................................... 28
1.3 MassLynx 4.0 Software......................................................... 29
Chapter 2
Installing .......................................................................................... 30
2.1 Site Selection and Power Requirements............................... 31
2.2 Unpacking and Inspecting..................................................... 32
2.3 Installing the Detector........................................................... 33
2.3.1 Installing the Rotary Pump ........................................ 33
2.3.2 Installing the Oil Return Connection Kit..................... 34
2.3.3 Connecting the Nitrogen Supply and Exhaust........... 35
2.3.4 Connecting the Rheodyne Injector (for Manual
Injections).................................................................. 37
2.3.5 Installing the ESI Probe............................................. 38
2.3.6 Connecting the Workstation....................................... 39
2.3.7 Preparing the Syringe and Syringe Pump................. 40
Table of Contents

Table of Contents 16
Chapter 3
Tuning ............................................................................................ 41
3.1 Opening MassLynx and Starting the Instrument................... 41
3.2 Tuning in ESI Mode............................................................... 43
3.2.1 Specifying Parameter Settings on the ES+
Source Page.............................................................. 44
3.2.2 Specifying Parameter Settings on the
Analyser Page ........................................................... 46
3.3 Tuning in APCI Mode ............................................................ 47
3.3.1 Preparing the Source for APCI Operation ................. 48
3.3.2 Installing the Tee Fitting............................................. 49
3.3.3 Specifying Parameters on the APCI+ Source
Page .......................................................................... 49
3.4 Readbacks............................................................................ 52
Chapter 4
Calibrating ....................................................................................... 54
4.1 Setting Up the Calibration File .............................................. 54
4.2 Setting Calibration Parameters ............................................. 55
4.2.1 Tune Window Settings ............................................... 55
4.2.2 Instrument Threshold Settings Dialog Box ................ 58
4.2.3 Automatic Calibration Check Dialog Box ................... 59
4.2.4 Calibration Parameters Dialog Box............................ 60
4.2.5 Mass Measure Dialog Box......................................... 62
4.2.6 Automatic Calibration Dialog Box .............................. 63
4.2.7 Calibration Acquisition Dialog Box............................. 64

Table of Contents 17
Chapter 5
Maintaining ...................................................................................... 73
5.1 Considerations...................................................................... 73
5.2 Routine Maintenance............................................................ 75
5.2.1 Checking the Rotary Pump Oil .................................. 75
5.2.2 Replacing the Pump Oil............................................. 75
5.2.3 Gas-Ballasting the Rotary Pump............................... 78
5.2.4 Replacing the Oil Mist Filter....................................... 79
5.2.5 Cleaning the Source Assembly.................................. 80
5.2.6 Cleaning the APCI Probe Tip..................................... 91
5.2.7 Cleaning and Replacing the Corona Discharge
Needle....................................................................... 91
5.3 Replacing Parts..................................................................... 92
5.3.1 Replacing the Ion Block Cartridge Heater................. 92
5.3.2 Replacing the Stainless Steel Capillary..................... 93
5.3.3 Replacing the ESI Probe Tip ..................................... 95
5.3.4 Replacing the APCI Fused Silica Capillary and
Filter Pad ................................................................... 96
5.3.5 Replacing the APCI Probe Heater............................. 98
Chapter 6
Troubleshooting ............................................................................... 99
6.1 Safety and Handling.............................................................. 99
6.2 Component Hardware Troubleshooting............................... 101
6.3 Inspecting the APCI Probe.................................................. 107

Table of Contents 18
Appendix A
Using the ESCi Multi-Mode Ionization Source................................ 108
A.1 Preparing for Operation ..................................................... 108
A.1.1 Installing the Corona Discharge Needle.................. 108
A.1.2 Setting Up MassLynx .............................................. 110
A.2 Daidzein Test ..................................................................... 117
A.2.1 Test Conditions ...................................................... 118
A.2.2 Signal-to-Noise Ratio .............................................. 118
Appendix B
Specifications ................................................................................. 119
B.1 ZQ Detector Specifications ................................................ 119
B.2 ESCi Multi-Mode Ionization Source Specifications ........... 121
Appendix C
Accessories and Spare Parts ......................................................... 122
Index ..................................................................................... 129

List of Figures 19
2-1 Installing the Detector....................................................................30
2-2 Pump Oil Level............................................................................... 33
2-3 Fitting the Gas Ballast and Hose adaptors to the Rotary Pump.... 35
2-4 ZQ Detector Rear Panel ................................................................36
2-5 Nitrogen Stud.................................................................................36
2-6 Drying Gas Exhaust Bottle ............................................................37
2-7 Rheodyne Injector..........................................................................38
2-8 ESI Probe in Situ ...........................................................................39
2-9 Syringe Pump................................................................................40
3-1 MassLynx Login Dialog Box........................................................... 41
3-2 MassLynx Main Window................................................................42
3-3 Tune Window Displaying the ES+ Source Page ............................43
3-4 Syringe Selection Dialog Box ........................................................45
3-5 Tune Window Displaying the Analyser Page..................................47
3-6 Combined Flow into the Tee ..........................................................49
3-7 Tune Window Displaying the APCI+ Source Page.........................50
3-8 Readbacks Dialog Box...................................................................52
3-9 Diagnostics Page Readbacks........................................................53
4-1 Calibration Window........................................................................54
4-2 Open Dialog Box............................................................................55
4-3 Tune Window Displaying the ES+ Source Page ............................57
4-4 Tune Window Displaying Analyser Page Parameters....................58
4-5 Instrument Threshold Settings Dialog Box ....................................59
4-6 Automatic Calibration Check Dialog Box .......................................59
4-7 Calibration Parameters Dialog Box................................................60
4-8 Mass Measure Dialog Box.............................................................62
4-9 Automatic Calibration Dialog Box .................................................. 63
4-10 Calibration Acquisition Setup Dialog Box ......................................65
List of Figures

List of Figures 20
4-11 Display Calibration Graphs Dialog Box..........................................67
4-12 Calibrate Window Showing ZQ-4000 Calibration Graphs..............69
5-1 Rotary Pump Assembly Fitted with Oil Mist Filter..........................76
5-2 Rotary Pump Oil Filler Plug, Drain Plug, and Sight Glass.............77
5-3 Isolation Valve................................................................................79
5-4 Oil Mist Filter Assembly.................................................................80
5-5 Pumping Block Assembly ..............................................................82
5-6 Ion Block Assembly .......................................................................83
5-7 Probe Assembly in Position on the Source....................................84
5-8 ZQ Detector Front View.................................................................85
5-9 Source Showing the Corona Discharge Needle ............................86
5-10 Ion Block........................................................................................86
5-11 Sample Cone and Cone Gas Nozzle.............................................87
5-12 Ion Block Rear View ......................................................................88
5-13 Hexapole Assembly.......................................................................89
5-14 Ion Block Cartridge Heater............................................................92
5-15 Replacing the Heater Cartridge.....................................................93
5-16 ESI Probe Tip with Capillary Protruding 0.5 mm...........................95
A-1 ZQ Mass Detector, Front View ...................................................109
A-2 Installing the Corona Needle ...................................................... 110
A-3 Tune Window .............................................................................. 110
A-4 Tune Window Showing Options List with ESCi Mode Selected . 111
A-5 Tune Window, Diagnostics Page ................................................ 112
A-6 Selecting the ESCi+ or ESCi- Ionization Mode ........................... 112
A-7 Selecting the Ion Mode in the MassLynx Peak Editor ................ 113
A-8 Tune Window as it Appears During ESCi Operation .................. 114
A-9 Function List Editor Window (Blank) ...........................................115
A-10 Function:nMS Scan Dialog Box ................................................. 115
A-11 Function List Editor Window Showing Specified Functions ........ 116
A-12 ESCi Mode Disabled ................................................................... 117
A-13 Daidzein (m/z = 255.2 [M + H] and 253.2 [M – H]) .....................117