Introduction to Proteome Wide Identification

We also performed proteome-wide identification of circadian proteins in two cereal crops namely, Oryza sativa and Sorghum bicolor , followed by the functional annotation of the predicted circadian proteins with Gene Ontology (GO) terms.

Here, we present a proteome-wide identification of reversibly oxidized cysteine sites in oxidant-treated cells using a maleimide-based bioswitch method coupled to mass spectrometry analysis.

Herein, we employed isotope-coded ATP acyl-phosphate probes, in conjunction with a multiple-reaction monitoring (MRM)-based targeted proteomic method for proteome-wide identifications of endogenous kinases that can bind to two N6-modified ATP derivatives, N6-methyl-ATP (N6-Me-ATP), and N6-furfuryl-ATP (a.

Here we review how recent advances in proteomic technologies, mass spectrometry instrumentation, and bioinformatics spurred the proteome-wide identification of PTM crosstalk through measurements of PTM sites.

Basic Protocol 1: Live-cell labeling of substrates of protein methyltransferases GLP1 and PRMT1 with lcBPPM-feasible enzymes and SAM analogue precursors Support Protocol: Gram-scale synthesis of Hey-Met Basic Protocol 2: Click labeling of lcBPPM cell lysates with a biotin-azide probe Alternate Protocol: Click labeling of small-scale lcBPPM cell lysates with a TAMRA-azide dye for in-gel fluorescence visualization Basic Protocol 3: Enrichment of biotinylated lcBPPM proteome with streptavidin beads Basic Protocol 4: Proteome-wide identification of lcBPPM targets with mass spectrometry Basic Protocol 5: Validation of individual lcBPPM targets by western blot.

We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells.

However, proteome-wide identification of CTP-binding proteins remains challenging.

However, proteome-wide identification of persulfidation sites is of great challenge due to the difficulties to accurately differentiate persulfide groups with disulfide and thiol groups in proteins, as well as the extremely low abundance of persulfidated peptides.

In contrast, mass spectrometric screening approaches enable the proteome-wide identification of minor protein changes in biofluids.

However, proteome-wide identification of methylated proteins in plants remains unexplored.

Herein we developed a chemical proteomic method for the proteome-wide identification of LPA-binding proteins.