Dinosaur: A Refined Open-Source Peptide MS Feature Detector

Research output: Contribution to journalArticle

Abstract

In bottom-up mass spectrometry (MS)-based proteomics, peptide isotopic and chromatographic traces (features) are frequently used for label-free quantification in data-dependent acquisition MS but can also be used for the improved identification of chimeric spectra or sample complexity characterization. Feature detection is difficult because of the high complexity of MS proteomics data from biological samples, which frequently causes features to intermingle. In addition, existing feature detection algorithms commonly suffer from compatibility issues, long computation times, or poor performance on high-resolution data. Because of these limitations, we developed a new tool, Dinosaur, with increased speed and versatility. Dinosaur has the functionality to sample algorithm computations through quality-control plots, which we call a plot trail. From the evaluation of this plot trail, we introduce several algorithmic improvements to further improve the robustness and performance of Dinosaur, with the detection of features for 98% of MS/MS identifications in a benchmark data set, and no other algorithm tested in this study passed 96% feature detection. We finally used Dinosaur to reimplement a published workflow for peptide identification in chimeric spectra, increasing chimeric identification from 26% to 32% over the standard workflow. Dinosaur is operating-system-independent and is freely available as open source on https://github.com/fickludd/dinosaur.

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Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Other Medical Engineering
  • Biological Sciences

Keywords

  • algorithm, chimeric spectra, electrospray ionization, feature detection, mass spectrometry, proteomics, software
Original languageEnglish
Pages (from-to)2143-2151
Number of pages9
JournalJournal of Proteome Research
Volume15
Issue number7
Publication statusPublished - 2016 Jul 1
Publication categoryResearch
Peer-reviewedYes