A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases

Praveen Kumar, James E. Johnson, Caleb Easterly, Subina Mehta, Ray Sajulga, Brook Nunn, Pratik D. Jagtap, Timothy J. Griffin

Research output: Contribution to journalArticlepeer-review

18 Scopus citations

Abstract

Multiomics approaches focused on mass spectrometry (MS)-based data, such as metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a comprehensive protein sequence database. These databases can be very large, containing millions of sequences, which reduces the sensitivity of matching tandem mass spectrometry (MS/MS) data to sequences to generate peptide spectrum matches (PSMs). Here, we describe and evaluate a sectioning method for generating an enriched database for those protein sequences that are most likely present in the sample. Our evaluation demonstrates how this method helps to increase the sensitivity of PSMs while maintaining acceptable false discovery rate statistics-offering a flexible alternative to traditional large database searching, as well as previously described two-step database searching methods for large sequence database applications. Furthermore, implementation in the Galaxy platform provides access to an automated and customizable workflow for carrying out the method. Additionally, the results of this study provide valuable insights into the advantages and limitations offered by available methods aimed at addressing challenges of genome-guided, large database applications in proteomics. Relevant raw data has been made available at https://zenodo.org/ using data set identifier "3754789"and https://arcticdata.io/catalog using data set identifier "A2VX06340".

Original languageEnglish (US)
Pages (from-to)2772-2785
Number of pages14
JournalJournal of Proteome Research
Volume19
Issue number7
DOIs
StatePublished - Jul 2 2020

Bibliographical note

Publisher Copyright:
Copyright © 2020 American Chemical Society.

Keywords

  • Galaxy
  • false discovery rate
  • metaproteomics
  • peptide spectrum match
  • proteogenomics
  • tandem mass spectrometry

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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