Thermo Scientific Prima PRO User manual

Part of Thermo Fisher Scientific
Prima PRO / Sentinel PRO
Mass Spectrometers
User Guide
P/N 209-230-510
Revision 10

©2013 Thermo Fisher Scientific Inc. All rights reserved.
Thermo Fisher Scientific Inc. (Thermo Fisher) makes every effort to ensure the accuracy and
completeness of this manual. However, we cannot be responsible for errors, omissions, or any loss of data
as the result of errors or omissions. Thermo Fisher reserves the right to make changes to the manual or
improvements to the product at any time without notice.
The material in this manual is proprietary and cannot be reproduced in any form without expressed written
consent from Thermo Fisher.

Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide v
Revision History
Revision
Level
Date
Comments
Rev 10
17/02/2016
Ex label changes

Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide vii
Contents
Introduction.........................................................................1-1
Safety Information..............................................................2-1
Overview.......................................................................................2-1
Safety Conventions and Symbols .................................................2-2
System Safety ...............................................................................2-3
Connecting the Instrument to the Electrical Supply..................2-4
Repair & Maintenance...............................................................2-4
Changing the Rotary Pump Oil..................................................2-4
Switching on the Rotary Pump..................................................2-4
High Temperatures ....................................................................2-5
Rotary Pump Exhaust Outlet .....................................................2-5
Inlet System Exhaust .................................................................2-5
Gas Mixtures in the Inlet System...............................................2-6
Protective Clothing....................................................................2-6
Hazardous Materials..................................................................2-6
Hazardous Area Systems...........................................................2-7
Fan Noise...................................................................................2-7
Site Requirements..............................................................3-1
Physical Installation......................................................................3-1
Cable Entries.................................................................................3-2
Safe Area Systems.....................................................................3-2
Hazardous Area Systems...........................................................3-2
Computer and Communications ...................................................3-2
Fibre Optic Communication ......................................................3-3
Hazardous Area Systems........................................................3-3
Environment..................................................................................3-4
General.......................................................................................3-4
Temperature...............................................................................3-4
Humidity....................................................................................3-4
Vibration....................................................................................3-4
Particulate Contamination..........................................................3-4
Altitude ......................................................................................3-5
Inlet Gas Connections...................................................................3-5
Calibration Gases.......................................................................3-5
Sample Gases.............................................................................3-6
Exhaust Gas Connections .............................................................3-7
Power............................................................................................3-8
Voltage and Frequency..............................................................3-8
Requirements.............................................................................3-8
Over-current Protection ...........................................................3-10
Chapter 1
Chapter 2
Chapter 3

Contents
viii Prima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
Power Quality ..........................................................................3-10
Power Connection....................................................................3-10
Other Services.............................................................................3-10
Safe Area Systems ...................................................................3-10
Dry Gas Vent ........................................................................3-10
Enclosure Purge....................................................................3-10
Hazardous Area Systems .........................................................3-11
Dry Gas Vent ........................................................................3-11
Rotary Pump Purge...............................................................3-11
Compressed Air Requirements.............................................3-12
Options........................................................................................3-13
Pump Purge Gas.......................................................................3-13
Rotary Oil Box Purge............................................................3-13
Rotary Pump Ballast.............................................................3-13
Turbo Pump Bearing Purge ..................................................3-13
External I/O Unit......................................................................3-14
Handling & Storage............................................................4-1
Receiving the Instrument..............................................................4-1
Unpacking the Instrument.............................................................4-2
Storing the Instrument...................................................................4-2
Installation & Interconnection...........................................5-1
Introduction...................................................................................5-1
Positioning the Instrument............................................................5-1
Cable Connections........................................................................5-1
General Requirements................................................................5-1
Safe Area Systems ..................................................................5-1
Hazardous Area Systems ........................................................5-2
Power Connection......................................................................5-2
Safe Area Systems ..................................................................5-2
Hazardous Area Systems ........................................................5-3
Sentinel PRO Sample Pump Power Connection.....................5-4
Signal Connection......................................................................5-4
Safe Area Systems ..................................................................5-4
Hazardous Area Systems ........................................................5-4
Gas Connections ...........................................................................5-4
Other Services...............................................................................5-4
Computer System..........................................................................5-5
Commissioning ..................................................................6-1
General..........................................................................................6-1
Procedure ......................................................................................6-1
Startup & Shutdown...........................................................7-1
Startup...........................................................................................7-1
Procedure ......................................................................................7-1
Vacuum Gauge Trip Level.........................................................7-4
Chapter 4
Chapter 5
Chapter 6
Chapter 7

Contents
Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide ix
Starting Scheduled Analysis......................................................7-4
Checking Instrument Tuning and Mass Alignment...................7-5
Emission..................................................................................7-6
Peak Shape..............................................................................7-6
Sensitivity ...............................................................................7-7
Detectors.................................................................................7-8
Mass Alignment......................................................................7-8
Heaters..................................................................................7-10
Checking Instrument Status Parameters..................................7-10
Shutdown....................................................................................7-11
Introduction..............................................................................7-11
Shutdown Procedure................................................................7-11
Emergency Shutdown..............................................................7-12
Status & Tuning Parameters..............................................8-1
Instrument Status ..........................................................................8-1
Source Tab....................................................................................8-2
Electron Energy .........................................................................8-2
Emission.....................................................................................8-2
Filament Current........................................................................8-2
Filament Current Limit..............................................................8-2
Filament Integrity ......................................................................8-3
Half Plate 1 and 2 Output Voltages...........................................8-3
In Current Limit.........................................................................8-3
Ion Energy..................................................................................8-3
Repeller Voltage........................................................................8-4
Source Current...........................................................................8-4
Source Temperature...................................................................8-4
Trap Current...............................................................................8-4
Analyser Tab.................................................................................8-5
ASU Controller Status...............................................................8-5
Cabinet Temperature..................................................................8-5
Electronics Temperature............................................................8-5
Magnet Controller Status...........................................................8-5
Mass Filter .................................................................................8-6
Pressure Set Point ......................................................................8-6
System Pressure.........................................................................8-6
System Pressure Trip.................................................................8-7
Turbo Motor Current .................................................................8-7
Turbo Operating Hours..............................................................8-7
Turbo Speed...............................................................................8-7
Turbo Speed Interlock ...............................................................8-8
Vacuum......................................................................................8-8
Vent Valve.................................................................................8-8
Inlet...............................................................................................8-8
Pressure Raw..............................................................................8-8
RMS Ambient Temperature.......................................................8-8
RMS Body Temp.......................................................................8-8
RMS Controller Status...............................................................8-8
Chapter 8

Contents
xPrima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
RMS Sample Flow Sensor.........................................................8-8
RMS Flow Zero .........................................................................8-8
RMS Position.............................................................................8-8
Sample Tube Current.................................................................8-8
Sample Tube Temperature.........................................................8-9
Collector Tab ................................................................................8-9
Faraday Deflector.......................................................................8-9
Multiplier Deflector...................................................................8-9
Multiplier Voltage......................................................................8-9
Negative and Positive Quad Lens Voltages...............................8-9
Resolution..................................................................................8-9
Power ..........................................................................................8-10
Amplifier +24V........................................................................8-10
Analyser Supplies +24V..........................................................8-10
Instrument CPU 24V................................................................8-10
Fan 24V....................................................................................8-10
Inlet Probe Current...................................................................8-10
Magnet Supply Current............................................................8-11
Magnet Sync AC......................................................................8-11
Power Controller Status...........................................................8-11
Turbo 24V................................................................................8-11
User IO 24V.............................................................................8-11
Vent Valve 24V .......................................................................8-11
Communications.........................................................................8-11
Host Comms Quiet...................................................................8-11
User I/O 0 Comms Quiet .........................................................8-11
User I/O 1 Comms Quiet .........................................................8-11
User I/O 2 Comms Quiet .........................................................8-11
User I/O 3 Comms Quiet .........................................................8-12
VGiNet.....................................................................................8-12
Checking Mass Alignment..........................................................8-12
Fault Diagnosis...................................................................9-1
Introduction...................................................................................9-1
Alarm Conditions..........................................................................9-1
Leak Detection..............................................................................9-4
Mass Spectrometer Faults.............................................................9-5
No Peaks ....................................................................................9-5
Poor Sensitivity..........................................................................9-6
Poor Stability on Startup............................................................9-6
Poor Results Following Calibration...........................................9-7
Ion Source and Magnet Pole Pieces Assembly..........................9-8
Filament Failure............................................................................9-8
Maintenance......................................................................10-1
Maintenance Schedule................................................................10-1
Procedures...................................................................................10-1
Rotary Pump Oil Level............................................................10-1
Cleaning the Cooling Fans.......................................................10-2
Chapter 9
Chapter 10

Contents
Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide xi
Lubricating the Turbo Molecular Pump ..................................10-3
Dismantling and Cleaning Procedures........................................10-3
Filament...................................................................................10-3
Ion Source................................................................................10-5
Magnet Pole Piece Assembly ..................................................10-8
Fuses ......................................................................................10-10
Hazardous Area Operation ............................................... A-1
Introduction..................................................................................A-1
Installation ................................................................................A-2
General Hazardous Area Work.................................................A-3
Commissioning and Maintenance.............................................A-3
Routine Checks.........................................................................A-4
Hazardous Area –General...........................................................A-4
Area Classification....................................................................A-4
Gas Classification.....................................................................A-5
Methods of Protection...............................................................A-5
Purge/Pressurisation...............................................................A-5
Flameproof (Europe) or Explosion Proof (North America) ..A-6
Increased Safety.....................................................................A-7
Non-Electrical........................................................................A-7
Purge Operation...........................................................................A-8
Purge Overview ........................................................................A-8
Purge Operation Requirements.................................................A-9
Parameter Measurement ......................................................A-10
Sample Containment System..................................................A-11
Definition and Description...................................................A-11
Parameters............................................................................A-11
Leakage Handling................................................................A-11
Inspection and Testing.........................................................A-13
Enclosure Leak Testing ..........................................................A-14
Purge Operation and Testing ..................................................A-15
All System Types.................................................................A-15
ATEX, IECEx and X-Purge Systems ..................................A-15
Z-Purge Systems..................................................................A-16
Other Hazardous Area Considerations ......................................A-16
Temperature............................................................................A-16
Over-Temperature Protection..............................................A-16
Batteries..................................................................................A-17
Dry Gas Vent..........................................................................A-17
Rotary Vacuum Pump.............................................................A-18
General.................................................................................A-18
Thermal Trip........................................................................A-18
Purge....................................................................................A-18
Calibration Panels...................................................................A-19
Air Conditioner.......................................................................A-20
Remote / Dual RMS................................................................A-20
RMS and Instrument in Hazardous Area.............................A-20
RMS in Hazardous Area and Instrument in Safe Area........A-20
Appendix A

