Dataset Information

P-VIS: internally-controlled validation of mass spectrometry-based peptide identifications

ABSTRACT: 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.

INSTRUMENT(S): 6550 iFunnel Q-TOF LC/MS

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

SUBMITTER: Timothy Wiles

LAB HEAD: Thomas Delong

PROVIDER: PXD020901 | Pride | 2020-09-21

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	200727_benchmarking_nano_rpt1_PVISresults.zip	Other
	200728_benchmarking_nano_rpt2_PVISresults.zip	Other
	200729_benchmarking_nano_rpt3_PVISresults.zip	Other
	200806_benchmarking_micro_rpt2_PVISresults.zip	Other
	200807_benchmarking_micro_rpt3_PVISresults.zip	Other

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Publications

Peptide-Spectrum Match Validation with Internal Standards (P-VIS): Internally-Controlled Validation of Mass Spectrometry-Based Peptide Identifications.

Wiles Timothy Aaron TA Saba Laura M LM Delong Thomas T

Journal of proteome research 20200929 1

Liquid chromatography-tandem mass spectrometry is an increasingly powerful tool for studying proteins in the context of disease. As technological advances in instrumentation and data analysis have enabled deeper profiling of proteomes and peptidomes, the need for a rigorous, standardized approach to validate individual peptide-spectrum matches (PSMs) has emerged. To address this need, we developed a novel and broadly applicable workflow: PSM validation with internal standards (P-VIS). In this ap ...[more]

PMID: 32924495

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