PRIMA: peptide robust identification from MS/MS spectra.
In proteomics, tandem mass spectrometry is the key technology for peptide sequencing. However, partially due to the deficiency of peptide identification software, a large portion of the tandem mass spectra are discarded in almost all proteomics centers because they are not interpretable. The problem is more acute with the lower quality data from low end but more popular devices such as the ion trap instruments. In order to deal with the noisy and low quality data, this paper develops a systematic machine learning approach to construct a robust linear scoring function, whose coefficients are determined by a linear programming. A prototype, PRIMA, was implemented. When tested with large benchmarks of varying qualities, PRIMA consistently has higher accuracy than commonly used software MASCOT, SEQUEST and X! Tandem.
Liu
Jian
J
Department of Biomedical Engineering, McGill University, Montreal, QC H3A 2B2, Canada. jian.liu4@mcgill.ca
Ma
Bin
B
Li
Ming
M
D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D019295:Computational Biology; D013058:Mass Spectrometry / Q000379:methods* / Q000706:statistics & numerical data; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D011382:Programming, Linear; D040901:Proteomics / Q000706:statistics & numerical data*; D020539:Sequence Analysis, Protein / Q000706:statistics & numerical data; D012984:Software
D010455:Peptides