Contents
xii Prima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
Sample Pump (Sentinel PRO Applications)...........................A-21
Fibre Optic Communications..................................................A-21
Service Replacement Items........................................................A-21
Troubleshooting.........................................................................A-23
Standards Conformance.............................................................A-25
Technical Description: Hardware......................................B-1
Introduction to the Prima PRO Hardware....................................B-1
Main Components.....................................................................B-1
Principle of Operation..................................................................B-2
Vacuum System...........................................................................B-4
Ion Source....................................................................................B-5
Filaments...................................................................................B-7
Mass Analyser..............................................................................B-9
Collector.......................................................................................B-9
Ion Detection..............................................................................B-10
MCP Detector Assembly ........................................................B-10
MCP Operation.......................................................................B-11
Faraday Detector.....................................................................B-13
Introduction of a Gas Sample ....................................................B-13
Mass Spectrometer Parameters..................................................B-15
Sensitivity ...............................................................................B-15
Resolution...............................................................................B-15
Cracking Patterns.......................................................................B-17
Ion Types ................................................................................B-17
Molecular Ion.......................................................................B-17
Isotope Ions..........................................................................B-17
Fragment Ions ......................................................................B-18
Multiple-Charged Ions.........................................................B-18
Rearrangement and Recombination Peaks...........................B-18
Definitions...............................................................................B-19
Technical Description: Inlet...............................................C-1
Rapid Multi-Stream Sampler (RMS)...........................................C-1
Introduction...............................................................................C-1
Safety ........................................................................................C-1
Inlet Specification.....................................................................C-2
Inlet Operation..........................................................................C-3
General Description...............................................................C-3
Connection to the Mass Spectrometer ...................................C-4
Seals.......................................................................................C-4
Inlet Selection ........................................................................C-5
Calibration Gas Control.........................................................C-5
Gas Connection......................................................................C-6
Exhaust Connection...............................................................C-7
Heating...................................................................................C-8
Hazardous Area Systems .......................................................C-9
Inlet Controller........................................................................C-10
General.................................................................................C-10
Appendix B
Appendix C

Contents
Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide xiii
Calibration Valve Drives.....................................................C-10
Main Body Heater................................................................C-10
Sample Tube Heater.............................................................C-11
Flow Sensor .........................................................................C-11
Digital Inputs .......................................................................C-11
VGiNet.................................................................................C-11
Inlet Testing............................................................................C-12
Functional Testing ...............................................................C-12
Cross Port Leakage.................................................................C-14
External Leakage ....................................................................C-15
Maintenance............................................................................C-15
Routine Maintenance...........................................................C-16
Sample Tube Removal............................................................C-19
Inlet Ports................................................................................C-21
Cleaning Procedure.................................................................C-21
Inlet Options ...........................................................................C-22
Remote Mounting................................................................C-22
Dual RMS...............................................................................C-23
Solenoid Inlet.............................................................................C-27
Introduction.............................................................................C-27
Safety......................................................................................C-27
Inlet Operation........................................................................C-28
Valve Operation...................................................................C-30
Capillary Connection...........................................................C-30
Heating.................................................................................C-31
Inlet Controller........................................................................C-31
General.................................................................................C-31
Valve Drives ........................................................................C-32
Manifold Heater...................................................................C-32
Microcapillary Block Heater ...............................................C-32
Flow Sensor .........................................................................C-32
Digital Inputs .......................................................................C-32
VGiNet.................................................................................C-33
Testing ....................................................................................C-33
Capillary Testing..................................................................C-33
Valve Function.....................................................................C-34
Cross Seat Leakage..............................................................C-34
External Leakage .................................................................C-35
Maintenance............................................................................C-36
Calibration Inlet...................................................................C-36
Sample Inlet.........................................................................C-38
Cleaning Procedure..............................................................C-39
Local I/O ............................................................................. D-1
Introduction..................................................................................D-1
Serial I/O......................................................................................D-1
Serial Link Type Selection .......................................................D-1
Indicators ..................................................................................D-2
Fibre Optic Serial Connection ..................................................D-2
Appendix D

Contents
xiv Prima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
Discrete I/O..................................................................................D-4
Supplying Power to the External I/O Circuit............................D-4
Indicators...................................................................................D-4
Analogue I/O.............................................................................D-5
Air Conditioner ...................................................................E-1
Introduction.................................................................................. E-1
Normal Operation ........................................................................E-1
Fault Conditions........................................................................... E-2
Fault Diagnosis ............................................................................E-3
Regulatory...........................................................................F-1
FCC.............................................................................................. F-1
WEEE .......................................................................................... F-2
China RoHS................................................................................. F-3
Appendix E
Appendix F

Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide 1-1
Chapter 1
Introduction
This manual is provided for users, operators, and owners of Thermo
Scientific Mass Spectrometers.
This manual covers both the Thermo Scientific Prima PRO,
Sentinel PRO, Prima PRO Ex (hazardous area), and Sentinel PRO Ex
(hazardous area) instrumentation.
Note: The name Prima PRO will be used exclusively in subsequent
chapters. Sentinel PRO is identical to Prima PRO except for the
following:
Inlet: A membrane assembly replaces the Prima PRO
capillary, molecular leak, and bypass.
Collector slits: Are 0.36 mm / 0.69 mm as opposed to the
standard 1.0 mm / 4.0 mm on the Prima PRO.
Information in this is organized in chapters and covers site
preparation, installation, commissioning, operation, and
maintenance. Technical descriptions of the instrument and various
inlet configurations are provided as individual appendices.
For sales and support of the Prima PRO / Sentinel PRO
instrumentation, the Thermo Fisher Process Instruments main offices
are detailed below.
Americas
Thermo Fisher Scientific
Process Instruments Division
1410 Gillingham Lane
Sugar Land, Texas 77478 USA
Phone: [phone]
Fax: [phone]
Contacts

Introduction
Contacts
1-2 Prima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
Europe, Middle East, Asia, Africa
Thermo Fisher Scientific, Europe
Process Instruments Division
Ion Path
Road Three
Winsford Industrial Estate
Winsford
Cheshire
CW7 3GA
UK
Phone: [phone]
Fax: [phone]
China
Thermo Fisher Scientific, China
Process Instruments Division
Building 6,
No.27 Xin Jinqiao Rd.
Shanghai
China 201206
Tel: [phone]
Fax: [phone]
Web Site
www.thermofisher.com

Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide 2-1
Chapter 2
Safety Information
This chapter contains general safety and operating information
applicable to analytical systems that must be understood by all
persons installing, using, or maintaining the system. This information
is designed to aid personnel in the safe installation, operation, and
service of the analyser and sample systems. It is not designed to
replace or limit appropriate safety measures applicable to work
performed by personnel. Any additional safety and operating
measures that are required must be determined by and followed by
personnel performing work on the system.
It is the responsibility of the user / operator / integrator (hereon
referred to as user) to perform risk assessments of the site location,
installation and operation of the instrumentation. This manual
highlights hazards associated with the instrument and provides
details of precautions to be taken to ensure safe operation. The user
must account for the information provided and put in place
procedures to ensure for the safety of personnel and plant.
To ensure personal safety, system integrity, and optimum
performance, users should thoroughly understand the content of this
manual before installing, using, or performing maintenance on this
product.
Failure to follow appropriate safety procedures or inappropriate
use of the equipment described in this manual can lead to
equipment damage or injury to personnel.
Any person working with or on the equipment described in this
manual is required to evaluate all functions and operations for
potential safety hazards before commencing work. Appropriate
precautions must be taken as necessary to prevent potential damage
to equipment or injury to personnel.
Only qualified technical personnel should access the analyser
enclosure.
If in doubt as to the instructions and information provided or if you
have additional questions regarding the product, a service or support
request, contact your nearest Thermo Fisher Scientific representative
for process mass spectrometers.
Overview

