Proteome Profiling Using Orbitrap Mass Spectrometry

Aims: Identify as many proteins and protein modifications as possible with maximum reliability and reproducible relative quantities as determined by label-free quantification

Procedures: Cell and tissue fractionation, proteolytic digests with various enzymes, protein separation by 2D-PAGE, chromatographic separation of peptides using nano-LC and peptide identification by high-resolution mass spectrometry (QEXACTIVE orbitrap) including MS/MS fragmentation.

Results:  > 100 000 distinct peptides (FDR<0.01) corresponding to >8000 distinct proteins (FDR<0.01) typically identified by us in a single cell type when combining different fractions and cell activity states.