PXD040449-2

PXD040449 is an original dataset announced via ProteomeXchange.

Title	A causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics
Description	We thoroughly characterize isobaric labeling (TMT)-associated reporter ion interference at the MS2 level using a defined two-proteome experimental system with known ground truth. We discover remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2-scans - a discrepancy that we find resolved by considering co-fragmentation of peptide ions hidden within the spectral “noise” of the MS1 isolation window. On this basis, we establish a comprehensive regression modeling strategy for predicting accurate, feature-wise estimates of reporter ion interference. Finally, we demonstrate the utility of accurate ion purity estimates for accurate fold change estimation and unbiased PTM site-to-protein normalization.
HostingRepository	PRIDE
AnnounceDate	2024-04-02
AnnouncementXML	Submission_2024-04-02_06:41:05.561.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Moritz Madern
SpeciesList	scientific name: Saccharomyces cerevisiae; NCBI TaxID: NCBITaxon:4932; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	phosphorylated residue; acetylated residue
Instrument	Orbitrap Eclipse; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-27 06:08:54	ID requested
1	2023-12-19 03:38:17	announced
⏵ 2	2024-04-02 06:41:06	announced	2024-04-02: Updated project metadata.
3	2024-10-22 06:18:04	announced	2024-10-22: Updated project metadata.

10.1016/J.MCPRO.2023.100694;

10.1016/j.mcpro.2023.100694;

Madern M, Reiter W, Stanek F, Hartl N, Mechtler K, Hartl M, A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics. Mol Cell Proteomics, 23(1):100694(2024) [pubmed]

submitter keyword: ion interference, TMT, ratio compression,isobaric label

Markus Hartl
contact affiliation	Mass Spectrometry Facility, Max Perutz Labs Vienna, University of Vienna, Vienna Biocenter, Dr.-Bohr-Gasse 7, 1030 Vienna
contact email	markus.hartl@univie.ac.at
lab head
Moritz Madern
contact affiliation	Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna
contact email	moritz.madern@gmx.at
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/2023/12/PXD040449

PRIDE project URI

• PRIDE
  1. PXD040449
     1. Label: PRIDE project
     2. Name: A causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics