Comparison of proteomic and phospho-proteomic analysis upon urea extraction and triple extraction

ABSTRACT: The goal of the present project was to investigate the applicability of a triple extraction (”TE”), which yields RNA, DNA and protein in a single procedure, for gel-free mass spectrometry-based proteomics. Proven successful for large-scale transcriptomics and genomics, we examined TE compatibility with mass spectrometry-based proteomics and phospho-proteomics by comparison to a urea standard processing. For whole proteome, peptides were fractionated using SAX; for phosphorylation analysis, modifications were enriched using TiO2 columns. We here demonstrate the efficiency of TE protocol for shotgun proteomics, providing similar results as urea-derived samples both at the qualitative and quantitative levels. The study of phosphorylation events is likewise compatible with TE, which actually results in a higher number of correctly localized sites than urea, while the nature of extracted sites appears somewhat distinct between both techniques. We thus conclude that our protocol is well suited for proteomics and as efficient as other more widely used workflows for mass spectrometry-based analysis.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

DISEASE(S): Urinary Bladder Cancer

SUBMITTER: Guillaume Arras  

LAB HEAD: Damarys Loew

PROVIDER: PXD011971 | Pride | 2021-07-20

REPOSITORIES: Pride