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PXD020901

PXD020901 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleP-VIS: internally-controlled validation of mass spectrometry-based peptide identifications
DescriptionPeptide-Spectrum Match (PSM) Validation with Internal Standards (P-VIS) is an objective approach to validating individual PSMs. A biological sample is analyzed by LC-MS/MS and the data are searched using a traditional approach such as a database search or de novo sequencing. A PSM of interest is identified, and a synthetic version of the putative peptide is obtained. Internal standard peptides (ISPs) are spiked into both the biological sample and the validation peptide sample and both samples are analyzed by LC-MS/MS. Using PSM_validator (https://github.com/Delong-Lab/PSM_validator/releases), an open-source program we created to implement the P-VIS workflow, both the fragmentation spectrum and the chromatographic retention time for the peptide of interest in the biological sample are compared to those of the validation peptide. The same comparisons are made for each of the ISPs, and these results are used to establish a prediction interval for valid matches. If the values for the comparisons between the biological and validation peptide fall within the prediction intervals, the match is considered valid. This submission contains the data and P-VIS results from a study aimed at benchmarking the P-VIS workflow.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:12:29.341.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTimothy Wiles
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
Instrument6550 iFunnel Q-TOF LC/MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-08-13 22:42:56ID requested
12020-09-20 23:10:53announced
22024-10-22 05:12:30announced2024-10-22: Updated project metadata.
Publication List
10.1021/acs.jproteome.0c00355;
Keyword List
submitter keyword: peptidomics, hybrid insulin peptides,peptide-spectrum match, post-translational modification, validation, immunotherapy, peptide splicing, immunopeptidomics
Contact List
Thomas Delong
contact affiliationDepartment of Pharmaceutical Sciences University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences
contact emailthomas.delong@cuanschutz.edu
lab head
Timothy Wiles
contact affiliationUniversity of Colorado
contact emailtimothy.wiles@ucdenver.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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