Dinosaur: A Refined Open-Source Peptide MS Feature Detector

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Dinosaur : A Refined Open-Source Peptide MS Feature Detector. / Teleman, Johan; Chawade, Aakash; Sandin, Marianne; Levander, Fredrik; Malmström, Johan.

I: Journal of Proteome Research, Vol. 15, Nr. 7, 01.07.2016, s. 2143-2151.

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Teleman, Johan ; Chawade, Aakash ; Sandin, Marianne ; Levander, Fredrik ; Malmström, Johan. / Dinosaur : A Refined Open-Source Peptide MS Feature Detector. I: Journal of Proteome Research. 2016 ; Vol. 15, Nr. 7. s. 2143-2151.

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TY - JOUR

T1 - Dinosaur

T2 - Journal of Proteome Research

AU - Teleman, Johan

AU - Chawade, Aakash

AU - Sandin, Marianne

AU - Levander, Fredrik

AU - Malmström, Johan

PY - 2016/7/1

Y1 - 2016/7/1

N2 - 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.

AB - 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.

KW - algorithm

KW - chimeric spectra

KW - electrospray ionization

KW - feature detection

KW - mass spectrometry

KW - proteomics

KW - software

UR - http://www.scopus.com/inward/record.url?scp=84977108911&partnerID=8YFLogxK

U2 - 10.1021/acs.jproteome.6b00016

DO - 10.1021/acs.jproteome.6b00016

M3 - Article

VL - 15

SP - 2143

EP - 2151

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 7

ER -