PXD028558

PXD028558 is an original dataset announced via ProteomeXchange.

Title	APIR: a universal FDR-control framework for boosting peptide identification power by aggregating multiple proteomics database search algorithms
Description	Advances in mass spectrometry (MS) have enabled high-throughput analysis of proteomes in biological systems. The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide-spectrum matches (PSMs), which convert mass spectra to peptide sequences. Different database search algorithms use distinct search strategies and thus may identify unique PSMs. However, no existing approaches can aggregate all user-specified database search algorithms with guaranteed control on the false discovery rate (FDR) and guaranteed increase in the identified peptides. To fill in this gap, we propose a statistical framework, Aggregation of Peptide Identification Results (APIR), that is universally compatible with all database search algorithms. Notably, under a target FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual database search algorithms do. Evaluation of APIR on a complex protein standard shows that APIR outpowers individual database search algorithms and guarantees the FDR control. Realdata studies show that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms. Note that the APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis, e.g., differential gene expression analysis on RNA sequencing data.
HostingRepository	PRIDE
AnnounceDate	2021-09-21
AnnouncementXML	Submission_2021-09-20_23:34:25.685.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yiling Chen
SpeciesList	scientific name: Pyrococcus furiosus; NCBI TaxID: 2261;
ModificationList	methylthiolated residue; monohydroxylated residue; deaminated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-16 07:40:07	ID requested
⏵ 1	2021-09-20 23:34:26	announced

Dataset with its publication pending

submitter keyword: Pyrococcus furiosus (Pfu), complex proteomic standard, proteomics

Leo David Wang
contact affiliation	Departments of Pediatrics and Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte CA 91010
contact email	lewang@coh.org
lab head
Yiling Chen
contact affiliation	University of California, Los Angeles
contact email	yiling0210@ucla.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/2021/09/PXD028558

PRIDE project URI

• PRIDE
  1. PXD028558
     1. Label: PRIDE project
     2. Name: APIR: a universal FDR-control framework for boosting peptide identification power by aggregating multiple proteomics database search algorithms