PXD004188

PXD004188 is an original dataset announced via ProteomeXchange.

Title	High precision iRT retention time prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation
Description	Targeted analysis of DIA data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires a spectral library, which contains for all considered peptide precursor ions empirically determined fragment ion intensities and their predicted retention time. Retention times, however, are not comparable on an absolute scale, especially if heterogeneous measurements are combined. Here we present a method for high-precision prediction of retention time, which significantly improves the quality of targeted DIA analysis compared to in silico retention time prediction and the state of the art indexed retention time (iRT) normalization approach. We describe a high precision normalized retention time algorithm, which is implemented in the Spectronaut software. We furthermore investigate the influence of nine different experimental factors, such as chromatographic mobile and stationary phase, on iRT precision. In summary we show that using targeted analysis of DIA data with high precision iRT significantly increases sensitivity and data quality. The iRT values are generally transferable across a wide range of experimental conditions. Best results, however, are achieved if library generation and analytical measurements are performed on the same system.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:29:39.694.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roland Bruderer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-19 04:23:02	ID requested
1	2016-07-14 06:30:37	announced
⏵ 2	2024-10-22 04:29:43	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201500488;

Bruderer R, Bernhardt OM, Gandhi T, Reiter L, High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation. Proteomics, 16(15-16):2246-56(2016) [pubmed]

curator keyword: Technical

submitter keyword: DIA,Retention time prediction

Lukas Reiter
contact affiliation	Biognosys AG, Schlieren, Schweiz
contact email	lukas.reiter@biognosys.ch
lab head
Roland Bruderer
contact affiliation	Biognosys AG
contact email	roland.bruderer@biognosys.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/2016/07/PXD004188

PRIDE project URI

• PRIDE
  1. PXD004188
     1. Label: PRIDE project
     2. Name: High precision iRT retention time prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation