IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Degnan, David J.; Zemaitis, Kevin J.; Lewis, Logan A.; McCue, Lee Ann; Bramer, Lisa M.; Fulcher, James Michael; Veličković, Dušan; Paša-Tolić, Ljiljana; Zhou, Mowei

doi:10.1021/jasms.3c00180

IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Journal Article · Mon Jul 31 00:00:00 EDT 2023 · Journal of the American Society for Mass Spectrometry

DOI:https://doi.org/10.1021/jasms.3c00180· OSTI ID:2202633

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Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Environmental Molecular Sciences Laboratory (EMSL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2202633

Report Number(s):: PNNL-SA--184623

Journal Information:: Journal of the American Society for Mass Spectrometry, Journal Name: Journal of the American Society for Mass Spectrometry Journal Issue: 9 Vol. 34; ISSN 1044-0305

Publisher:: American Society for Mass SpectrometryCopyright Statement

Country of Publication:: United States

Language:: English

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47 OTHER INSTRUMENTATION
MALDI-MS
R package
isotope profile
mass spectrometry
trelliscope

IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

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