PXD020901 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | P-VIS: internally-controlled validation of mass spectrometry-based peptide identifications |
Description | Peptide-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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_05:12:29.341.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Timothy Wiles |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | 6550 iFunnel Q-TOF LC/MS |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-08-13 22:42:56 | ID requested | |
1 | 2020-09-20 23:10:53 | announced | |
⏵ 2 | 2024-10-22 05:12:30 | announced | 2024-10-22: Updated project metadata. |
Publication List
Keyword List
submitter keyword: peptidomics, hybrid insulin peptides,peptide-spectrum match, post-translational modification, validation, immunotherapy, peptide splicing, immunopeptidomics |
Contact List
Thomas Delong |
contact affiliation | Department of Pharmaceutical Sciences University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences |
contact email | thomas.delong@cuanschutz.edu |
lab head | |
Timothy Wiles |
contact affiliation | University of Colorado |
contact email | timothy.wiles@ucdenver.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/09/PXD020901 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD020901
- Label: PRIDE project
- Name: P-VIS: internally-controlled validation of mass spectrometry-based peptide identifications