PXD020901

PXD020901 is an original dataset announced via ProteomeXchange.

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

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.

10.1021/acs.jproteome.0c00355;

Wiles TA, Saba LM, Delong T, Peptide-Spectrum Match Validation with Internal Standards (P-VIS): Internally-Controlled Validation of Mass Spectrometry-Based Peptide Identifications. J Proteome Res, 20(1):236-249(2021) [pubmed]

submitter keyword: peptidomics, hybrid insulin peptides,peptide-spectrum match, post-translational modification, validation, immunotherapy, peptide splicing, immunopeptidomics

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

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

• PRIDE
  1. PXD020901
     1. Label: PRIDE project
     2. Name: P-VIS: internally-controlled validation of mass spectrometry-based peptide identifications