{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kitata RB"],"funding":["Ministry of Science and Technology, Taiwan","NCI NIH HHS","NIGMS NIH HHS"],"pagination":["2539"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8099862"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["12(1)"],"pubmed_abstract":["Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values."],"journal":["Nature communications"],"pubmed_title":["A data-independent acquisition-based global phosphoproteomics system enables deep profiling."],"pmcid":["PMC8099862"],"funding_grant_id":["R01 GM094231","U24 CA210967","MOST 107-2113-M-001-023-MY3"],"pubmed_authors":["Lin PY","Tsai CF","Sung TY","Kitata RB","Choong WK","Chen BS","Chen YJ","Nesvizhskii AI","Chang YC"],"additional_accession":[]},"is_claimable":false,"name":"A data-independent acquisition-based global phosphoproteomics system enables deep profiling.","description":"Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve deep and robust quantitative phosphoproteomics profiling for minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within two hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values.","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 May","modification":"2025-04-26T07:25:12.309Z","creation":"2025-04-06T12:16:30.875Z"},"accession":"S-EPMC8099862","cross_references":{"pubmed":["33953186"],"doi":["10.1038/s41467-021-22759-z"]}}