PXD057758-1

PXD057758 is an original dataset announced via ProteomeXchange.

Title	Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation
Description	We present a method for FDR control of PIP, called “PIP-ECHO” (PIP Error Control via Hybrid cOmpetition) and devise a rigorous protocol for evaluating FDR control of any PIP method. Using three different datasets, we evaluate PIP-ECHO alongside the PIP procedures implemented by FlashLFQ, IonQuant, and MaxQuant. These analyses show that PIP-ECHO can accurately control the FDR of PIP at 1% across multiple datasets. Only PIP-ECHO was able to control the FDR in data with injected sample size equivalent to a single-cell dataset. The three other methods fail to control the FDR at 1%, yielding false discovery proportions ranging from 2-6%. We demonstrate the practical implications of this work by performing differential expression analyses on spike-in datasets, where different known amounts of yeast or E. coli peptides are added to a constant background of HeLa cell lysate peptides. In this setting, PIP-ECHO increases both the accuracy and sensitivity of differential expression analysis: our implementation of PIP-ECHO within FlashLFQ can detect twice as many differentially abundant proteins as MaxQuant and three times as many as IonQuant in the spike-in dataset. This repository contains the raw data for one of the datasets used to evaluate the error rate of PIP, as well as the database search and quantitative results obtained for all of the datasets examined.
HostingRepository	PRIDE
AnnounceDate	2025-10-06
AnnouncementXML	Submission_2025-10-05_18:06:30.172.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD057758
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Solivais
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-11 12:58:44	ID requested
⏵ 1	2025-10-05 18:06:31	announced

10.1021/acs.jproteome.5c00065;

Solivais AJ, Boekweg H, Smith LM, Noble WS, Shortreed MR, Payne SH, Keich U, Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation. J Proteome Res, 24(9):4437-4449(2025) [pubmed]

10.6019/PXD057758;

submitter keyword: MBR, E. coli, Human,LFQ, Quantification, PIP

Lloyd M. Smith
contact affiliation	University of Wisconsin - Madison
contact email	smith@chem.wisc.edu
lab head
Alexander Solivais
contact affiliation	University of Wisconsin-Madison
contact email	alexsolivais@gmail.com
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/2025/10/PXD057758

PRIDE project URI

• PRIDE
  1. PXD057758
     1. Label: PRIDE project
     2. Name: Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation