Wiki

Saturation - of the source, the quad, and the electron multiplier
Isotope ratio problems
Invalid quantitation results as a result of space charging effects (excessive saturation)
Continual improper use could damage the system! Don't abuse your GCMS...

Here are the steps to figure out how much you can run on a 7010x system:

1. Run each new sample type in full scan mode (ie MS1Scan) with EM gain set to ~0.5.

If any of the peaks in the scan total ion chromatogram are flat topping (ie overloading the detector), including matrix peaks that you do not need to analyze, please do one or more combinations of the following:

a. Inject less until the chromatogram comes on scale.

b. Run the sample in split mode (use ultra-inert split liners) or even higher split ratios

c. Dilute the sample

d. Do further sample clean up

2. Make sure column flow rate is <1.5 mL/min into the MS while the filament is on

3. Always run constant flow mode methods. ALL GCMS sources work better under stable vacuum.

4. Make sure the solvent delay is long enough that all the solvent has eluted before the filament is turned on.

5. Make sure that there are no leaks. If you are using any CFT devices, Purged Ultimate Union, splitter, Deans Switch, there are more places leaks can occur.

6. Always make sure the quad temps are 150C or less. There is no reason to run the quads too hot. They really only need to be hot enough to be stable and eliminate water condensation. Anywhere between 106 and 150 will work up to the maximum source temperature.

7. Only certain applications need a source temperature >280C, so use 280C as a maximum temperature for the source when running samples.

The 7010 High Efficiency Source system is more sensitive than a 7000. This may require trade-offs in your methodology. Use that sensitivity to reduce the amount of sample injected and analyzed - that reduces the amount of normal user maintenance required. Less liners, gold seals, columns, filaments, and multipliers replaced and less source cleanings save you money and time!

Tags: GC/MS, 7010, 7000, upgrade

Common GC/MS Contaminants and their Source

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

The source of GC/MS contamination can sometimes be determined by identifying the contaminates. Learn more about common GC/MS contaminants on pages 59 - 60 in the 5977B Series MSD Troubleshooting and Maintenance Manual.

5977B Series MSD Troubleshooting and Maintenance Manual (agilent.com)

Tags: Troubleshooting, contamination, Maintenance

Extending Gauge Tube Life

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

The gauge tube on the 5975 can fail in what the user feels is a short life span because it is on all the time. Failure is indicated by the LED status on the tube and readings of 9.99 or 0. The gauge tube life can be extended by using a command, pre run macro. In the method information box make sure pre-Run macro is selected. Place gauge_off in the instrument control field. The gauge will turn off for every run and back on when the run is finished.

42062

Tags: green operation, GC/MS, extending life, instrument lifetime, durability, lifetime, 5975

Minimum Parts Required to Add an MSD to a 6890, 7890 or 8890 GC

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

Parts Required for an Agilent 6890 or 7890 GC

Part Description	Part Number	Quantity
Valve Driver Bracket	G1580-00070	1
Capture screws M4x12mm, Torx T20	1390-1023	2
Valve Driver Wiring Harness	G1530-60660	1
MSD Cable, heated zone	G1530-60790	1

Parts Required for an Agilent 8890 GC*

Part Description	Part Number	Quantity
AUX Heater Hardware Kit (includes 1 Heater/Sensor Panel Mount Assembly, 1 Aux A and Valves Cable, 2 Machine Pan-HD Torx T-20 Screws)	G3450-60024	1
Interface Cable	G1530-60790	1

*The Agilent 8890 GC utilizes the ELVS if connected to a 5977B where an LVDS cable is needed. The part numbers for these are G3450-60019, GC cable, and G7077-60807, MS cable.

Tags: GC/MS transfer line interface, Mass Spec transfer line

What to Consider When Evaluating Hydrogen User as a Carrier Gas with Agilent EI GC/MS Systems

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

The purpose of this document is to help users of Agilent EI GC/MS systems determine if hydrogen can be used as a carrier gas for their analyses and what considerations and procedures are necessary to make the transition successful.

