title: Combinatorial libraries of synthetic peptides as a model for shotgun proteomics.
abstract: A synthetic approach to model the analytical complexity of biological proteolytic digests has been developed. Combinatorial peptide libraries ranging in length between 9 and 12 amino acids that represent typical tryptic digests were designed, synthesized, and analyzed. Individual libraries and mixtures thereof were studied by replicate liquid chromatography-ion trap mass spectrometry and compared to a tryptic digest of Deinococcus radiodurans. Similar to complex proteome analysis, replicate study of individual libraries identified additional unique peptides. Fewer novel sequences were revealed with each additional analysis in a manner similar to that observed for biological data. Our results demonstrate a bimodal distribution of peptides sorting to either very low or very high levels of detection. Upon mixing of libraries at equal abundance, a length-dependent bias in favor of longer sequence identification was observed. Peptide identification as a function of site-specific amino acid content was characterized with certain amino acids proving to be of considerable importance. This report demonstrates that peptide libraries of defined character can serve as a reference for instrument characterization. Furthermore, they are uniquely suited to delineate the physical properties that influence identification of peptides, which provides a foundation for optimizing the study of samples with less defined heterogeneity.
authors.affiliation: Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Bohrer
authors.forename: Yong Fuga
authors.initials: YF
authors.lastname: Li
authors.forename: James P
authors.initials: JP
authors.lastname: Reilly
authors.forename: David E
authors.initials: DE
authors.lastname: Clemmer
authors.forename: Richard D
authors.initials: RD
authors.lastname: DiMarchi
authors.forename: Predrag
authors.initials: P
authors.lastname: Radivojac
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Arnold
mesh_terms: D000595:Amino Acid Sequence; D002853:Chromatography, Liquid / Q000379:methods; D034301:Deinococcus / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods; D019151:Peptide Library; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D014357:Trypsin / Q000378:metabolism
chemical_list: D019151:Peptide Library; D010455:Peptides; D014357:Trypsin