PXD008029-1

PXD008029 is an original dataset announced via ProteomeXchange.

Title	An adaptive pipeline to maximize isobaric tagging data in large-scale MS-based proteomics
Description	Isobaric tagging is a method of choice in Mass Spectrometry (MS)-based proteomics for comparing multiple conditions at a time. Despite its multiplexing capabilities, when multiple experiments are merged for comparison in large sample-size studies, some drawbacks appears, due to the presence of missing values, which result from the stochastic nature of the Data-Dependent Acquisition (DDA) mode. Another indirect cause of data incompleteness might derive from the proteomic-typical data processing workflow that first identifies proteins in individual experiments and then only quantifies those identified proteins, leaving a large number of unmatched spectra with quantitative information unexploited. Inspired by untargeted metabolomic and label-free proteomic workflows, we developed a quantification-driven bioinformatic pipeline (Quantify then Identify – QtI) that optimizes the processing of isobaric Tandem Mass Tag (TMT) data from large-scale studies. This pipeline includes innovative modules, such as the Peptide Match Rescue (PMR) and the Optimized Post-Translational Modification (OPTM) and outperforms a classical benchmark workflow in terms of quantification and identification rates, significantly reducing missing data while preserving unmatched features for quantitative comparison. The number of unexploited tandem mass spectra was reduced by 77% and 62% for two human cerebrospinal fluid (CSF) and plasma datasets, respectively.
HostingRepository	PRIDE
AnnounceDate	2018-05-01
AnnouncementXML	Submission_2018-05-01_02:58:21.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008029
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Charlotte Macron
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Ammonia-loss; Deamidated; TMT6plex; Dehydrated; Oxidation; Acetyl; Carbamidomethyl
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-24 02:54:44	ID requested
⏵ 1	2018-05-01 02:58:23	announced
2	2024-10-22 04:41:25	announced	2024-10-22: Updated project metadata.

Corth, é, sy J, Theofilatos K, Mavroudi S, Macron C, Cominetti O, Remlawi M, Ferraro F, N, ú, ñ, ez Galindo A, Kussmann M, Likothanassis S, Dayon L, An Adaptive Pipeline To Maximize Isobaric Tagging Data in Large-Scale MS-Based Proteomics. J Proteome Res, 17(6):2165-2173(2018) [pubmed]

curator keyword: Technical

submitter keyword: Algorithms

Bioinformatics

Biomarkers

Discovery

Isobaric tagging

Machine learning

Protein identification

Quantification

Tandem mass spectrometry

Tandem mass tag

Loïc Dayon
contact affiliation	Proteomics Team Leader of Nestlé Institute of Health Sciences
contact email	loic.dayon@rd.nestle.com
lab head
Charlotte Macron
contact affiliation	NIHS
contact email	charlotte.macron@rd.nestle.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/2018/05/PXD008029

PRIDE project URI

• PRIDE
  1. PXD008029
     1. Label: PRIDE project
     2. Name: An adaptive pipeline to maximize isobaric tagging data in large-scale MS-based proteomics