Evaluation of scoring functions and peptide exposure by fractionation

UID: 11092

Author(s): Kentsis, Alex* * MSK affiliated

Description: Evaluation of sensitivity and accuracy of widely used scoring functions Sequest, MaxQuant, Peaks, and Byonic. Spectra from E. coli were matched to human sequences, and human spectra from K052 cells were matched to A. loki sequences to determine specificity of matching and FDR estimation. A subsampling analysis of SCX-RP fractionation was performed.

Subject of Study

Subject(s)

Access via PRIDE

Accession #: PXD008463
Access Restrictions: Free to All
Access Instructions: All public datasets available in PRIDE Archive in the repository can be accessed via the website by FTP link, Web Service (for programmatic access), and the PRIDE Inspector stand-alone tool.
Associated Publications: Cifani P, Dhabaria A, Chen Z, Yoshimi A, Kawaler E, Abdel-Wahab O, Poirier J, Kentsis A. ProteomeGenerator: A framework for comprehensive proteomics based on de novo transcriptome assembly and high-accuracy peptide mass spectral matching. Journal of Proteome Research. 2018; 17(11):3681-3692.
Equipment Used: Orbitrap Fusion Lumos
Software Used: Byonic
Full MS/MS search engine for comprehensive peptide and protein identification

MaxQuant
A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.

Peaks
a software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post-translational modifications (PTMs) and sequence variants (mutations), and peptide/protein de novo sequencing

SEQUEST®
A tandem mass spectrometry database search program that correlates tandem mass spectra of peptides against peptide sequences from a sequence database.
Dataset Format(s): FASTA, RAW, zip
Dataset Size: 96 GB (does not include zip files for software packages)

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