EI GC/MS Instrument Helium to Hydrogen Carrier Gas Conversion User Guide (agilent.com)

Tags: GC/MS, Hydrogen carrier gas

Fixing a Corrupt Tune File

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

If you suspect a corruption in your MSD tune file, the current process is to delete Inst 1/Add Inst 1. There is a nifty command that may solve this without the hassle. Try the command [freshtune]. This should reset the currently loaded tune file to default.

If this does not work then open explore c:\msdchem\X\59XX and rename the tune to .old <atune.u to atune.old>, them mschem\mssetup\59xx and copy the correct tune (dc pol pos or neg) to the orginal directory you were at then rename the file to .u removing the .pu or .nu from the file name.

Applies to : 5973, 5975

41107

Tags: corrupt tune file, tune file, GC/MS, 5973, MSD, error reset, 5975

EI filament P/N G7005-60061 replaces both previous EI filaments

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

(dated March 2015)

Background:

Currently there are 2 EI filaments for the GCMS:

EI (P/N G3170-60050)

EI RIS (P/N G7005-60050)

Beginning May 1, 2013 only one filament was sold:

EI (P/N G7005-60061)

Situation:

As of March 2015, there were two EI filaments. They are different in the dimensions of the base and the length of the ss posts below the base.

Solution/Action:

Today, the standard filament and the RIS version of that filament differ only in the dimensions of the base and the length of the ss posts below the base. The filaments were replaced with one that fits the requirements of both the Ei and EI RIS. The newer filament, (G7005-60061) shares the alumina base that fits the dimensional requirements of the RIS source.

BEFORE: 2 filaments for the EI GCMS:

EI (P/N G3170-60050)

EI RIS (P/N G7005-60050)

AFTER May 1, 2015. only one filament:

EI (P/N G7005-60061)

In addition to the simplification of the portfolio, which eliminates the need for a unique EI RIS filament,there are advantages to use of the new alumina base. Through the insertions and removal of the Ion Source, the RIS filament can be subject to torsional stress and strain which in some cases can result in breakage of the base. The new alumina base is up to 5 times stronger and eliminates almost all breakage risk to the filament. In addition the new EI filament will have chamfered tips on the post to ease insertion

Additional Information:

The serial number on the EI had been on the tab welded to the post. The serial number now will be laser etched on the base. The functional component of the EI filament is the four coil rhenium wire - this part is not changing

41648

Tags: electron ionization, ei, filament part number, filament, 5973X, 5977X, ion source, 5975X

How to clean an Agilent GCMS Ion Source

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

During the normal course of operation GCMS sources require cleaning due to sample throughput. This can be indicated by:

Loss in analyte response not improved by normal inlet and column maintenance.
Poor calibrant ion peak shapes during tuning, especially for the 502 ion.
Escalating tune repeller voltage.
Escalating tune Electron Multiplier voltage.

Sample residue, gas contaminants, and pump oil vapor all form an adsorbed organic film that must be removed. This film is often semi-insulating and causes a loss of the required electric fields necessary for optimum performance. Thoroughly cleaning all metal surfaces of the source removes this coating. The care taken during this activity becomes more critical as our instruments become more sensitive. The attached document contains the latest up-to-date way to do this, including tips and tricks you may have not seen before. The R&D engineers added some very interesting tidbits!

Source cleaning is normal user maintenance and is only covered under the contract during scheduled preventative maintenance. Customers can add extra source cleaning visits onto their contract if they want Agilent to do it for them; customers may do it themselves if the symptoms point to that as the first step. Customers need to be trained on the best way to accomplish this recurring task, and this document is a good supplement to the information in the operations manuals and the available videos.

Refer to this guide:

How to clean an Agilent GCMS Ion Source

and for the High Efficiency Source:

How to clean an Agilent GCMS High Efficiency Ion Source

Tags: GC/MS, Maintenance, preventive maintenance, ion source, cleaning

Agilent 7200 GC Q/TOF Application Notes

kristen.sensabaugh — Mon, 03 May 2021 19:36:14 GMT

Revision 1 posted to Wiki by kristen.sensabaugh on 5/3/2021 7:36:14 PM

GC/Q-TOF workflows for comprehensive pesticide analysis

GC/Q-TOF Screening of Pesticides in Food

GC/Q-TOF MS Surveillance of Pesticides in Food

Comprehensive Food Profiling Combining High Resolution LC/MS and GC/MS Analyses

Association of Nosema ceranae Infection with Honey Bee (Apis meillfera) Exposome Profiles and Affected Biological Pathways

A New Approach to the Analysis of Chlorinated Paraffins by Gas Chromatography Quadrupole Time-of-Flight Mass Spectrometry

A multi-omic approach to reveal the effect of low-level gamma radiation on rice seeds

The Use of High Resolution Accurate Mass GC/Q-TOF and Chemometrics in the Identification of Environmental Pollutants in Wastewater Effluents

Using GCxGC and the Agilent 7200 GC/Q-TOF for an Untargeted Metabolomics Study

Differential Analysis in Screening Assays for Extractables and Leachables Study

Identification and comparison of extractables in drug container closure systems

Analysis of IV Bag Systems

Tracing the origin of Lambrusco sparkling wines by a metabolomics approach using a HS-SPME-GC-CI-QTOF-MS method

Advanced Techniques in Gas Chromatography-Mass Spectrometry (GC-MS-MS and GC-TOF-MS) for Environmental Chemistry

Gas Chromatography–Timeof-Flight Mass Spectrometry in Food and Environmental Analysis

Tags: 7200 Application Notes

Collection of 7250 GC/Q-TOF Resources

kristen.sensabaugh — Mon, 03 May 2021 19:27:08 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 7:27:08 PM

Here is a collection of Agilent GC/Q-TOF Resources. Links to user manuals, reference guides, application notes and videos for the 7250 GC/Q-TOF on Agilent.com.

User Manuals

Agilent PN	Title	Type
G3430-90038	Agilent 7890B GC, GC/MS, and ALS Site Preparation Guide	Site Preparation
G3540-90012	Agilent 8890 Gas Chromatograph Site Preparation Guide	Site Preparation
G7250-90014	Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight (Q-TOF) GC/MS System Quick Start	Quick Start
G7250-90008	Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System Concepts Guide	Concepts
G7250-90006	Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System Operating Manual	Operation
G7250-90007	Agilent 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS System Troubleshooting and Maintenance Manual	Troubleshooting and Maintenance
G7250-90013	Agilent MassHunter Workstation Software - 7250 Accurate-Mass Quadrupole Time-of-Flight GC/MS Familiarization Guide	Familiarization Guide
G3335-90176	Molecular Structure Correlator (MSC) Quick Start Guide	Quick Start Guide

Reference Guides

Agilent PN	Title	Type
5991-8048EN	Agilent SureMass	Technical Overview
5994-1890EN	Agilent MassHunter Classifier	Technical Overview
5994-0157EN	Agilent Reversed Flow Modulator	Technical Overview

Application Notes

Agilent PN	Title
5994-2280	Workflow for Food Classification and Authenticity using Yerba Mate and High-Resolution GC/Q-TOF
5994-2264	Black Pepper Authenticity Workflow Using the High-Resolution Agilent 7250 GC/Q-TOF
5994-1346	Contaminants Screening Using High‑Resolution GC/Q-TOF and an Expanded Accurate Mass Library of Pesticides and Environmental Pollutants
5994-1429	Short Chain Chlorinated Paraffins (SCCP) Analysis Using Negative Chemical Ionization (CI) and Low Energy EI by High-Resolution 7250 GC/Q-TOF
5994-1345EN	Analysis of Wastewater Effluent Samples to Identify Toxic Chemicals Using the High-Resolution Agilent 7250 GC/Q-TOF
5994-1371EN	Comprehensive Profiling of Environmental Contaminants in Surface Water Using High-Resolution GC/Q-TOF
5994-0290EN	Combination of Chemical Ionization (CI) and Low Energy Ionization (EI) Capabilities with High-Resolution Q-TOF GC/MS

