PXD053241

PXD053241 is an original dataset announced via ProteomeXchange.

Title	Unifying the analysis of bottom-up proteomics data with CHIMERYS
Description	Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography–tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent, data-independent or parallel reaction monitoring, separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in data-dependent, data-independent or parallel reaction monitoring experiments.
HostingRepository	PRIDE
AnnounceDate	2025-04-16
AnnouncementXML	Submission_2025-04-16_12:39:47.850.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martin Frejno
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Halobacterium salinarum; NCBI TaxID: 2242; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion Lumos; LTQ Orbitrap Velos; Orbitrap Exploris 480; Q Exactive HF-X; Q Exactive Plus; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-19 13:06:34	ID requested
⏵ 1	2025-04-16 12:39:48	announced

10.1038/S41592-025-02663-W;

submitter keyword: DIA, human, FDR, CHIMERYS, entrapment, multi-species,LC-MSMS, DDA

Martin Frejno
contact affiliation	MSAID GmbH
contact email	martin.frejno@msaid.de
lab head
Martin Frejno
contact affiliation	MSAID GmbH
contact email	martin.frejno@msaid.de
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/2025/04/PXD053241

PRIDE project URI

• PRIDE
  1. PXD053241
     1. Label: PRIDE project
     2. Name: Unifying the analysis of bottom-up proteomics data with CHIMERYS