PXD014913

PXD014913 is an original dataset announced via ProteomeXchange.

Title	Automated identification of the Cowpox virus (Brighton Red) strain in HEp-2 cells using nLC-MS/MS spectra
Description	Accompanying benchmarking sample for "TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples": Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to non-iterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:03:27.700.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mathias Kuhring
SpeciesList	scientific name: Cowpox virus (Brighton Red); NCBI TaxID: 265872; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Discovery

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-05 02:22:36	ID requested
1	2020-05-10 22:18:37	announced
⏵ 2	2024-10-22 05:03:29	announced	2024-10-22: Updated project metadata.

Kuhring M, Doellinger J, Nitsche A, Muth T, Renard BY, TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples. J Proteome Res, 19(6):2501-2510(2020) [pubmed]

10.1021/acs.jproteome.9b00714;

submitter keyword: Cowpox virus (Brighton Red), Human, nLC-MS/MS

Bernhard Y. Renard
contact affiliation	Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
contact email	RenardB@rki.de
lab head
Mathias Kuhring
contact affiliation	Robert Koch Institute
contact email	mathias.kuhring@live.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/2020/05/PXD014913

PRIDE project URI

• PRIDE
  1. PXD014913
     1. Label: PRIDE project
     2. Name: Automated identification of the Cowpox virus (Brighton Red) strain in HEp-2 cells using nLC-MS/MS spectra