title: Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics.
abstract: The aim of the work was to explore usefulness of artificial neural network (ANN) analysis for the evaluation of proteomics data. The analysis was applied to the data generated by the widely used protein identification program Sequest, completed with several structural parameters readily calculated from peptide molecular formulas. Proteins from yeast cells were identified based on the MS/MS spectra of peptides. The constructed ANN was demonstrated to classify automatically as either "good" or "bad" the peptide MS/MS spectra otherwise classified manually. An appropriately trained ANN proves to be a high-throughput tool facilitating examination of Sequest's results. ANNs are recommended as a means of automatic processing of large amounts of MS/MS data, which normally must be considered in the analysis of complex mixtures of proteins in proteomics.
authors.affiliation: Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen J Hallera 107, 80-416 Gdańsk, Poland. tbaczek@amg.gda.pl
authors.forename: Tomasz
authors.initials: T
authors.lastname: Baczek
authors.forename: Adam
authors.initials: A
authors.lastname: Buciński
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Ivanov
authors.forename: Roman
authors.initials: R
authors.lastname: Kaliszan
mesh_terms: D001185:Artificial Intelligence; D013058:Mass Spectrometry / Q000379:methods / Q000592:standards; D016571:Neural Networks, Computer; D010455:Peptides / Q000032:analysis*; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis*; D020539:Sequence Analysis, Protein / Q000379:methods / Q000592:standards; D012986:Software Validation; D013997:Time Factors
chemical_list: D010455:Peptides; D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins