{"database":"iProX","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Piliang Hao"],"species":["Homo Sapiens","Escherichia Coli"],"full_dataset_link":["http://www.iprox.org/page/project.html?id=IPX0001174000"],"submitter_email":["haopl@shanghaitech.edu.cn"],"submitter_affiliation":["ShanghaiTech University"],"sample_protocol":[""],"repository":["iProX"],"data_protocol":[""],"pubmed_abstract":["High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation.<h4>Methods</h4>In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry.<h4>Results</h4>Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol.<h4>Conclusions</h4>The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol."],"pubmed_title":["Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation."],"pubmed_authors":["Lin Zhilong Z, Ren Yan Y, Shi Zhaomei Z, Zhang Keren K, Yang Huanming H, Liu Siqi S, Hao Piliang P"],"additional_accession":[]},"is_claimable":false,"name":"Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation","description":"Dataset for evaluation of nonspecific cleavages and  artificial modifications using E.coli and A549 cells","dates":{"publication":"Sun Jan 19 00:00:00 GMT 2020"},"accession":"PXD017186","cross_references":{"TAXONOMY":["562","9606"],"pubmed":["32031715"]}}