Videos

See the Whole Picture with the NEW 7250 GC/Q-TOF | Agilent

Low Energy EI Innovation Minute | Agilent

Mass Spectrometry - Food Safety at EURL | Agilent

Persistent Environmental Pollutants and Emerging Contaminants Testimonial | Agilent

Tags: 7250, GC/Q-TOF, GC/Q-TOF User Manuals, 7250 User Manuals, GC/Q-TOF Application Notes

GCMS Wiki

kristen.sensabaugh — Mon, 03 May 2021 16:05:50 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 4:05:50 PM

Agilent 5977B Series MSD Ion Source Cleaning and Scheduled Maintenance

kristen.sensabaugh — Mon, 03 May 2021 16:04:02 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 4:04:02 PM

Check out the Agilent 5977B Series MSD Laboratory Operation Quick Reference Guide about Ion Source Cleaning and Scheduled Maintenance!

5977B Series MSD Laboratory Operator Quick Reference Guide (agilent.com)

Tags: Ion Source Cleaning, Mass Spec Source, Scheduled Maintenance, Source Maintenance

Collection of GC/MS Resources Home

kristen.sensabaugh — Mon, 03 May 2021 16:04:02 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 4:04:02 PM

Explore Agilent 5977B GC/MS, 7000D GC/TQ, 7010B GC/TQ, and 7250 GC/Q-TOF resources. More links will be posted soon!

Collection of 5977B GC/MS Resources - Wiki - GC/MS - Agilent Community

Collection of 7000D and 7010B GC/TQ Resources - Wiki - GC/MS - Agilent Community

Collection of 7250 GC/Q-TOF Resources - Wiki - GC/MS - Agilent Community

Tags: 7250, 7010B, 5977B, GC/Q-TOF User Manuals, 7000D, GC/TQ User Manuals, GC/MS User Manuals

Collection of 5977B GC/MS Resources

kristen.sensabaugh — Mon, 03 May 2021 16:01:26 GMT

Current Revision posted to Wiki by kristen.sensabaugh on 5/3/2021 4:01:26 PM

Here is a collection of Agilent GC/MS Single Quad Resources. Links to user manuals, reference guides, videos, and application notes on Agilent.com. Available resources about JetClean and QuickProbe are also included!

Hardware User Manuals

Agilent PN	Title	Type
G7003-90053	Agilent GC/MS Hydrogen Safety	Safety
G3430-90038	Agilent 7890B GC, GC/MS, and ALS Site Preparation Guide	Site Preparation
G3540-90012	Agilent 8890 Gas Chromatograph Site Preparation Guide	Site Preparation
G4580-90006	Agilent Intuvo 9000 GC, GC/MS, and ALS Site Preparation Guide	Site Preparation
G7077-90036	Agilent 5977 Series MSD System Concepts Guide	Concepts Guide
G7077-90034	Agilent 5977B Series MSD Operating Manual	Operation
G7077-90035	Agilent 5977 Series MSD Troubleshooting and Maintenance Manual	Maintenance and Troubleshooting

Are you using MassHunter Software to control your GC/MS? Refer to these User Manuals.

Agilent PN	Title	Type
G7077-90019	Agilent 5977 Series MSD with MassHunter Quick Start	Quick Start
G7077-90020	Agilent MassHunter GCMS Data Acquisition for the 5977 Series MSD System – Getting Started	Getting Started
G7077-90021	Agilent MassHunter Data Acquisition Software for 5975/5977 Series GC/MSD Familiarization Guide	Software Familiarization
G3335-90187	Agilent MassHunter Workstation– Unknowns Analysis	Software Familiarization

Are you using OpenLab CDS Software to control your GC/MS? Refer to this User Manual.

