PXD034534

PXD034534 is an original dataset announced via ProteomeXchange.

Title	IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides
Description	In mass spectrometry (MS)-based quantitative proteomics, labeling with isobaric mass tags such as iTRAQ and TMT can substantially improve sample throughput and reduce peptide missing values. Nonetheless, the quantification of labeled peptides tends to suffer from reduced quantitative accuracy due to the co-isolation of co-eluting precursors of similar mass-to-charge. Acquisition approaches such as MS3 level quantification or ion mobility separation address this problem, yet are difficult to audit and limited to expensive instrumentation. Here we introduce IsobaricQuant, an open-source software tool for the quantification, visualization, and filtering of peptides labeled with isobaric mass tags, with specific focus on precursor interference. IsobaricQuant is compatible with MS2- and MS3 level acquisition strategies, has a viewer that allows assessing interference, and provides several scores to aid the filtering of scans with compression. We demonstrate that IsobaricQuant quantifications are accurate by comparing it with commonly used software. We further show that its QC scores can successfully filter scans with reduced quantitative accuracy at MS2- and MS3 level, removing inaccurate peptide quantifications and decreasing protein CVs. Finally, we apply IsobaricQuant to a PISA dataset and show that QC scores improve the sensitivity of the identification of protein targets of a kinase inhibitor. IsobaricQuant is available at https://github.com/Villen-Lab/isobaricquant.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:57:16.113.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexander Hogrebe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-15 03:56:35	ID requested
1	2022-07-11 16:37:23	announced
⏵ 2	2023-11-14 08:57:19	announced	2023-11-14: Updated project metadata.

Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA, TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat Methods, 17(4):399-404(2020) [pubmed]

Paulo JA, Navarrete-Perea J, Gygi SP, Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT. J Proteomics, 210():103531(2020) [pubmed]

Navarrete-Perea J, Gygi SP, Paulo JA, HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments. J Am Soc Mass Spectrom, 32(1):247-254(2021) [pubmed]

submitter keyword: reanalysis

Judit Villen
contact affiliation	Department of Genome Sciences, University of Washington, USA
contact email	jvillen@uw.edu
lab head
Alexander Hogrebe
contact affiliation	MSAID GmbH
contact email	ahogrebe@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/2022/07/PXD034534

PRIDE project URI

• PRIDE
  1. PXD034534
     1. Label: PRIDE project
     2. Name: IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides