The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. Proteomic analysis for each CPTAC study is carried out independently by Proteomic Characterization Centers (PCCs) using a variety of protein fractionation techniques, instrumentation, and workflows. Mass spectrometry and...

Summary from ProteomeXchange: "Protein arginine methyltransferase 5 (PRMT5) belongs to the class II arginine methyltransferases and catalyzes monomethylation and symmetrical dimethylation of arginines on proteins. It has recently emerged as a promising cancer drug target, and two PRMT5 inhibitors are currently in clinical trials for a range malignancies. Despite the recognized therapeutic potential,...

Summary from the GEO: "Protein arginine methyltransferase 5 (PRMT5) belongs to the class II arginine methyltransferases and catalyzes monomethylation and symmetrical dimethylation of arginines on proteins. It has recently emerged as a promising cancer drug target, and three PRMT5 inhibitors are currently in clinical trials for a range of malignancies. In this study, we aimed to further elucidate the...

Description from the ProteomeXchange: "Exo1 tagged with the TAP sequence was pulled down from synchronous ndt80∆ meiotic cells after induction of the CDC5 kinase at t = 8 h 15 in meiosis (1 h 15 after CDC5 induction), in order to identify its phosphorylated residues" PRIDE Sample Processing Protocol: "2.1010 cells of VBD2070 strain were harvested after 8 h 15 min in sporulation medium and processed...

Description from Proteome Xchange: "Mlh3 internally tagged with Flag was pulled down from synchronous meiotic cells at t = 4 h in meiosis, in order to identify its interacting partners involved in meiotic crossover formation" Sample Processing Protocol from PRIDE: "2.1010 cells of VBD1674 strain at 4 h in meiosis were harvested, washed two times with ice-cold TNG buffer (50 mM Tris/HCl pH 8; 150...

Description from PRIDE: "To find differentially expressed protein in colorectal cancer compared with normal colon tissue, we performed global proteome analysis using LC-MS."

This dataset was generated to model discovery of uncommon and non-canonical PTM by agnostic analysis. Synthetic DFSAFILVEFCR peptides were obtained in three chemoforms, all with carbamidomethylated C12: 1) with unmodified phenylalanines, 2) with fluoro-F2, and 3) with fluoro-F11. Peptide composition and chemical modifications were confirmed using mass spectrometry. Peptides were analyzed in neat solvent...

Unanticipated regulatory protein modifications can be discovered from the unbiased comprehensive analysis of biological systems using SAMPEI. To explore this idea, we sought to map protein modifications induced during mammalian cell differentiation, modeled by the response of mouse RAW264.7 macrophage cells to lipopolysaccharide (LPS), a potent inducer of macrophage activation and differentiation...

This dataset was generated to parametrize and benchmark software for unbiased discovery of post-translationally modified peptides.

Inorganic phosphate is an essential nutrient acquired by cells from their environment. Here we characterize the adaptative responses of fission yeast to chronic phosphate starvation, during which cells enter a state of quiescence, initially fully reversible upon replenishing phosphate after 2 days but resulting in gradual loss of viability during 4 weeks of starvation. Time-resolved analyses of changes...