PXD024405

PXD024405 is an original dataset announced via ProteomeXchange.

Title	Protamine characterization by top-down proteomics: Boosting proteoform identification with DBSCAN
Description	Protamines replace histones as the main nuclear protein in sperm cells having a crucial role in compacting the paternal genome. Human spermatozoa contain the protamine 1 (P1) and the family of protamine 2 (P2) proteins. Alterations in protamine PTMs or on the P1/P2 ratio could be associated with male infertility. Top-down proteomics enables large-scale analysis of intact proteforms derived from alternative splicing, missense or nonsense genetic variants or PTMs. In contrast to current gold standard techniques, top-down allows a more in-depth analysis of protamine PTMs and proteoforms, opening up new perspectives to unravel their impact on male fertility. We analyzed two normozoospermic semen samples by top-down and discussed in detail the difficulties we found in the data analysis and the suggested solutions, as this step is one of the current bottlenecks in top-down proteomics with currently available bioinformatic tools. Our strategy for the data analysis combines two different software, ProSight PD (PS) and TopPIC suite (TP), with a clustering algorithm to decipher protamine proteoforms. We identified up to 32 protamine proteoforms at different levels of characterization. This in-depth analysis of the protamine proteoform landscape of an individual boosts personalized diagnosis of male infertility.
HostingRepository	PRIDE
AnnounceDate	2021-05-13
AnnouncementXML	Submission_2021-05-13_02:55:12.813.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marina Gay
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	O4'-phospho-L-tyrosine; O-phospho-L-threonine; monohydroxylated residue; O-phospho-L-serine; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-26 06:21:43	ID requested
⏵ 1	2021-05-13 02:55:13	announced

Arauz-Garofalo G, Jodar M, Vilanova M, de la Iglesia Rodriguez A, Castillo J, Soler-Ventura A, Oliva R, Vilaseca M, Gay M, Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN. Proteomes, 9(2):(2021) [pubmed]

submitter keyword: Male Infertility

Sperm

Protamine

LC-MS/MS

Top Down Proteomics

Proteoform

Post-Translational Modifications

Bioinformatics

DBSCAN.

Marta Vilaseca
contact affiliation	Mass Spectrometry and Proteomics Core Facility Institute for Research in Biomedicine (IRB Barcelona)
contact email	marta.vilaseca@irbbarcelona.org
lab head
Marina Gay
contact affiliation	Institute for Research in Biomedicine
contact email	marina.gay@irbbarcelona.org
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/2021/05/PXD024405

PRIDE project URI

• PRIDE
  1. PXD024405
     1. Label: PRIDE project
     2. Name: Protamine characterization by top-down proteomics: Boosting proteoform identification with DBSCAN