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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Quattro Ultima
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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Quattro Ultima
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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Quattro Ultima
User's Guide

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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Quattro Ultima
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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Quattro Ultima
User's Guide

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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Quattro Ultima
User's Guide

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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Quattro Ultima
User's Guide

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
Table of Contents
Quattro Ultima
User's Guide