Journal
ANALYTICAL CHEMISTRY
Volume 82, Issue 15, Pages 6559-6568Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ac100910a
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Funding
- NCI NIH HHS [U24 CA126480-01, U24 CA126480] Funding Source: Medline
- NCRR NIH HHS [R01 RR024236-01A1, R01 RR024236] Funding Source: Medline
- NIGMS NIH HHS [R01 GM103725] Funding Source: Medline
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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.
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