PXD024584

PXD024584 is an original dataset announced via ProteomeXchange.

Title	Pipelines and Systems for Threshold Avoiding Quantification of LC-MS/MS data
Description	The accurate processing of complex LC-MS/MS data from biological samples is a major challenge for metabolomics, proteomics and related approaches. Here we present the Pipelines and Systems for Threshold Avoiding Quantification (PASTAQ) LC-MS/MS pre-processing toolset, which allows highly accurate quantification of data-dependent acquisition (DDA) LC-MS/MS datasets. PASTAQ performs compound quantification using single-stage (MS1) data and implements novel algorithms for high-performance and accurate quantification, retention time alignment, feature detection, and linking annotations frommultiple identification engines. PASTAQ offers straightforward parametrization and automatic generation of quality control plots for data and pre-processing assessment. This design results in smaller variance when analyzing replicates of proteomes mixed with known ratios, and allows the detection of peptides with a larger dynamic concentration range compared to widely used proteomics preprocessing tools. The performance of the pipeline is also demonstrated in a biological human serum dataset for the identification of gender related proteins.
HostingRepository	PRIDE
AnnounceDate	2021-08-18
AnnouncementXML	Submission_2021-08-18_05:09:04.698.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024584
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Horvatovich Péter
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-08 04:47:00	ID requested
⏵ 1	2021-08-18 05:09:05	announced

S, á, nchez Brotons A, Eriksson JO, Kwiatkowski M, Wolters JC, Kema IP, Barcaru A, Kuipers F, Bakker SJL, Bischoff R, Suits F, Horvatovich P, Pipelines and Systems for Threshold-Avoiding Quantification of LC-MS/MS Data. Anal Chem, 93(32):11215-11224(2021) [pubmed]

submitter keyword: LC-MS/MS pre-processing, proteomics, label-free, isotope quantification

Peter Horvatovich
contact affiliation	University of Groningen, Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
contact email	p.l.horvatovich@rug.nl
lab head
Horvatovich Péter
contact affiliation	Faculty of Mathematics and Natural Sciences, Department of Pharmacy, Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
contact email	p.l.horvatovich@rug.nl
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/2021/08/PXD024584

PRIDE project URI

• PRIDE
  1. PXD024584
     1. Label: PRIDE project
     2. Name: Pipelines and Systems for Threshold Avoiding Quantification of LC-MS/MS data