Micromass Quattro Ultima User manual

Quattro Ultima
User's Guide
Code: 6666511
Issue 3
© Micromass Ltd.
Micromass UK Limited
Floats Road
Wythenshawe
M23 9LZ
Tel: [phone] Fax: [phone]
Tudor Road
Altrincham
WA14 5RZ
Tel: [phone] Fax: [phone]
http://www.micromass.co.uk
The instrument is marked with this symbol where high voltages are
present.
The instrument is marked with this symbol where hot surfaces are
present.
The instrument is marked with this symbol where the user should refer to
this User's Guide for instructions which may prevent damage to the
instrument.
Warnings are given throughout this manual where care is required to avoid personal
injury.
If the instrument is used in a manner not specified by the manufacturer, the protection
provided by the equipment may be impaired.
This manual is a companion to the MassLynx NT User's Guide supplied with the
instrument.
All information contained in these manuals is believed to be correct at the time of
publication. The publishers and their agents shall not be liable for errors
contained herein nor for incidental or consequential damages in connection with
the furnishing, performance or use of this material. All product specifications, as
well as the information contained in this manual, are subject to change without
notice.

Quattro Ultima
User's Guide

Contents
Hardware Specifications
Dimensions 11
Weights 11
Lifting and Carrying 12
Power 13
Environment 13
Water Cooling 13
Exhausts 13
Rotary Pumps 13
API Gas Exhaust 13
Nitrogen 14
CID Gas 14
Instrument Description
Overview 15
Vacuum System 16
Ionisation Techniques 17
Atmospheric Pressure Chemical Ionisation 17
Electrospray 17
Nanoflow Electrospray 17
Sample Inlet 17
MS Operating Modes 18
MS-MS Operating Modes 18
The Daughter Ion Spectrum 19
The Parent Ion Spectrum 20
MRM: Multiple Reaction Monitoring 21
The Constant Neutral Loss Spectrum 22
Data System 22
Front Panel Connections 23
Desolvation Gas and Probe Nebuliser Gas 23
Capillary / Corona 23
ESI / APcI 23
Front Panel Controls and Indicators 24
Status Display 24
Vacuum LED 24
Operate LED 24
Flow Control Valves 25
Divert / Injection Valve 25
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User's Guide

Rear Panel Connections 26
Event Out 26
Contact Closure In 26
Analog Channels 26
MUX 27
Data System 27
Water 28
Nitrogen Gas In 28
Exhausts 29
CID Gas 29
Power Cord 29
Mains Switch 29
Fuses 29
Rotary Control 29
ESD Earth Facility 29
Internal Layout 30
Electronics 30
Mechanical Components 32
Routine Procedures
Start Up Following a Complete Shutdown 33
Preparation 33
Pumping 36
Measuring the Analyser Pressure 37
Using the Instrument 37
Start Up Following Overnight Shutdown 37
Preparation for Electrospray Operation 38
Preparation for APcI Operation 40
Operate 42
Automatic Pumping and Vacuum Protection 42
Overview 42
Protection 42
Transient Pressure Trip 42
Pump Fault 43
Power Failure 43
Tuning 44
Calibration 44
Data Acquisition 44
Data Processing 44
Setting Up for MS-MS Operation 44
Parent Ion Selection 44
Fragmentation 45
Shutdown Procedures 46
Emergency Shutdown 46
Overnight Shutdown 46
Complete Shutdown 47
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User's Guide

Automatic Start up and Shutdown 48
The Shutdown Editor 48
The Auto Control Tasks Page 49
The Shutdown Editor Toolbar 51
Loading Startup and Shutdown Files 52
Saving a Startup or Shutdown File 52
Printing Startup and Shutdown Files 53
Creating Startup and Shutdown Files 54
Running Startup and Shutdown Files 54
Tuning
Overview 55
The Tune Page 56
Printing Tune Information 56
Experimental Record 56
Saving and Restoring Parameter Settings 56
Modifying the Peak Display 58
Changing the Display 60
Customise Plot Appearance 60
Trace 61
Intensity 61
Grid 61
AutoTune 62
Ion Mode 63
Scope Parameters 64
Gas Controls 64
Ramp Controls 64
Resetting the Zero Level 65
Controlling Readbacks 66
Changing Tune Parameter Settings 67
Source Voltages 67
Data Acquisition
Starting an Acquisition 69
Starting an Acquisition from the Tune Page 69
Parameters 70
Multiple Samples 71
Process 72
Automated Analysis of Sample List 72
Monitoring an Acquisition 74
The Acquisition Status Window 74
Chromatogram Real-Time Update 74
Spectrum Real-Time Update 74
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Instrument Data Thresholds 75
MaxEnt 76
Profile Data 76
Centroid Data 76
SIR Data 76
Ion Counting Threshold 77
Profile Data - Spike Removal 78
Analog Data 79
System Manager 79
Stopping an Acquisition 80
The Function List Editor 80
Introduction 80
The Function List Editor Toolbar 82
Adding a New Function 82
Modifying an Existing Function 83
Copying an Existing Function 83
Removing a Function 83
Changing the Order of Functions 83
Setting a Solvent Delay 84
Analog Channels 84
Saving and Restoring a Function List 85
Setting up a Full Scan Function 86
Mass (m/z) 86
Cone Voltage 86
Method 86
Scan Duration (secs) 87
APcI Probe 87
Setting up a SIR Function 88
Channels 88
Method 89
Retention Window 89
Setting up MS-MS Scanning Functions 90
Mass 90
Collision Energy 92
Setting up a MRM Function 93
Setting up a Survey Function 93
Survey and MSMS Template Pages 94
MS to MSMS Switching 95
MSMS to MS Switching 97
Including and Excluding Masses 98
Monitoring Acquisitions 99
Mass Calibration
Introduction 101
Overview 102
Calibration Types 102
The Calibration Process 103
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User's Guide

Electrospray 103
Introduction 103
Preparing for Calibration 104
Reference Compound Introduction 104
Tuning 104
Instrument Threshold Parameters 105
Calibration Options 106
Selecting the Reference File 106
Removing Current Calibrations 106
Selecting Parameters 107
Automatic Calibration Check 107
Calibration Parameters 108
Mass Measure Parameters 109
Performing a Calibration 110
Acquisition Parameters 112
Starting the Calibration Process 114
Checking the Calibration 116
Calibration Failure 118
Incorrect Calibration 120
Manual Editing of Peak Matching 121
Saving the Calibration 121
Verification 122
Electrospray Calibration with PEG 124
Atmospheric Pressure Chemical Ionisation 125
Introduction 125
Preparing for Calibration 126
Reference Compound Introduction 126
Tuning 126
Calibration Options 126
Selecting Reference File 126
Removing Current Calibrations 126
Selecting Calibration Parameters 126
Performing a Calibration 127
Static Calibration 127
Scanning Calibration and Scan Speed Compensation 132
Calibration Failure 135
Incorrect Calibration 136
Manual Editing of Peak Matching 137
Saving the Calibration 137
Manual Verification 138
Electrospray
Introduction 141
Post-column Splitting 144
Megaflow 145
Changing Between Flow Modes 145
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Operation 146
Checking the ESI Probe 147
Obtaining an Ion Beam 148
Tuning and Optimisation 148
Megaflow Hints 154
Removing the Probe 154
Sample Analysis and Calibration 155
General Information 155
Typical ES Positive Ion Samples 156
Typical ES Negative Ion Samples 156
Chromatographic Interfacing 157
LC-MS Sensitivity Enhancement 158
Nanoflow Electrospray
Overview 159
Installing the Interface 160
Operation of the Camera System 163
Using the Microscope 163
Glass Capillary Option 164
Restarting the Spray 165
Nano-LC Option 166
Installation 166
Operation 167
Changing Options 168
Atmospheric Pressure Chemical Ionisation
Introduction 169
Preparation 170
Checking the Probe 171
Obtaining a Beam 172
Calibration 173
Hints for Sample Analysis 174
Tuning for General Qualitative Analysis 174
Specific Tuning for Maximum Sensitivity 174
Corona Current 175
Probe Position 175
Probe Temperature 175
Desolvation Gas 175
Removing the Probe 176
Maintenance and Fault Finding
Introduction 177
Cooling Fans and Air Filters 177
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The Vacuum System 178
Vacuum Leaks 179
Pirani Gauge 179
Active Inverted Magnetron Gauge 179
Gas Ballasting and Rotary Pump Oil Recirculation 180
Oil Mist Filter 181
Foreline Trap 181
Rotary Pump Oil 182
The Source 183
Overview 183
Cleaning the Cone Gas Nozzle and Sample Cone 184
Removing and Cleaning the Ion Block 188
Removing and Cleaning the Ion Tunnel Assembly 192
Reassembling and Checking the Source 194
The Discharge Pin 195
The Electrospray Probe 196
Overview 196
Replacement of the Stainless Steel Sample Capillary 198
The APcI Probe 200
Cleaning the Probe Tip 200
Replacing the Probe Tip Heater 201
Replacing the Fused Silica Capillary 202
The Analyser 204
The Detector 204
Electronics 205
Fuses 205
Analog PCB 205
RF Power PCB 205
Power Backplane #2 205
Pumping Logic PCB 205
Power Sequence PCB 205
Rear Panel 205
Fault Finding Check List 206
No Beam 206
Unsteady or Low Intensity Beam 206
Ripple 206
High Noise Level in MRM Analyses 207
Chemical Noise 207
Electronic Noise 208
High Back Pressure 208
General Loss of Performance 209
Cleaning Materials 210
Preventive Maintenance Check List 211
Weekly 211
Monthly 211
Three-Monthly 211
Four-Monthly 211
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Reference Information
Overview 213
Editing a Reference File 214
Positive Ion 215
Horse Heart Myoglobin 216
Polyethylene Glycol 216
PEG + NH4+216
Sodium Iodide and Caesium Iodide Mixture 217
Sodium Iodide and Rubidium Iodide Mixture 217
Negative Ion 218
Horse Heart Myoglobin 218
Mixture of Sugars 218
Sodium Iodide and Caesium Iodide (or Rubidium Iodide) Mixture 219
Preparation of Calibration Solutions 220
PEG + Ammonium Acetate for Positive Ion Electrospray and APcI 220
PEG + Ammonium Acetate for Positive Ion Electrospray
(Extended Mass Range) 220
Sodium Iodide Solution for Positive Ion Electrospray 221
Method 1 221
Method 2 221
Sodium Iodide Solution for Negative Ion Electrospray 221
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Quattro Ultima
User's Guide