Agilent PN	Title	Type
G7077-90031	Agilent 5975/5977 MSD for OpenLAB CDS Operating Manual	Software Operation

Reference Guides

Agilent PN	Title	Type
G7077-90038	Agilent 5977B Series MSD Laboratory Operator Quick Reference Guide	Ion Source Cleaning and Scheduled Maintenance
5991-2105EN	A Quick-Start Guide to Optimizing Detector Gain for GC/MSD	Technical Overview
N/A - eSeminar	Mass Spectrometer Optimization	eSeminar Slides
5994-2312EN	Agilent EI GC/MS Instrument Helium to Hydrogen Carrier Gas Conversion	User Guide

Videos

MS Explained – Spectral Interpretation

MS Explained – Method Development

MS Explained - Relative Abundance

MS Explained - Evaluation of Acquired Spectra

MS Explained - Library Search

MS Explained - Mass of a Water Molecule

MS Explained - Setting the Proper Threshold

MS Explained - Maintaining System Performance

MS Explained – The Ion Source

MS Explained – The Mass Spectrometer

MS Explained – Initial Evaluation

MS Explained – The Data System

MS Explained – Simple Mass Spectrum

MS Explained – Tuning

MS Explained – Scan Mode and SIMM Mode

MS Explained - Accountability

MS Explained – The Detector

JetClean - How it Works

Refer to the resources below, and learn more by viewing this video and exploring Agilent.com.

Agilent PN	Title	Type
G7077-90033	Agilent JetClean Operating Manual	Operation
G7077-90032	Agilent JetClean for OpenLAB Operating Manual	Software Operation
5944-0656EN	Phthalates Analysis With Method GB 5009.271-2016 Using the Agilent 8890 GC and MSD with Agilent JetClean	Application Note

QuickProbe - How it Works

Refer to the resources below, and learn more by viewing this video and exploring Agilent.com.

Agilent PN	Title	Type
G3971-90002	Agilent G3971 QuickProbe User Manual	User Manual
5994-1357EN	Maximizing Efficiency of the Agilent QuickProbe GC/MS System	White Paper
5994-2025EN	Increasing Throughput for Forensic Screening of Raw Case Samples Using the Agilent QuickProbe GC/MS System	Application Note
5994-1505EN	60-Second Screening of Foods Using the Agilent QuickProbe GC/MS System	Application Note
5994-0874EN	Fast Analysis Workflow with No Sample Preparation for Forensic Applications Using QuickProbe GC/MS	Application Note

General Application Notes

Agilent PN	Title
5994-2551EN	Accelerated Determination of Microplastics in Environmental Samples using Thermal Extraction Desorption-Gas Chromatography/Mass Spectrometry (TED-GC/MS)
5994-2725EN	Estimation of beta-sitosterol in Milk Fat (Ghee) by Agilent 8890 GC and 5977B MS
5994-2757EN	Quantitation of Cannabinoids in Hemp Flower by Derivatization GC/MS
5994-2252EN	Analysis of US EPA TO-15 for Ambient Air Monitoring Using Cryogen-Free Thermal Desorption and Gas Chromatography Coupled to a Single Quadrupole Mass Spectrometer (GC/MSD)
5994-2199EN	Quantification of microplastics in environmental samples using pyrolysis and GC/MSD
5994-2077EN	Rapid Rinse & Shoot, Screening Workflow of Pesticides in Fruit by GC/MSD in 6 Minutes
5994-2032EN	Terpenes Analysis in Cannabis Products by Liquid Injection using the Agilent Intuvo 9000/5977B GC/MS System
5994-2179EN	Comparison of Fritted and Wool Liners for Analysis of Semivolatile Organic Compounds by Gas Chromatography/Mass Spectrometry
5994-1967EN	A High Performance and Cost‑Effective GC/MS Solution for Measuring Aromatics in Gasoline Using ASTM Method D5769
5994-1926EN	Novel Residual Solvents Analysis of Cannabinoid Products with the Agilent Headspace-GC/MS System
5994-1463EN	Determination of Volatile Organic Compounds in the Cabins of Vehicles by Agilent 8890 GC/5977B MSD and Thermal Desorption Sampler
5994-1488EN	Analysis of USP <467> Residual Solvents of Class 1, Class 2, and Class 3 using the Agilent 8890 GC/ FID /5977B MSD System
5994-1500EN	EPA 8270E with Pulsed Split Injection and Retention Time Locking on an 8890 GC with a 5977 Series MSD
5994-0916EN	Pesticide Screening in Strawberries Using the Agilent 8860 GC with the Agilent 5977B GC/MSD and SureTarget Deconvolution
5994-0915EN	GC/MSD Pesticide Screening in Strawberries at Tolerance Levels Using Library Searching Deconvoluted Spectra
5994-1132EN	Combined Analysis of N-Nitrosodimethylamine (NDMA) and N-Nitrosodiethylamine (NDEA) using the Agilent 7697A Headspace Sampler, 8890 GC System, and 5977 GC/MSD
5994-1012EN	Analysis of Drugs of Abuse by GC/MS Using Ultra Inert Universal Sintered Frit Liners
5994-0833EN	US EPA Method 524.2: Successful Measurement of Purgeable Organic Compounds in Drinking Water by Agilent 8860/5977B GC/MSD
5994-0953EN	Analysis of Semivolatile Organic Compounds with Agilent Sintered Frit Liner by Gas Chromatography/Mass Spectrometry
5994-0951EN	Determination of Aromatic Amines Derived from Azo Colorants by GC/MS using Supported Liquid Extraction Chem Elut S Cartridges
5994-0626EN	Determination of Off-Odor Compounds in Drinking Water Using an SPME Device with GC/MS
5994-0590EN	Analysis of Low-Level PAHs in Drinking Water with an Agilent PAL3 equipped with SPME ARROW
5994-0646EN	Analysis of Semivolatile Organic Compounds in Drinking Water on the Agilent 8890 GC and 5977 GC/MSD with Extended Calibration Range
5994-0444EN	Endrin and DDT Stability Study for Drinking Water Methods with an Agilent 8890 GC/5977B GC/MSD
5994-0483EN	Phthalate Analysis Using an Agilent 8890 GC and an Agilent 5977A GC/MSD
5994-0499EN	Optimized GC/MS Analysis for PAHs in Challenging Matrices
5991-9103EN	GC/MS detection of short chain fatty acids from mammalian *** using automated sample preparation in aqueous solution
5991-9107EN	Analysis of Oil and Fat containing foods by fully automated sample preparation using a PAL3 coupled with a 7890 GC and a 5977 MSD system according to AOAC 996.01
5994-0013EN	Analysis of Semivolatile Organic Compounds in Drinking Water on the Agilent Intuvo and 5977 with Extended Calibration Range
5994-0291EN	Analysis of Hydraulic Fracturing Fluids with the Agilent Intuvo 9000 GC and Agilent 5977B GC/MSD
5994-0350EN	EPA 8270 Re-optimized for Widest Calibration Range on the 5977 Inert Plus GC/MSD
5994-0489EN	Determination of Volatile Organic Compounds in Soil and Sediment by Purge and Trap GC/MS
5991-8499EN	Analysis of Terpenes in Cannabis Using the Agilent 7697A/7890B/5977B Headspace GC-MSD System

Tags: GC/MS, JetClean, 5977B, GC/MS Site Preparation, QuickProbe, GC/MS User Manuals