PXD022124

PXD022124 is an original dataset announced via ProteomeXchange.

Title	A Bothrops jararaca venom subproteome to benchmark a spectral clustering algorithm by controlling the selection bias
Description	The clustering of mass spectra is a critical component of many proteomics applications. The clustering validation science is just as important, having evolved side by side with the clustering algorithms themselves. In this work, we build on Rieder et al. 's cluster validation framework, and we discuss the problem of selection bias in cluster validation measures; we introduce an assessment measure that is biased toward the number of peptide ion species; we introduce a cluster assessment framework for proteomics and demonstrate its importance by evaluating the performance of 8 clustering algorithms in 7 proteomics datasets, and we discuss the tradeoff between assessment measures. Finally, the validation methods presented here can be of broad applicability be-yond the clustering of mass spectra. This PRIDE entry describes in detail sample preparation, LC-MS/MS analysis, and protein identification of one of the proteomics datasets used in this work (> 10 kDa Bothrops jararaca snake venom proteome).
HostingRepository	PRIDE
AnnounceDate	2022-03-16
AnnouncementXML	Submission_2022-03-16_03:04:28.609.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Hemmi Valente
SpeciesList	scientific name: Bothrops jararaca; NCBI TaxID: 8724;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-21 22:31:53	ID requested
⏵ 1	2022-03-16 03:04:29	announced

Silva ARF, Lima DB, Kurt LU, Dupr, é M, Chamot-Rooke J, Santos MDM, Nicolau CA, Valente RH, Barbosa VC, Carvalho PC, Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra. J Proteomics, 245():104282(2021) [pubmed]

submitter keyword: Venomics, Bothrops jararaca, Spectral clustering, Algorithm

Richard Hemmi Valente
contact affiliation	Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
contact email	richardhemmi@gmail.com
lab head
Richard Hemmi Valente
contact affiliation	Fundação Oswaldo Cruz
contact email	richardhemmi@gmail.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/2022/03/PXD022124

PRIDE project URI

• PRIDE
  1. PXD022124
     1. Label: PRIDE project
     2. Name: A Bothrops jararaca venom subproteome to benchmark a spectral clustering algorithm by controlling the selection bias