{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/x01/MSV000080875/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":2,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"submitter":["Alexey I. Nesvizhskii"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=1c684d9c89074706b78449f10d259e2e"],"submitter_email":["nesvi@umich.edu"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["133"],"ptm_modification":["MOD:00425 - \"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\"","MOD:00397 - \"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["Q Exactive"],"species":["Homo Sapiens (ncbitaxon:9606)"],"submitter_affiliation":["University of Michigan, Ann Arbor, MI, US"],"pubmed_abstract":["We describe an improved version of the data-independent acquisition (DIA) computational analysis tool DIA-Umpire, and show that it enables highly sensitive, untargeted, and direct (spectral library-free) analysis of DIA data obtained using the Orbitrap family of mass spectrometers. DIA-Umpire v2 implements an improved feature detection algorithm with two additional filters based on the isotope pattern and fractional peptide mass analysis. The targeted re-extraction step of DIA-Umpire is updated with an improved scoring function and a more robust, semiparametric mixture modeling of the resulting scores for computing posterior probabilities of correct peptide identification in a targeted setting. Using two publicly available Q Exactive DIA datasets generated using HEK-293 cells and human liver microtissues, we demonstrate that DIA-Umpire can identify similar number of peptide ions, but with better identification reproducibility between replicates and samples, as with conventional data-dependent acquisition. We further demonstrate the utility of DIA-Umpire using a series of Orbitrap Fusion DIA experiments with HeLa cell lysates profiled using conventional data-dependent acquisition and using DIA with different isolation window widths."],"pubmed_title":["Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers."],"pubmed_authors":["Tsou Chih-Chiang CC, Tsai Chia-Feng CF, Teo Guo Ci GC, Chen Yu-Ju YJ, Nesvizhskii Alexey I AI"],"pubmed_abstract_synonyms":["293 cell, Networks, CDF, human being, Family Member, Kinship, GRP1/cytohesin 1, ion, determination, Feature, FBN, Network, Human, jecur, CG11633, peptide, cytohesin/GRP1, Polypeptides, POF, peptido, posterior, Homo sapiens, sensitive, ECTOL1, DmelCG1768, GRP1, Grp1, HILDA, Life Cycle, AGAMOUS-like 61, HEK 293, Human Embryonic Kidney 293, sensitivity, Man, WMS, DiA, Family Life Cycle, l(2)k07135, Kinship Network, Man (Taxonomy), peptides, Research, iones, PTPSTEP, HeLa, l(2)SH2 0323, iecur, purification, DIASP, ions, DIA, Dia, Probabilities, OCTD, allergic reaction, isolation and purification, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Neural-specific protein-tyrosine phosphatase, l(2)k08110, 38E.16, peptidos, Characteristics, DIA2, Kinship Networks, Family Life Cycles, Family, GPHYSD2, posterior end of organism, SGS, GPH, 293 HEK, Family Research, Desmoplastic astrocytoma of infancy, Modern, stepk, function, CG1768, Mischung, DRF2, isolation., Peptide, Cell, ACMICD, Family Members, polypeptide, Isotope, ms(2)04138, Desmoplastic infantile astrocytoma, Characteristic, HeLa Cell, Ionen, Algorithm, MLPLI, chemical analysis, 3.1.3.48, MFS1, HELA cell, Dias, Filiation, l(2)SH0323, WMS2, CYH1, DDA, Step, CG11628, 293, POF2, F27C12_24, F27C12.24, HEK293, Striatum-enriched protein-tyrosine phosphatase, MASS, HEK-293, Features, human, DmelCG11628, Life Cycles, Livers, Ion, STEP, Families, Modern Man, SSKS, Cells, DIANA, Peptid, assay, Polypeptide, Relatives, humans"],"name_synonyms":["CDF, l(2)k07135, determination, Peptidomics, POF2, F27C12_24, Desmoplastic astrocytoma of infancy, F27C12.24, FBN, MASS, CG1768, DIASP, DRF2, DIA, ACMICD, OCTD, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, ms(2)04138, Desmoplastic infantile astrocytoma, POF, ECTOL1, DmelCG1768, chemical analysis, SSKS, MLPLI, DIANA, 38E.16, HILDA, Dia., MFS1, AGAMOUS-like 61, assay, DIA2, Dias, GPHYSD2, WMS, WMS2, DiA, SGS"],"pubmed_title_synonyms":["ACMICD, OCTD, determination, Peptidomics, ECTOL1, chemical analysis, FBN, MFS1, assay, MASS, GPHYSD2, WMS, DIA, WMS2, SGS, SSKS."],"description_synonyms":["CDF, l(2)k07135, determination, Peptidomics, POF2, F27C12_24, Desmoplastic astrocytoma of infancy, F27C12.24, FBN, MASS, CG1768, DIASP, DRF2, DIA, ACMICD, OCTD, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, ms(2)04138, Desmoplastic infantile astrocytoma, POF, ECTOL1, DmelCG1768, chemical analysis, SSKS, MLPLI, DIANA, 38E.16, HILDA, Dia., MFS1, AGAMOUS-like 61, assay, DIA2, Dias, GPHYSD2, WMS, WMS2, DiA, SGS"],"citation_count":["2"],"additional_accession":["PXD003179"]},"is_claimable":true,"name":"Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire","description":"Untargeted data independent acquisition proteomics analysis using Orbitrap mass spectrometers and DIA-Umpire","dates":{"publication":"Sat Apr 01 04:29:00 BST 2017"},"accession":"MSV000080875","cross_references":{"pubmed":["27246681"]}}