Protein citrullination in human tissues

ABSTRACT: Citrullination is a post-translational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations and while the modification has been linked to several diseases including rheumatoid arthritis and cancer, its physiological or pathophysiological roles remain largely unclear. In part this is owing to limitations in available methodology able to robustly enrich, detect and localize the modification. As a result, only few citrullination sites have been identified on human proteins with high confidence. In this study, we mined data from mass spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Database searching of ~70 million tandem mass spectra yielded ~13,000 candidate spectra which were further triaged by spectrum quality metrics and the detection of the specific neutral loss of isocyanic acid from citrullinated peptides to reduce false positives. Because citrullination is easily confused with deamidation, we synthetised ~2,200 citrullinated and 1,300 deamindated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new and for 56% of the proteins, citrullination was detected for the first time. Sequence motif analysis revealed a strong preference for Asp and Gly, residues around the citrullination site. Interestingly, while the modification was detected in 26 human tissues with the highest levels found in brain and lung, citrullination levels did not correlate well with protein expression of the PAD enzymes. Even though the current work represents the largest survey of protein citrullination to date, the modification was mostly detected on high abundance proteins arguing that the development of specific enrichment methods would be required in order to study the full extent of cellular protein citrullination.

OTHER RELATED OMICS DATASETS IN: MODEL1109130000 MODEL1311110000 MODEL1909260003 MODEL1311110001 MODEL1909260004 MODEL1703310000 MODEL1909260005 MODEL1909260006

INSTRUMENT(S): Thermo Scientific instrument model, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Heart, Testis, Brain, Liver, Lung, Uterine Endometrium, Lymph Node, Vermiform Appendix, Salivary Gland, Smooth Muscle, Kidney, Ovary, Colon, Pancreas, Bone Marrow, Spleen, Stomach, Duodenum, Tonsil, Gall Bladder, Fat Body, Esophagus, Placenta, Rectum, Urinary Bladder, Adrenal Gland, Small Intestine

SUBMITTER: Chien-Yun Lee  

LAB HEAD: Bernhard Kuster

PROVIDER: PXD008970 | Pride | 2018-04-04

REPOSITORIES: Pride