title: In silico analysis of accurate proteomics, complemented by selective isolation of peptides.
abstract: Protein identification by mass spectrometry is mainly based on MS/MS spectra and the accuracy of molecular mass determination. However, the high complexity and dynamic ranges for any species of proteomic samples, surpass the separation capacity and detection power of the most advanced multidimensional liquid chromatographs and mass spectrometers. Only a tiny portion of signals is selected for MS/MS experiments and a still considerable number of them do not provide reliable peptide identification. In this article, an in silico analysis for a novel methodology of peptides and proteins identification is described. The approach is based on mass accuracy, isoelectric point (pI), retention time (t(R)) and N-terminal amino acid determination as protein identification criteria regardless of high quality MS/MS spectra. When the methodology was combined with the selective isolation methods, the number of unique peptides and identified proteins increases. Finally, to demonstrate the feasibility of the methodology, an OFFGEL-LC-MS/MS experiment was also implemented. We compared the more reliable peptide identified with MS/MS information, and peptide identified with three experimental features (pI, t(R), molecular mass). Also, two theoretical assumptions from MS/MS identification (selective isolation of peptides and N-terminal amino acid) were analyzed. Our results show that using the information provided by these features and selective isolation methods we could found the 93% of the high confidence protein identified by MS/MS with false-positive rate lower than 5%.
authors.affiliation: Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cubanacán, Playa, Ciudad de la Habana, Cuba. yasset.perez@biocomp.cigb.edu.cu
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.forename: Aniel
authors.initials: A
authors.lastname: Sánchez
authors.forename: Yassel
authors.initials: Y
authors.lastname: Ramos
authors.forename: Alex
authors.initials: A
authors.lastname: Schmidt
authors.forename: Markus
authors.initials: M
authors.lastname: Müller
authors.forename: Lázaro
authors.initials: L
authors.lastname: Betancourt
authors.forename: Luis J
authors.initials: LJ
authors.lastname: González
authors.forename: Roberto
authors.initials: R
authors.lastname: Vera
authors.forename: Gabriel
authors.initials: G
authors.lastname: Padron
authors.forename: Vladimir
authors.initials: V
authors.lastname: Besada
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D007526:Isoelectric Point; D008970:Molecular Weight; D010455:Peptides / Q000302:isolation & purification*; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins