PXD022778-1

PXD022778 is an original dataset announced via ProteomeXchange.

Title	Improving power while controlling the false discovery rate when only a subset of peptides are relevant
Description	The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are reDR control strategies are needed. Recently, two methods were proposed to address this problem: subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of “neighbor” peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. Not considering neighbors compromises the FDR estimate because a spectrum generated by an irrelevant peptide can incorrectly match well to a relevant peptide. Therefore, we have developed a new method, “filter then subset-neighbor search” (FSNS), that accounts for neighbor peptides. We show evidence that FSNS properly controls the FDR when neighbors are present and that FSNS outperforms group-FDR, the only other method able to control the FDR relative to a subset of relevant peptides
HostingRepository	PRIDE
AnnounceDate	2021-06-18
AnnouncementXML	Submission_2021-06-18_03:55:24.402.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andy Lin
SpeciesList	scientific name: Ricinus communis (Castor bean); NCBI TaxID: 3988; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos; LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-26 22:52:51	ID requested
⏵ 1	2021-06-18 03:55:24	announced
2	2021-07-11 21:51:33	announced	2021-07-12: Updated project metadata.

Dataset with its publication pending

submitter keyword: human, yeast, UPS1, castor, ricin

Willian Stafford Noble
contact affiliation	University of Washington
contact email	william-noble@uw.edu
lab head
Andy Lin
contact affiliation	University of Washington
contact email	linandy@uw.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/2021/06/PXD022778

PRIDE project URI

• PRIDE
  1. PXD022778
     1. Label: PRIDE project
     2. Name: Improving power while controlling the false discovery rate when only a subset of peptides are relevant