Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT.

ABSTRACT: Ideally, shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, the large dynamic range and complexity of cellular proteomes results in oversampling of abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested the proteome equalization technology, ProteoMiner, in conjunction with Multidimensional Protein Identification Technology (MudPIT) to determine how the equalization of protein dynamic range could improve shotgun proteomics methods for the analysis of cellular proteomes. Our results suggest low abundance protein identifications were improved by two mechanisms: (1) depletion of high abundance proteins freed ion trap sampling space usually occupied by high abundanc

SUBMITTER: Fonslow BR 

PROVIDER: S-EPMC3161494 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature