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PXD011353 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePROTEOFORMER 2.0: MS validation
DescriptionPROTEOFORMER is a pipeline for generating a search space of candidate translation products based on ribosome profiling data. The pipeline was published in 2014, but since then, several features have been added. For this project, the PROTEOFORMER pipeline 2.0 was tested on human HCT116 and Jurkat cell ribosome profiling data with all its new features and then compared to raw MS data of both cell lines, validating its use as a proteogenomic tool. In this study, results of 3 proteoform calling methods were combined (classical PROTEOFORMER proteoform calling, PRICE and SPECtre). Afterwards, results were eventually combined with the canonical or splicing-included version of human UniProt. The different described combinations were exported as a FASTA file and used as search space for searching matching MS data.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSteven Verbruggen
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; acetylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-10-15 02:01:55ID requested
12019-05-03 13:37:56announced
Publication List
Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G, PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Mol Cell Proteomics, 18(8 suppl 1):S126-S140(2019) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: HCT116, Jurkat, MSMS, PROTEOFORMER
Contact List
Gerben Menschaert
contact affiliationBioBix, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, Belgium
contact emailGerben.Menschaert@UGent.be
lab head
Steven Verbruggen
contact affiliationBioBix
contact emailSteven.Verbruggen@UGent.be
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
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