NITPICK: Peak Identification for Mass Spectrometry Data

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2008 Aug 30

PMID 18755032

Citations 37

Authors

Bernhard Y Renard

Marc Kirchner

Hanno Steen

Judith A J Steen

Fred A Hamprecht

Affiliations

Soon will be listed here.

Abstract

Background: The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments.

Results: This contribution proposes a sparse template regression approach to peak picking called NITPICK. NITPICK is a Non-greedy, Iterative Template-based peak PICKer that deconvolves complex overlapping isotope distributions in multicomponent mass spectra. NITPICK is based on fractional averaging, a novel extension to Senko's well-known averaging model, and on a modified version of sparse, non-negative least angle regression, for which a suitable, statistically motivated early stopping criterion has been derived. The strength of NITPICK is the deconvolution of overlapping mixture mass spectra.

Conclusion: Extensive comparative evaluation has been carried out and results are provided for simulated and real-world data sets. NITPICK outperforms pepex, to date the only alternate, publicly available, non-greedy feature extraction routine. NITPICK is available as software package for the R programming language and can be downloaded from (http://hci.iwr.uni-heidelberg.de/mip/proteomics/).

Citing Articles

TIHI Toolkit: A Peak Finder and Analyzer for Spectroscopic Data.

Han K, Boziki A, Tkatchenko A, Berryman J ACS Omega. 2024; 9(50):49397-49410.

PMID: 39713663 PMC: 11656381. DOI: 10.1021/acsomega.4c06830.

AdductHunter: identifying protein-metal complex adducts in mass spectra.

Long D, Eade L, Sullivan M, Dost K, Meier-Menches S, Goldstone D J Cheminform. 2024; 16(1):15.

PMID: 38321500 PMC: 10845562. DOI: 10.1186/s13321-023-00797-7.

The isotope distribution: A rose with thorns.

Claesen J, Rockwood A, Gorshkov M, Valkenborg D Mass Spectrom Rev. 2023; 44(1):22-42.

PMID: 36744702 PMC: 11624904. DOI: 10.1002/mas.21820.

Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.

James E, Murphree T, Vorauer C, Engen J, Guttman M Chem Rev. 2021; 122(8):7562-7623.

PMID: 34493042 PMC: 9053315. DOI: 10.1021/acs.chemrev.1c00279.

Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine.

Teo G, Polasky D, Yu F, Nesvizhskii A J Proteome Res. 2020; 20(1):498-505.

PMID: 33332123 PMC: 8864561. DOI: 10.1021/acs.jproteome.0c00544.

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