Hardware Specifications
Dimensions
Weights
Instrument: 150kg (330lb)
Data system
(computer, monitor and printer): 60kg (130lb)
Rotary pumps
E2M28: 40kg (90lb)
E1M18: 32kg (72lb)
Transformer (optional): 100kg (220lb)
Hardware Specifications
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Quattro Ultima
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535mm
700mm
120mm
(ventilation)
1325mm
180mm
200mm
(pumping line)

Lifting and Carrying
Warning: Persons with a medical condition, for example a back injury, which
prevents them from handling heavy loads should not attempt to lift the
instrument.
Before lifting the instrument proceed as follows:
Vent and power down the instrument.
Disconnect the instrument from the power and water supplies.
Disconnect power and tubing connections to the rotary pump from the rear of
the instrument.
Disconnect the API gas inlet and the exhaust lines from the rear of the
instrument.
Disconnect all connections to LC equipment.
If the instrument is to be moved over a large distance or in a confined space it is
recommended that any probes are removed from the API source.
The weight of the instrument is 150kg (330lb). Lifting equipment or suitably trained
personnel are required to lift or lower the instrument.
UK Health and Safety guidelines recommend that a minimum of six trained and
suitable personnel are required to lift a unit of this weight. The instrument should be
lifted from underneath the frame with one person at each corner of the instrument
supporting the instrument in line with, or close to, the feet upon which the instrument
stands. Two further people should support the instrument centrally.
Caution: Under no circumstances should the instrument be lifted by the probe or
the source enclosure.
Before undertaking any lifting, lowering or moving of the instrument:
•Assess the risk of injury.
•Take action to eliminate the risk.
•Plan the operation.
•Use trained people.
•Refer to local or company guidelines before attempting to lift the instrument.
Micromass accept no responsibility for any injuries or damage sustained while lifting
the instrument.
Hardware Specifications
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User's Guide

