Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes.

ABSTRACT: Human cancer cell lines are widely used in pharmacological and systems biological studies. The rapid documentation of the steady-state gene expression landscape of the cells used in a particular experiment may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library-free data analysis workflow, to measure both the proteome and phosphoproteome of a melanoma cell line panel with different metastatic properties. For each cell line, the single-shot DIA-MS detected 8100 proteins and almost 40 000 phosphopeptides in the respective measurements of two hours. Benchmarking the DIA-MS data towards the RNA-seq data and tandem mass tag (TMT)-MS results from the same set of cell

SUBMITTER: Gao E 

PROVIDER: S-EPMC8205956 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature