Effects of gradient lengths and acquisition frequency on the number of protein identifications in nanoflow LCMSMS of complex proteomic sample homo sapiens

ABSTRACT: A liquid chromatography-tandem mass-spectrometry LC-MS/MS is now an indispensable method for shotgun proteomics. The combination of chromatographic separation and MS/MS identification provides valuable information about protein compositions from different biological samples. In this article, we examined the relationship between gradient length and MS acquisition on examples of three complex peptide mixtures. We found that combining long gradient and higher MS acquisitions resulted in more protein identifications for human plasma, Escherichia coli, and Chinese hamster ovary cell lines. We also evaluated the efficiency of Mascot and PEAKS proteomic tools for the analysis of LC-MS/MS data.

INSTRUMENT(S): impact II

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Arman Kulyyassov  

PROVIDER: MSV000094936 | MassIVE | Wed Jun 05 06:00:00 BST 2024

SECONDARY ACCESSION(S): PXD052860

REPOSITORIES: MassIVE