Thermo Scientific iCAP Q User manual

Part of Thermo Fisher Scientific
Revision B - 1288090
Thermo Fisher Scientific
iCAP Q
Operating Manual

© 2012 Thermo Fisher Scientific Inc. All rights reserved.
Original Operating Instructions
Leybonol and Sogevac are a registered trademarks of Oerlikon Leybold Vacuum GmbH. Santoprene
is a registered trademark of Monsanto, Inc. Viton is a registered trademark of DuPont Dow
Elastomers.
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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use
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any part of this document is strictly prohibited, except with the written authorization of Thermo
Fisher Scientific Inc.
Release History: Revision A released in March 2012.
Revision B released in June 2012.

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Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) i
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Suggestions to the Manual
ii iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific

Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) iii
Contents
Chapter 1 Using this Manual.....................................................................1-1
About this Manual ............................................................ 1-1
Typographical Conventions .............................................. 1-2
Signal Word................................................................... 1-2
Viewpoint Orientation................................................... 1-2
Data Input ..................................................................... 1-2
Topic Headings.............................................................. 1-3
Reference Documentation................................................. 1-4
Chapter 2 Scope of Delivery......................................................................2-1
Standard System Components .......................................... 2-1
Optional System Components .......................................... 2-2
Chapter 3 System Description...................................................................3-1
General Description.......................................................... 3-2
Instrument Layout ......................................................... 3-3
Sample Introduction System ............................................. 3-4
Peristaltic Pump............................................................. 3-4
Nebulizer ....................................................................... 3-5
Spray Chamber .............................................................. 3-5
Injector .......................................................................... 3-6
Torch............................................................................. 3-6
Interface............................................................................ 3-7
Sample Cone and Skimmer Cone .................................. 3-7
Extraction Lens .............................................................. 3-8
Ion Optics......................................................................... 3-9
RAPID Lens................................................................... 3-9
QCell............................................................................. 3-9
DA Assembly ............................................................... 3-10
Mass Analyzer ................................................................. 3-10
Quadrupole.................................................................. 3-10
Detector....................................................................... 3-10
Vacuum System .............................................................. 3-11
Forepump .................................................................... 3-12
Turbomolecular Pump................................................. 3-12
Pressure Measurement.................................................. 3-12
Gas Supply...................................................................... 3-13
Connections................................................................. 3-13
Plasma and Cooling Gas .............................................. 3-14
CCT Gas ..................................................................... 3-15
Additional Gas ............................................................. 3-17

Contents
iv iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
Cooling System............................................................... 3-19
Connections for Water Supply..................................... 3-19
Recirculating Chiller .................................................... 3-20
Exhaust System ............................................................... 3-21
Connections.................................................................... 3-22
Main Power Switch...................................................... 3-23
Power Connections ...................................................... 3-23
Fore Vacuum Pump Connections ................................ 3-24
Connection to Computer and Peripherals.................... 3-25
Chapter 4 Safety.......................................................................................... 4-1
Safety Symbols and Signal Words in this Manual.............. 4-2
Observing this Manual................................................... 4-2
Safety Symbols on the Instrument..................................... 4-3
Rating Plate....................................................................... 4-5
Intended Use..................................................................... 4-6
Qualified Personnel........................................................ 4-7
Permitted Materials........................................................... 4-7
Electrical Safety Precautions.............................................. 4-8
Residual Hazards............................................................... 4-9
Personal Protective Equipment ....................................... 4-10
EMC Information........................................................... 4-11
In Case of Emergency ..................................................... 4-12
Chapter 5 System Setup............................................................................. 5-1
Safety Guidelines for Installation....................................... 5-2
Placing the System ............................................................ 5-3
Instrument Dimensions ................................................. 5-3
Moving the Instrument.................................................. 5-4
Workbench for Instrument ............................................ 5-5
Laboratory Conditions...................................................... 5-7
Power Supply................................................................. 5-7
Gas Supply..................................................................... 5-7
Laboratory Temperature ................................................ 5-8
Humidity....................................................................... 5-8
Ventilation and Fume Exhaust....................................... 5-9
Vibration ....................................................................... 5-9
Airborne Noise Emission ............................................... 5-9
Chapter 6 Operation ................................................................................... 6-1
Safety Guidelines for Operation ........................................ 6-2
System Controls................................................................ 6-4
System Status LEDs ....................................................... 6-4
Power Panel ................................................................... 6-5
Starting Up the System ..................................................... 6-6
Shutting Down the System ............................................... 6-7
Switching to Standby Mode........................................... 6-7