Power
Instrument: 230V (+10%, -14%), 13A
Data system: 100-120V or 200-240V, 13A
Pumps: 230V (+10%, -14%), 13A
Environment
Ambient temperature: 15-28°C (59-82°F)
Short term variance (1.5 hours): ≤2°C (≤4°F)
Overall heat dissipation
(excluding LC
and optional water chiller): 4.2kW maximum
Humidity: Relative humidity ≤70%
Water Cooling
Heat dissipation into the water: 200W
Exhausts
Rotary Pumps
The rotary pumps must be vented to atmosphere (external to the laboratory) via a
fume hood or industrial vent.
API Gas Exhaust
The API gas exhaust must be vented to atmosphere (external to the laboratory).
Caution: The API gas exhaust line must not be connected to the rotary pump
exhaust line. In the event of an instrument failure, rotary pump exhaust could be
admitted into the source chamber producing severe contamination.
Hardware Specifications
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Nitrogen
A supply of dry, oil-free nitrogen at 6-7 bar (90-100 psi) is required.
Caution: The lines supplying nitrogen to the instrument must be clean and dry.
If plastic tubing is used it must be made of Teflon. The use of other types of
plastic leads to contamination of the instrument.
CID Gas
Argon is required as collision gas. The supplied gas should be dry, of high purity
(99.9%) and at a pressure of approximately 350 mbar (5 psi).
Caution: Operating with the CID gas at a significantly higher pressure results in
a fault.
Hardware Specifications
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Instrument Description
Overview
The Micromass Quattro Ultima is a high performance benchtop triple quadrupole mass
spectrometer designed for routine LC-MS-MS operation. Quattro Ultima may be
coupled to:
•a HPLC system with or without an autosampler.
•an infusion pump.
•a syringe pump.
Ionisation takes place in the source at atmospheric pressure. These ions are sampled
through a series of orifices into the first quadrupole where they are filtered according
to their mass to charge ratio (m).
The mass separated ions then pass into the hexapole collision cell where they either
undergo collision induced decomposition (CID) or pass unhindered to the second
quadrupole. The fragment ions are then mass analysed by the second quadrupole.
Finally the transmitted ions are detected by a conversion dynode, phosphor and
photomultiplier detection system. The output signal is amplified, digitised and
presented to the data system.
Instrument Description
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Samples
from the liquid
introduction system
are introduced at
atmospheric pressure into the
ionisation source.
Ions are sampled through a series of orifices.
The ions are filtered according to their mass to charge
ratio ( ).
The mass separated ions undergo collision induced decomposition.
The fragment ions are filtered according to their mass to charge ratio.
The transmitted ions are detected by the photomultiplier detection system.
The signal is amplified, digitised and presented to the MassLynx NT™ data system.
m
MassLynx NT
Data System
Sample Inlet
Sampling Cone
and Ion Block
Ion Tunnels
Prefilter 1
Quadrupole 1
Collision Cell
Prefilter 2
Quadrupole 2
Detector

Vacuum System
Vacuum is achieved using two direct drive rotary pumps, and two turbomolecular
pumps.
The rotary pumps are mounted on the floor external to the instrument. The E1M18
pumps the ion source block, while the E2M28 pumps the first ion tunnel and also
backs the turbomolecular pumps. The E1M18 has an automatic gas ballast control
valve mounted in the oil return line from the mist filter. This solenoid valve is opened
whenever the E1M18 is switched on, allowing continuous recirculation of the pump
oil provided that the manual gas ballast valve on the pump is left open.
The turbomolecular pumps evacuate the analyser and ion transfer region. These pumps
are both water cooled.
Vacuum measurement is by an active inverted magnetron (Penning) gauge for the
analyser and a Pirani gauge for the gas cell. The Penning gauge acts as a vacuum
switch, switching the instrument out of the OPERATE mode if the pressure is too high.
The speed of each turbomolecular pump is also monitored and the system is fully
interlocked to provide adequate protection in the event of a fault in the vacuum
system, a failure of the power supply or vacuum leaks.
Instrument Description
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Ionisation Techniques
Two atmospheric pressure ionisation techniques are available.
Atmospheric Pressure Chemical Ionisation
Atmospheric pressure chemical ionisation (APcI) generally produces protonated or
deprotonated molecular ions from the sample via a proton transfer (positive ions) or
proton abstraction (negative ions) mechanism. The sample is vaporised in a heated
nebuliser before emerging into a plasma consisting of solvent ions formed within the
atmospheric source by a corona discharge. Proton transfer or abstraction then takes
place between the solvent ions and the sample. Eluent flows up to 2 ml/min can be
accommodated without splitting the flow.
Electrospray
Electrospray (ESI) ionisation takes place as a result of imparting a strong electrical
field to the eluent flow as it emerges from the nebuliser. producing an aerosol of
charged droplets. These undergo a reduction in size by solvent evaporation until they
have attained a sufficient charge density to allow sample ions to be ejected from the
surface of the droplet (“ion evaporation”).
A characteristic of ESI spectra is that ions may be singly or multiply charged. Since
the mass spectrometer filters ions according to their mass-to-charge ratio, compounds
of high molecular weight can be determined if multiply charged ions are formed.
Eluent flows up to 1 ml/min can be accommodated although it is often preferable with
electrospray ionisation to split the flow such that 100 to 200 µl/min of eluent enters
the mass spectrometer.
Nanoflow Electrospray
The optional nanoflow interface allows electrospray ionisation to be performed in the
flow rate range 5 to 1000 nanolitres per minute.
For a given sample concentration, the ion currents observed in nanoflow are
comparable to those seen in normal flow rate electrospray. Great sensitivity gains are
therefore observed when similar scan parameters are used, due to the great reductions
in sample consumption.
Sample Inlet
Sample is introduced from a suitable liquid pumping system along with the nebulising
gas to either the APcI probe or the electrospray probe. For nanoflow electrospray,
metal coated glass capillaries allow the lowest flow rates to be obtained while fused
silica capillaries are used for flow injection analyses or for coupling to nano-HPLC.
Instrument Description
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MS Operating Modes
MS1 Collision Cell MS2
MS Resolving RF Only (Pass all masses)
MS2 RF Only (Pass all masses) Resolving
The MS1 mode, in which MS1 is used as the mass filter, is the most common and
most sensitive method of performing MS analysis. This is directly analogous to using
a single quadrupole mass spectrometer.
The MS2 mode of operation is used, with collision gas present, when switching
rapidly between MS and MS-MS operation. It also provides a useful tool for
instrument tuning and calibration prior to MS-MS analysis, and for fault diagnosis.
MS-MS Operating Modes
The basic features of the four common MS-MS scan functions are summarised below.
MS1 Collision
Cell MS2
Daughter Ion
Spectrum
Static
(parent mass selection)
RF only
(pass all
masses)
Scanning
Parent Ion
Spectrum Scanning
Static
(daughter mass
selection)
Multiple Reaction
Monitoring
Static
(parent mass selection)
Static
(daughter mass
selection)
Constant Neutral
Loss Spectrum
Scanning (synchronised
with MS2)
Scanning (synchronised
with MS1)
Instrument Description
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Source MS1 Collision Cell MS2 Detector

The Daughter Ion Spectrum
This is the most commonly used MS-MS scan mode. Typical applications are:
•Structural elucidation (for example peptide sequencing).
•Method development for MRM screening studies:
Identification of daughter ions for use in MRM “transitions”.
Optimisation of CID tuning conditions to maximise the yield of a specific
daughter ion to be used in MRM analysis.
Example:
Daughters of the specific parent at m609 from reserpine in electrospray
positive ion mode.
The result:
Instrument Description
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MS1
static at m/z 609
(parent mass)
MS2
scanning from
m/z 100 to 650
Collision Cell
RF only
(pass all masses)

The Parent Ion Spectrum
Typical application:
•Structural elucidation.
Complementary or confirmatory information (for daughter scan data).
Example:
Parents of the specific daughter ion at m195 from reserpine in electrospray
positive ion mode.
The result:
Instrument Description
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MS1
scanning from
m/z 50 to 650
MS2
static at m/z 195
(daughter mass)
Collision Cell
RF only
(pass all masses)