Safety Information
Safety Conventions and Symbols
2-2 Prima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
The following conventions and symbols are used throughout this
manual to alert users to potential hazards or important information.
Failure to heed the warnings and cautions in this manual can
lead to injury or equipment damage.
Warning / Danger
Warning / Danger statements notify users of procedures, practices,
conditions, etc. which may result in serious injury or death if not
carefully observed or followed. The triangular icon displayed with a
warning varies depending on the type of hazard (only two are
displayed here).
Prohibited
These statements explicitly PROHIBIT an action. Ignoring an
instruction related to a hazard highlighted with this symbol may
cause an unsafe condition that could result in an accident.
Caution
Cautions notify users of operating procedures, practices, conditions,
etc. that may result in equipment damage or cause injury if not
carefully observed or followed.
Caution
Statements accompanied by this caution symbol explicitly require
an action be taken. Ignoring an instruction related to a hazard or
instruction highlighted with this symbol may cause an unsafe
condition which could result in an accident.
Note
Notes emphasize important or essential information or a statement of
company policy regarding an operating procedure, practice,
condition, etc. 
Safety
Conventions
and Symbols

Safety Information
System Safety
Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide 2-3
The information in this manual is designed to aid personnel to
correctly and safely install, operate, and / or maintain the system
described; however, personnel are still responsible for considering all
actions and procedures for potential hazards or conditions that may
not have been anticipated in the written procedures. If a procedure
cannot be performed safely, it must not be performed until
appropriate actions can be taken to ensure the safety of the
equipment and personnel.
The procedures in this manual are not designed to replace or
supersede required or common sense safety practices. All safety
warnings listed in any documentation applicable to equipment and
parts used in or with the system described in this manual must be
read and understood prior to working on or with any part of the
system.
Failure to correctly perform the instructions and procedures in
this manual or other documents pertaining to this system can
result in equipment malfunction, equipment damage, and / or
injury to personnel.
Warning! Deviation from the instructions may result in equipment
malfunction, equipment damage, and / or injury to personnel.
Read this manual before operating the instrument! In particular,
review the following cautionary statements.
Caution! Only qualified personnel trained in the safe operation of
the Prima PRO / Sentinel PRO hardware should have access to the
cabinet door keys.
Caution! Never disregard any cautionary or warning instructions.
Read and observe all instructions on printed labels fixed to the
instrument.
Caution! Failure to operate the instrument as specified could
impair the protection features provided and described in this guide.
Hazards exist within the instrument enclosure, and the remainder of
this chapter details any necessary precautions to be taken. Read the
following safety notes carefully before attempting to operate or work
on the instrument.
System
Safety

Safety Information
System Safety
2-4 Prima PRO & Sentinel PRO Mass Spectrometers User Guide Thermo Fisher Scientific
Caution!
Check that the mains supply satisfies the requirements
detailed in Chapter 3: Site Requirements.
Connection must be made by qualified personnel only.
Observe the instructions provided in Chapter 3: Site
Requirements, and ensure that the connection is consistent
with local safety regulations.
When performing repair or maintenance on the instrument:
Warning! Before attempting to carry out repairs or maintenance,
isolate the mains electrical supply.
Caution! Maintenance should be carried out by qualified personnel
only.
Warning! Allow the pump oil to cool before draining.
Caution! Check that the oil level is between the two markers on the
oil level window before switching on the rotary pump.
Connecting the
Instrument to the
Electrical Supply
Repair &
Maintenance
Changing the
Rotary Pump Oil
Switching on the
Rotary Pump

Safety Information
System Safety
Thermo Fisher Scientific Prima PRO & Sentinel PRO Mass Spectrometers User Guide 2-5
Warning! The following assemblies may attain a surface
temperature as listed:
Rapid Multi-Stream Sampler (RMS) and Single Point Inlet
System: 120°C.
Single Point Inlet System (High Temperature Version):
230°C.
RMS Sample Probe: 120°C.
Inlet Probe Assembly: 120°C.
Rotary pump operating temperature: 75°C.
Warning! Ensure that the rotary pump is unobstructed. Failure to
do so will cause dangerous internal pressures in the pump. This will
result in blown seals and bursting of the oil box and could result in
physical injury.
Warning! A leak-tight exhaust must be fitted to the inlet system
when sampling gas streams which are:
Explosive
Toxic
Asphyxiant
High
Temperatures
Rotary Pump
Exhaust Outlet
Inlet System
Exhaust