Combinatorial libraries of synthetic peptides as a model for shotgun proteomics.
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.
Bohrer
Brian C
BC
Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
Li
Yong Fuga
YF
Reilly
James P
JP
Clemmer
David E
DE
DiMarchi
Richard D
RD
Radivojac
Predrag
P
Tang
Haixu
H
Arnold
Randy J
RJ
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
D019151:Peptide Library; D010455:Peptides; D014357:Trypsin