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Searching MS MS Spectra for Lipid IDs

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Paul Hutchins edited this page May 1, 2018 · 5 revisions

Searching MS/MS Spectra for Lipid IDs (Spectrum Searcher)

Overview

Spectrum Searcher accepts MS/MS files in either .mgf or .mzXML format and identifies lipid spectra in the files using a two-step searching algorithm. Spectral searching results are generated as .csv files in the same directory as the MS/MS files and contain detailed information on each spectral match. These .csv files are necessary for peak identification in Peak Finder

If you use the embedded LipidBlast libraries, please cite the following publications:

Kind, T., Liu, K.-H., Lee, D.Y., DeFelice, B., Meissen, J.K., and Fiehn, O. (2013). LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat. Methods 10, 755–758.

Tsugawa, H., Ikeda, K., Tanaka, W., Senoo, Y., Arita, M., and Arita, M. (2017). Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library. J. Cheminform. 9, 1–12.

Instructions

  • Convert MS Files

    • Files must be centroided and be either .mgf or .mzXML. The majority of vendor-specific file formats can be converted to these file formats using Proteowizard. If original data was collected in profile mode, adding the Zero Samples Filter in MSConvert reduces the resulting centroided file size and greatly increases searching speed.

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  • Select MS/MS Files for Searching

    • Select the “Add” button and select the MS/MS files to search.

  • Select Libraries to Search Against

    • In the “Available Libraries” table, select all libraries to search against

    • The table will be populated with all .msp files found in src/msp_files

  • Update MS/MS Search Parameters as Needed

    • The “MS1 Search Tolerance” field denotes the absolute mass tolerance used to search for valid lipids for the precursor of each MS/MS spectrum

    • The “MS2 Search Tolerance” field denotes the absolute mass tolerance used for spectral similarity scoring

    • The “Max Search Results Returned” field denotes the maximum possible number of search results returned for each spectrum

    • The “MS2 Low Mass Cuttoff” field denotes the minimum m/z value in each ms/ms spectral which will be used for spectral similarity scoring. This value is useful for removing low mass acetate or formate fragments which are ubiquitous and can skew spectral similarity scoring.

  • Search Spectra

    • Select “Search Spectra”

    • MS/MS search results are written in the same directory as the input files and with “_Results.csv” appended to the input file as its name.

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Tutorials

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