SOP FOR THE GC-MS INSTRUMENT

CHM9011M
CHROMATOGRAPHY AND SEP SCIENCES
PAWANDEEP SINGH
(28409601)
MODULE COORDINATOR: NITIN SEETOHUL

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 SOP for the GC-MS Instrument
1. Purpose
 To set up an instrumental technique for separating 1-Ethyl-3-methylbenzene from the
mixture and to encourage the efficient use of the PerkinElmer Clarus 600 Gas
Chromatography and PerkinElmer Clarus 600 Mass Spectrometer.
 Lessen the likelihood of harm that could result from improper usage of the device.
 Make sure that chemical analysis yields trustworthy results.
 Contribute to rising to the position of preeminent researcher within the organization.
 Streamline the process of staff training and knowledge transfer.
 fostering a culture that priorities precision, accuracy, and continuous progress in our
analytical approaches
 Given the potential hazards posed by petrol canisters and high temperatures, it is essential
to get to know the specific equipment and read the operator's handbook carefully before
operating GC-MS.
2. Scope
This SOP covers all the technical details of the GC–MS, including setup, operation,
maintenance, and a wide range of analytical operations, such as sample preparation, injection,
separation, mass spectrometric detection, and general safety measures. This standard operating
procedure (SOP) lays out the necessary steps for troubleshooting, as well as for functioning and
maintenance. Finding and isolating combinations containing both organic volatile and thermally
stable components is within its purview. This Standard Operating Procedure (SOP) applies only
to the PerkinElmer Clarus 600 Gas Chromatography-Mass Spectrometry (GC-MS) apparatus
located in Room JLC2101 at the University of Lincoln's Janet Lane Claypon, Brayford Campus.
3. Introduction
As demonstrated in Figure 1, GC-MS analysis is a cornerstone in current laboratory practices,
providing a strong instrument for the identification and quantification of chemicals inside
complicated mixtures. Its importance stems from its adaptability, which allows for the study of a
wide variety of materials, from environmental toxins to biological specimens. This method
assimilates gas chromatography's separation aids with a mass spectrometer's mass-selective
recognition abilities to deliver a inclusive understanding of the sample composition (Zhu et al.,
2023).

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Figure 1. Photograph of the GC-MS instrument.
In a standard GC-MS system, the gas chromatograph separates components by their volatility,
while the mass spectrometer identifies and quantifies these components by detecting their mass-
to-charge ratios. The injection port for sample input, the chromatographic column for separation,
and the mass spectrometer for detection are all important components. The procedure starts with
the vaporization of the sample, followed by the separation of components as they pass through
the chromatographic column. Following that, the separated components enter the mass
spectrometer, where they are ionized and subjected to mass analysis. (Clifford et al., 2021).
The robustness of GC-MS analysis lies in its ability to handle complex mixtures and provide
high-resolution data essential for qualitative and quantitative analyses. This makes GC-MS an
indispensable tool across various scientific disciplines, including environmental science,
forensics, and pharmaceutical research. Its broad applications, coupled with the precision of its
analytical results, position GC-MS as a fundamental technique in advancing scientific inquiry
and problem-solving within the laboratory.

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 4. Definitions
Gas Chromatography (GC): A technique that uses an inert gas to vaporize a sample and then
moves it down a chromatographic column, allowing the components to be separated.
Standard Operating Procedure (SOP): The SOP for the utilization of GC-MS is clearly
outlined here.
Mass Spectrometry (MS): It is a procedure that use the mass-to-charge ratio to provide details
on the molecular structure of molecules (Buttinger and Wenzl, 2020).
Ionization: The conversion of non-ionic substances into ions for the purpose of detection in
mass spectrometry.
Retention Time: The duration during which a chemical remains in the chromatographic column
is a critical determinant for its identification (Rey-Stolle et al., 2022).
5. Procedure
5.1 Sample Preparation:
Guidelines: Outline suitable sample preparation processes in detail, emphasizing the need of
precision and repeatability.
Extraction: Describe the sample extraction techniques to ensure efficient recovery of target
chemicals.
If applicable, provide directions for derivatization processes, clarifying their role in improving
compound detectability.
Pretreatment: Include any pretreatment processes, such as filtration or concentration, that are
required to optimize sample integrity and instrument performance (Müller et al., 2002).
5.2 Instrumentation Setup:
Setup and Calibration: To begin, ensure that the GC-MS instrument is switched on and calibrated
in accordance with standard protocols.
Install the chromatographic column with care, making sure all connections are secure.
Detector Parameters: Enter detector parameters such as ionization source conditions and mass
spectrometer settings.
Additional Parameters: Address any additional relevant parameters that are critical for the
specific analysis, ensuring a thorough and precise instrument setup.

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 5.3 System Initialization:
Check that all of the components, including the gas chromatograph and mass spectrometer, are
turned on and stable.
Warm-up the GC-MS system for the appropriate length of time to guarantee temperature stability
for successful studies.
Software Setup: Run the control program to verify computer-GC-MS communication.
System Check: Perform a system check to verify proper starting and to remedy any issues.
Column Conditioning: Condition columns prior to sample analysis to stabilize performance.
5.4 Calibration Procedure:
a) Prepare a calibration standard solution that accurately represents the analytes of interest.
b) Load the GC-MS system with the standard solution.
c) Optimize equipment parameters to achieve optimal resolution and sensitivity.
d) Obtain mass spectra and chromatograms for each analyte.
e) Conduct calibration checks on a daily basis before analyzing samples.
f) Ensure instrument accuracy by doing a comprehensive calibration at least once each
week.
g) For comprehensive documentation of all calibration activities to maintain traceability and
for quality control.
5.5 Sample Injection:
a) Take Solubility and Volatility into Account When Preparing the Sample Make Sure the
samples are adequately prepared.
b) Method for Injecting: Fill the injection port with a predetermined amount of sample using
a syringe. To keep variances to a minimum, keep the injection speed constant.
c) To Keep Analyses Accurate, Always Rinse the Syringe After Each Injection to Stop
Cross-Contamination.
5.6 Chromatographic Separation:
a) Vaporized samples are sent down a column in chromatographic separation, which
separates substances according on how they react with the stationary phase.
b) In the event that it applies, please provide the kind of column, its size, and any
temperature programming specifics.
c) Prioritize exact regulation of column temperature to achieve ideal separation.

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 d) For reliable and repeatable chromatographic findings, make sure the process is well-
structured from sample injection to elution (Miller et al., 2022).
5.7 Mass Spectrometry Analysis:
a) Determine the kind of ionization to use, such as chemical ionization (CI) or electron
ionization (EI), according to the sample's composition.
b) Make sure to specify the mass-to-charge ratio scan range in order to cover all important
analyte masses thoroughly.
c) In order to characterize compounds accurately and thoroughly, it is necessary to include
any extra factors that are important to the particular study.
5.8 Data Acquisition:
a) Instrument Initialization: Start the GC-MS instrument, making that it is properly
calibrated and that the system is ready.
b) Configure parameters such as injection volume and chromatographic settings using
Chromeleon for instrument control and data collecting.
c) Execution of the Run Sequence: Carry out the run sequence, defining the sample
injection and analysis procedure.
d) Data Storage: Ensure that obtained data, including raw chromatograms and mass spectra,
is stored in a systematic manner for further analysis and review.

Figure 2. creating a GCMS method for sample analysis.

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Figure 3. Run Time.

Figure 4. Autosampler.

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Figure 5. Autosampler.

Figure 6. Injection port.

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Figure 7. He gas flow.

Figure 8. Temperature gradient.

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Figure 9. Isothermal.

Figure 10. capillary column information.

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Figure 11. Scan mode of blank.

Figure 12. SIM mode of blank.

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Figure 13. saving of GCMS method just created.

Figure 14. input sample information into data table.

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Figure 15. Scan mode of sample.

Figure 16. SIM mode data of sample.

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Figure 17. Temperature gradient vs. isothermal.
6. Sample Analysis
a) Data Handling:
To protect data integrity, clearly mark and trace samples throughout the analytical process.
Electronic Documentation: For traceability, record sample information in a specialised electronic
system and connect it to the gathered data.
Data Storage: Implement a systematic data storage policy that ensures organised archiving for
simple retrieval and auditing.
b) Accuracy:
Calibration: To ensure accurate quantitative findings, calibrate the GC-MS instrument on a
regular basis using suitable standards.
Internal Standards: Incorporate internal standards during sample preparation to improve accuracy
and adjust for instrument performance variances (Bremer et al., 2023).
c) Quality Control:
Quality Assurance Checks: Perform regular quality checks, including system suitability tests, to
ensure the GC-MS system's dependability and performance.
Validation Procedures: Follow validation processes for particular sample types to ensure findings
satisfy set accuracy and precision standards.

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 d) Comparing of Mass spectrum:
The mass spectra displayed above include both 1-Ethyl-3-methylbenzene and 1-Ethyl-2-
methylbenzene, encompassing the whole m/z range collected during the course of the run. Each
MS may be seen using the retention times from.
While this MS may be used to match chemicals in the NIST database, it should not be used for
confirmation (Zeki et al., 2020).

Figure 18. MS library search (Step #1).

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Figure 19. MS library search (Step #2).

Figure 20. MS library search (Step #3).

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b) Trailing feature measures for unanticipated events like as disasters, equipment faults, and
sample spills.
c) Trailing feature measures for unanticipated events like as disasters, equipment faults, and
sample spills.
d) Describe time-consuming GC-MS instrument maintenance processes.
e) Set maintenance frequency for system cleaning and column replacement.
f) Ensure operators follow maintenance schedules for each instrument (Dvořáková et al.,
2023).
g) Handle and provide hazardous items according to approved protocols. Handbags and
safety glasses are recommended PPE for sample grounding and instrument operation.
Emergency shutdown: Integrate backup tool shutdown and evacuation.
8. Documentation and Record Keeping:
a) Emphasize the importance of accurate record-keeping for traceability and audit purposes.
b) Specify the required documentation, including sample logbooks, instrument logs, and
analysis reports.
c) Ensure compliance with organizational and regulatory documentation standards
(Buttinger and Wenzl, 2020).

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References
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analysis tool for 156,000 GC–TOF MS metabolome samples. Journal of Cheminformatics, 15, 66.

BUTTINGER, G. & WENZL, T. 2020. Validation by collaborative trial of a method for the determination by

GC–MS and LC–MS/MS of boar taint marker compounds in pork tissue. Food chemistry: X, 6,

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CLIFFORD, B., LOCK, N., KARBOWSKI, R., JOHNSON, V., SANDY, A., LUGO-MORALES, L., OWENS, A. &

SHEEHAN, C. 2021. Utilizing GC-MS and GC Instrumentation for Residual Solvents in Cannabis

and Hemp. Cannabis Laboratory Fundamentals, 191-222.

DVOŘÁKOVÁ, M., SVOBODOVÁ, L., RUCKI, M., ŠEVČÍK, V., HOŠÍKOVÁ, B., CHRZ, J., BENDOVÁ, H.,

KEJLOVÁ, K., OČADLÍKOVÁ, D. & MALÝ, M. 2023. The Safety Assessment of Cosmetic Perfumes

by Using In Chemico and In Vitro Methods in Combination with GC-MS/MS Analysis. Alternatives

to Laboratory Animals, 51, 224-248.

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MÜLLER, A., DÜCHTING, P. & WEILER, E. W. 2002. A multiplex GC-MS/MS technique for the sensitive and

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REY-STOLLE, F., DUDZIK, D., GONZALEZ-RIANO, C., FERNÁNDEZ-GARCÍA, M., ALONSO-HERRANZ, V.,

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ZEKI, Ö. C., EYLEM, C. C., REÇBER, T., KıR, S. & NEMUTLU, E. 2020. Integration of GC–MS and LC–MS for

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