Contents
Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) v
Shutting Down the Complete System (Instrument
Vented).......................................................................... 6-7
Shutting Down the Instrument only (Instrument not
Vented).......................................................................... 6-8
Getting Ready................................................................... 6-9
Before Operating the System.......................................... 6-9
Getting Ready with the Experiment Editor .................... 6-9
Going to Operation Status with Instrument Control ... 6-13
Working with LabBooks ................................................. 6-14
Loading a LabBook ...................................................... 6-14
Submitting a LabBook ................................................. 6-15
Starting the Data Acquisition....................................... 6-15
After Operation............................................................... 6-16
Run the System with Blanks......................................... 6-16
Release Peristaltic Pump Tubing .................................. 6-16
Emptying the Waste Container.................................... 6-16
Chapter 7 Troubleshooting ........................................................................7-1
General Remarks............................................................... 7-2
Administrator/User ........................................................ 7-2
Safety Guidelines for Troubleshooting .............................. 7-2
Error Messages .................................................................. 7-4
Plasma not Lit................................................................... 7-5
Sensitivity Problems/No Signal ......................................... 7-7
Signal Drifts with Time .................................................... 7-8
Poor Signal Stability.......................................................... 7-9
Interlocks ........................................................................ 7-10
Door Lock ................................................................... 7-10
Interface Temperature.................................................. 7-10
Low Water Flow .......................................................... 7-10
Hardware Lock Open................................................... 7-11
Water Valve Closed...................................................... 7-11
Low Argon Pressure ..................................................... 7-11
Low Cool Gas Flow ..................................................... 7-11
Low Exhaust Gas Flow................................................. 7-12
Plasma Lit Sensor......................................................... 7-12
Chapter 8 Maintenance..............................................................................8-1
Safety Guidelines for Maintenance.................................... 8-2
General Advice for Maintenance ....................................... 8-4
Returning Parts.............................................................. 8-4
Servicing Plan ................................................................... 8-5
General Maintenance Routines ......................................... 8-7
Cleaning the Surface of the Instrument.......................... 8-7
Cleaning Agents............................................................. 8-7
Checking Warning Labels .............................................. 8-7
Checking Gas Lines for Leaks ........................................ 8-8
Maintaining the Air Filter ................................................. 8-9

Contents
vi iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
Maintaining the Inlet System .......................................... 8-11
Maintaining the Nebulizer ........................................... 8-11
Maintaining the Peristaltic Pump................................. 8-12
Maintaining the Spray Chamber .................................. 8-13
Maintaining the Injector .............................................. 8-14
Maintaining the Torch................................................. 8-15
Cleaning the Glassware ................................................ 8-16
Maintaining the Interface................................................ 8-17
Tools............................................................................ 8-17
Maintaining the Sample Cone...................................... 8-17
Maintaining the Skimmer Cone................................... 8-20
Maintaining the Extraction Lens.................................. 8-23
Thermo Fisher Scientific Service ..................................... 8-26
Health and Safety Form ............................................... 8-26
Services to be Performed by Thermo Fisher Scientific
Service Only................................................................. 8-26
Chapter 9 Additional Safety Information................................................ 9-1
Fore Vacuum Pump.......................................................... 9-2
Recirculating Chiller ......................................................... 9-4
Dionex ICS-5000.............................................................. 9-5
Legal Documents..................................................................... D-1
Glossary .................................................................................... G-1
Index ............................................................................................I-1

Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) 1-1
Chapter 1 Using this Manual
This chapter provides information about this operating manual. It
contains the following topics:
•“About this Manual” on page 1-1
•“Typographical Conventions” on page 1-2
•“Reference Documentation” on page 1-4
About this Manual
This iCAP Q Operating Manual contains precautionary statements that
can prevent personal injury, instrument damage, and loss of data if
properly followed. It describes the modes of operation and principle
hardware components of your iCAP Q mass spectrometer and provides
step-by-step instructions for cleaning and maintaining your instrument.

Using this Manual
Typographical Conventions
1-2 iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
Typographical Conventions
This section describes typographical conventions that have been
established for Thermo Fisher Scientific manuals.
Signal Word
Make sure you follow the precautionary statements presented in this
manual. The special notices appear different from the main flow of text:
NOTICE Points out possible material damage and other important
information in connection with the instrument. ▲
Viewpoint Orientation
Left and right used in this manual always refer to the viewpoint of a
person facing the front side of the instrument.
Data Input
Throughout this manual, the following conventions indicate data input
and output via the computer:
•Messages displayed on the screen are represented by capitalizing the
initial letter of each word and by italicizing each word.
•Input that you enter by keyboard is identified by quotation marks:
single quotes for single characters, double quotes for strings.
•For brevity, expressions such as “choose File > Directories” are used
rather than “pull down the File menu and choose Directories.”
•Any command enclosed in angle brackets < > represents a single
keystroke. For example, “press <F1>” means press the key labeled
F1.
•Any command that requires pressing two or more keys
simultaneously is shown with a plus sign connecting the keys. For
example, “press <Shift> +<F1>” means press and hold the <Shift>
key and then press the <F1> key.
•Any button that you click on the screen is represented in bold face
letters. For example, “click Close”.

Using this Manual
Typographical Conventions
Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) 1-3
Topic Headings
The following headings are used to show the organization of topics
within a chapter:
Chapter 1 Chapter Name
Second Level Topics
Third Level Topics
Fourth Level Topics

Using this Manual
Reference Documentation
1-4 iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
Reference Documentation
The iCAP Q Operating Manual represents the Original Operating
Instructions. Thermo Fisher Scientific provides additional reference
documents for the iCAP Q mass spectrometer that are not part of the
Original Operating Instructions. Reference documentation for the
iCAP Q mass spectrometer includes the following:
•iCAP Q Preinstallation Requirements Guide
•iCAP Q Consumables Catalog
You can access PDF files of most manuals from the data system
computer. The software also provides Help.
A printed version of the iCAP Q Operating Manual is shipped with the
instrument. A printed version of the iCAP Q Preinstallation
Requirements Guide is part of the Preinstallation Kit. This kit is sent to
your laboratory before the arrival of the iCAP Q mass spectrometer.
NOTICE If this manual is in another language than English:
Translations of the above are shown with their titles translated and the
English title in parentheses. You can download them from the Customer
Information Service (CIS) site. See the contact information at the
beginning of this manual. ▲
Refer also to the user documentation provided by the manufacturers of
third party components:
•Fore vacuum pump
•Turbomolecular pumps
•Water recirculating chiller
•Data system computer and monitor
•Safety data sheets

Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) 2-1
Chapter 2 Scope of Delivery
This chapter lists the standard components of your iCAP Q system and
frequently shipped optional components.
•“Standard System Components” on page 2-1
•“Optional System Components” on page 2-2
Standard System Components
The iCAP Q standard system comprises the following components:
•iCAP Q mass spectrometer
•Fore vacuum pump
•Data system computer and monitor
•CCT gas module (for iCAP Qc and iCAP Qs only)
•Additional gas kit (for iCAP Qs only)
•Installation Kit including
- Tools for installation and maintenance
-Spareparts
- Equipment for connecting the basic instrument
•Printed manuals
-iCAP Q Operating Manual
For a list of the manuals delivered with the iCAP Q mass spectrometer
and instructions on where to find PDF files of these manual, see
“Reference Documentation” on page 1-4.

