» Articles » PMID: 19338334

Accurate and Sensitive Peptide Identification with Mascot Percolator

Overview
Journal J Proteome Res
Specialty Biochemistry
Date 2009 Apr 3
PMID 19338334
Citations 181
Authors
Affiliations
Soon will be listed here.
Abstract

Sound scoring methods for sequence database search algorithms such as Mascot and Sequest are essential for sensitive and accurate peptide and protein identifications from proteomic tandem mass spectrometry data. In this paper, we present a software package that interfaces Mascot with Percolator, a well performing machine learning method for rescoring database search results, and demonstrate it to be amenable for both low and high accuracy mass spectrometry data, outperforming all available Mascot scoring schemes as well as providing reliable significance measures. Mascot Percolator can be readily used as a stand alone tool or integrated into existing data analysis pipelines.

Citing Articles

Cerebrospinal fluid proteomics reveals the innate immunity and blood-brain barrier dysregulation in a patient with multidrug-resistant ventriculitis treated with intrathecal and intravenous polymyxin B.

Li M, Liu D, Bergen P, Liang S, Chen J, Kho Z Heliyon. 2025; 10(24):e40893.

PMID: 39759273 PMC: 11699078. DOI: 10.1016/j.heliyon.2024.e40893.


Global Proteomics Indicates Subcellular-Specific Anti-Ferroptotic Responses to Ionizing Radiation.

Christopher J, Breckels L, Crook O, Vazquez-Chantada M, Barratt D, Lilley K Mol Cell Proteomics. 2024; 24(1):100888.

PMID: 39617061 PMC: 11780130. DOI: 10.1016/j.mcpro.2024.100888.


Validation and quantification of peptide antigens presented on MHCs using SureQuant.

Leddy O, Cui Y, Ahn R, Stopfer L, Choe E, Kim D Nat Protoc. 2024; .

PMID: 39438697 DOI: 10.1038/s41596-024-01076-x.


The MBO2/FAP58 heterodimer stabilizes assembly of inner arm dynein and reveals axoneme asymmetries involved in ciliary waveform.

Fu G, Augspurger K, Sakizadeh J, Reck J, Bower R, Tritschler D Mol Biol Cell. 2024; 35(5):ar72.

PMID: 38568782 PMC: 11151096. DOI: 10.1091/mbc.E23-11-0439.


TNF-α-induced Inhibition of Protein Myristoylation Binding Between NMT1 and Sorbs2 in Osteoblasts.

Kutsuna S, Sugiyama G, Komiyama T, Kamohara H, Ohyama Y, Kumamaru W In Vivo. 2023; 38(1):107-113.

PMID: 38148048 PMC: 10756471. DOI: 10.21873/invivo.13416.


References
1.
Elias J, Gygi S . Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007; 4(3):207-14. DOI: 10.1038/nmeth1019. View

2.
Keller A, Nesvizhskii A, Kolker E, Aebersold R . Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002; 74(20):5383-92. DOI: 10.1021/ac025747h. View

3.
Wolters D, Washburn M, Yates 3rd J . An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem. 2002; 73(23):5683-90. DOI: 10.1021/ac010617e. View

4.
Kall L, Canterbury J, Weston J, Noble W, MacCoss M . Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods. 2007; 4(11):923-5. DOI: 10.1038/nmeth1113. View

5.
Klammer A, MacCoss M . Effects of modified digestion schemes on the identification of proteins from complex mixtures. J Proteome Res. 2006; 5(3):695-700. PMC: 2535816. DOI: 10.1021/pr050315j. View