SpectiCal: m/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions

Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed SpectiCal, a software tool that can read mzML files from data-dependent acquisition proteomics experiments in parallel, compute m/z calibrations f...

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Bibliographic Details
Published in:	Journal of proteome research Vol. 23; no. 4; pp. 1519 - 1530
Main Authors:	Zhang, Nathan H., Deutsch, Eric W.
Format:	Journal Article
Language:	English
Published:	United States American Chemical Society 05-04-2024
Subjects:	Calibration Ions Peptides - analysis Software Tandem Mass Spectrometry - methods immonium ions spectral calibration SpectiCal proteomics Mass spectrometry low-mass ions
Online Access:	Get full text
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Summary:	Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed SpectiCal, a software tool that can read mzML files from data-dependent acquisition proteomics experiments in parallel, compute m/z calibrations for each file prior to identification analysis based on known low-mass ions, and produce information about frequently observed peaks and their explanations. Using calibration coefficients, the data can be corrected to generate new calibrated mzML files. SpectiCal was tested using five public data sets, creating a table of commonly observed low-mass ions and their identifications. Information about the calibration and individual peaks is written in PDF and TSV files. This includes information for each peak, such as the number of runs in which it appears, the percentage of spectra in which it appears, and a plot of the aggregated region surrounding each peak. SpectiCal can be used to compute MS run calibrations, examine MS runs for artifacts that might hinder downstream analysis, and generate tables of detected low-mass ions for further analysis. SpectiCal is freely available at https://github.com/PlantProteomes/SpectiCal.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1535-3893 1535-3907 1535-3907
DOI:	10.1021/acs.jproteome.3c00882