Scope of Delivery
Optional System Components
2-2 iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
Optional System Components
The following optional components are frequently shipped with the
standard iCAP Q MS system:
•Autosampler ESI, ESI FAST, or CETAC
•Autosampler housing
•NESLAB ThermoFlex 2500 Recirculating Chiller
•Dionex ICS Ion Chromatography System
•Noise reduction cover and drip pan for fore vacuum pump

Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) 3-1
Chapter 3 System Description
This chapter provides an overview of the functional elements of the
iCAP Q instrument. It contains the following topics:
•“General Description” on page 3-2
•“Sample Introduction System” on page 3-4
•“Ion Optics” on page 3-9
•“QCell” on page 3-9
•“Mass Analyzer” on page 3-10
•“Detector” on page 3-10
•“Vacuum System” on page 3-11
•“Gas Supply” on page 3-13
•“Cooling System” on page 3-19
•“Exhaust System” on page 3-21
•“Connections” on page 3-22

System Description
General Description
3-2 iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
General Description
The iCAP Q mass spectrometer is designed for direct analyses of liquid
samples and can be coupled to further devices for analyses of gases or
solid aerosols.
Three models are available: iCAP Qa, iCAP Qc and iCAP Qs.
Differences in the systems will be noted where applicable.
Figure 3-1 shows a front view of the instrument.
Figure 3-1. iCAP Q MS front view

System Description
General Description
Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) 3-3
Instrument Layout
The iCAP Q instrument can be divided into four main components,
which are described in the following topics:
•Sample introduction
•Interface (ion generation)
•Ion Optics (ion focussing)
•Mass Analyzer
Labeled Components: 1= sample introduction, 2=interface, 3=ion optics,
4=mass analyzer
Figure 3-2. Instrument schematics - front view
1
2
3
4

System Description
Sample Introduction System
3-4 iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
Sample Introduction System
The sample introduction system of the iCAP Q MS comprises the
peristaltic pump, the nebulizer, the Peltier-cooled spray chamber and the
torch with the injector. Figure 3-3 shows a schematic view of the sample
introduction system.
Peristaltic Pump
A peristaltic pump passes the liquid sample to the nebulizer. Figure 3-4
shows the peristaltic pump with sample and drain tubing:
Labeled Components: 1=ICP torch with injector, 2=spray chamber,
3=nebulizer, 4=drain to waste (peristaltic pump), 5=to waste, 6=sample to
nebulizer (peristaltic pump), 7=nebulizer gas
Figure 3-3. Schematics sample introduction
3
2
1
4
6
7
5
Figure 3-4. Peristaltic pump at inlet system

System Description
Sample Introduction System
Thermo Fisher Scientific iCAP Q Operating Manual (P/N 1288090, Revision B) 3-5
Nebulizer
The sample aerosol is generated by the nebulizer. The properties of the
aerosol can be influenced by the nebulizer gas flow and also by the type
of nebulizer employed. Depending on the model ordered, the nebulizer
is made of either polypropylene (PP) or perfluoroalkoxy (PFA), see
Table 3-1.
Spray Chamber
The spray chamber filters out larger aerosol droplets for improved signal
stability and low oxide rates. Depending on the model ordered, the
spray chamber is made of either quartz or PFA, see Table 3-1.
Table 3-1. Material used in different iCAP Q models
Model Item Material
iCAP Qa nebulizer PP
spray chamber quartz
injector quartz, 2.5 mm ID
iCAP Qc nebulizer PFA
spray chamber quartz
injector quartz, 2.5 mm ID
iCAP Qs nebulizer PFA
spray chamber PFA
injector sapphire, 2.0 mm ID
Labeled Components: 1=nebulizer, 2=spray chamber, 3=injector, 4=torch
Figure 3-5. Nebulizer, spray chamber, injector and torch
1
2
3
4

System Description
Sample Introduction System
3-6 iCAP Q Operating Manual (P/N 1288090, Revision B) Thermo Fisher Scientific
For the iCAP Q instrument, the spray chamber is cooled using a Peltier
cooled chiller to improve instrument performance.
Injector
The injector is available with various internal diameters (ID) and in
various material for different types of analysis. Injectors with smaller
inner diameters are, for example, employed with organic-based
solutions, see Table 3-1. Due to the semi-demountable design of the
torch, the injectors can easily be replaced, see Figure 3-6.
Torch
The torch consists of two concentric quartz tubes, each with variable
flow rates. The gas stream through the outer tube of the torch shapes the
plasma and shields the torch body against the high temperatures of the
plasma (cool gas). The auxiliary gas flows through the inner tube.
Figure 3-6. Torch and injector