Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression Data
| Autor: | Paul Kearney, Kevin Eng, Heather Butler, Patrice Hugo |
|---|---|
| Rok vydání: | 2007 |
| Předmět: |
Proteomics
Gene Expression Profiling Proteins General Chemistry Computational biology Biology Biochemistry Molecular biology Mass Spectrometry Peptide Fragments Protein expression Gene expression profiling Resolver Identification (biology) Protein identification Biomarker discovery Peptide expression Biomarkers Software |
| Zdroj: | Journal of Proteome Research. 7:234-244 |
| ISSN: | 1535-3907 1535-3893 |
| DOI: | 10.1021/pr0705439 |
| Popis: | Proteomic discovery platforms generate both peptide expression information and protein identification information. Peptide expression data are used to determine which peptides are differentially expressed between study cohorts, and then these peptides are targeted for protein identification. In this paper, we demonstrate that peptide expression information is also a powerful tool for enhancing confidence in protein identification results. Specifically, we evaluate the following hypothesis: tryptic peptides originating from the same protein have similar expression profiles across samples in the discovery study. Evidence supporting this hypothesis is provided. This hypothesis is integrated into a protein identification tool, PIPER (Protein Identification and Peptide Expression Resolver), that reduces erroneous protein identifications below 5%. PIPER's utility is illustrated by application to a 72-sample biomarker discovery study where it is demonstrated that false positive protein identifications can be reduced below 5%. Consequently, it is recommended that PIPER methodology be incorporated into proteomic studies where both protein expression and identification data are collected. |
| Databáze: | OpenAIRE |
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