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What are the best practices for creating and maintaining your own GC-MS library?

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Creating and maintaining your own GC-MS library can be a valuable asset for your analytical work, as it allows you to identify and quantify compounds of interest with greater accuracy and confidence. However, building a reliable and comprehensive GC-MS library requires some best practices to ensure its quality and usability. In this article, we will discuss some of these best practices, such as how to select and prepare reference standards, how to optimize and validate your GC-MS method, how to store and update your library data, and how to use your library effectively for matching and reporting.

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1 Select and prepare reference standards

The first step to creating your own GC-MS library is to obtain reference standards for the compounds you want to include in your library. Reference standards are pure samples of known identity and concentration that provide the basis for generating and comparing GC-MS spectra. You should choose reference standards that are relevant for your application, that are available and affordable, and that have sufficient purity and stability. You should also prepare your reference standards properly, by following the manufacturer's instructions, by using appropriate solvents and dilutions, and by storing them in suitable conditions.

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2 Optimize and validate your GC-MS method

The second step to creating your own GC-MS library is to optimize and validate your GC-MS method for the analysis of your reference standards. Optimizing your GC-MS method means adjusting the parameters of your instrument, such as the column, the carrier gas, the injection mode, the temperature program, the ionization mode, and the scan range, to achieve the best separation and detection of your compounds. Validating your GC-MS method means verifying that your method meets the criteria of accuracy, precision, sensitivity, selectivity, linearity, and robustness for your intended purpose. You should document your method optimization and validation steps and results, as they will affect the quality and reproducibility of your library spectra.

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3 Store and update your library data

The third step to creating your own GC-MS library is to store and update your library data in a secure and organized way. Storing your library data means saving your reference spectra, along with relevant information such as compound name, CAS number, molecular formula, retention time, peak area, and source, in a format that is compatible with your GC-MS software and hardware. Updating your library data means adding new compounds, deleting obsolete ones, or modifying existing ones, as your analytical needs change. You should also backup your library data regularly, and protect it from unauthorized access or modification.

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LaTasha Folmar

Quality Manager
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I've found it helpful to ID the primary and at leat two secondary mass peaks that you know have no interference in your typical matrix. This leaves less potential misinterpretation for future use.

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4 Use your library effectively for matching and reporting

The final step to creating your own GC-MS library is to use it effectively for matching and reporting your analytical results. Matching your library means comparing the spectra of your unknown samples with the spectra of your library compounds, using various algorithms and criteria, such as similarity index, mass accuracy, retention time, and peak shape. Reporting your library means presenting and interpreting your matching results, using various tools and formats, such as tables, charts, annotations, and comments. You should use your library with caution and critical thinking, as it is not a substitute for expert judgment or confirmation by other methods.

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Nekoda Harris

Scientific Software ?????| Mass Spectrometry ??| Spectral Databases ???
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There are a variety of search algorithms in the literature that could be implemented. The most popular of these are the 'identity' (composite) and 'similarity' (dot-product) algorithms developed by NIST. You will obtain slightly different results depending on your choice of algorithm, and whether or not you decide to implement pre-filters as well. Regardless of which algorithm you choose, it is always best to include replicates of each spectrum in your library collected under differing conditions so that you are more likely to obtain a solid match when querying the library later on. Once you choose an algorithm, results are typically reported using a weighted combination of HQI and RHQI (hit quality index and reverse hit quality index).

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5 Here’s what else to consider

This is a space to share examples, stories, or insights that don’t fit into any of the previous sections. What else would you like to add?

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Henry Lozano Pereira

Organic Mass spectrometist researcher
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Always consider adding the retention index to each mass spectrum since it can be an indication of the amount of carbons that unknown molecule may have and it is an important piece of information with which the retention time of the unknown compound is confirmed. And this parameter can tell us which column is used, because the retention index of a compound in column A is different for the same compound in column B.

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Nekoda Harris

Scientific Software ?????| Mass Spectrometry ??| Spectral Databases ???
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Some additional insights: If your lab is using a variety of instrumentation from different vendors, it may be a good idea to consider vendor-agnostic software to manage your spectral data. This will allow you to access and interpret your data in the same place regardless of instrument type.

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What are the best practices for creating and maintaining your own GC-MS library?

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1 Select and prepare reference standards

2 Optimize and validate your GC-MS method

3 Store and update your library data

4 Use your library effectively for matching and reporting

5 Here’s what else to consider

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