Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.

ABSTRACT:

Background

Onco-proteogenomics aims to understand how changes in a cancer's genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database.

Methods

We established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines.

Results

We developed a set of recommendations for the detection of variants using three searc

SUBMITTER: Alfaro JA 

PROVIDER: S-EPMC5514513 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature