Proteomics

Dataset Information

0

Protamine characterization by top-down proteomics: Boosting proteoform identification with DBSCAN

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Semen

SUBMITTER: Marina Gay  

LAB HEAD: Marta Vilaseca

PROVIDER: PXD024405 | Pride | 2021-05-13

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
3506_AS_SiP_PRM_Uniprot_Mox_Phos_STY_ThreeTier_newname_PrSMs.txt Txt
A_R01.raw Raw
A_R02.raw Raw
B_R03.raw Raw
B_R04.raw Raw
Items per page:
1 - 5 of 6
altmetric image

Publications

Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN.

Arauz-Garofalo Gianluca G   Jodar Meritxell M   Vilanova Mar M   de la Iglesia Rodriguez Alberto A   Castillo Judit J   Soler-Ventura Ada A   Oliva Rafael R   Vilaseca Marta M   Gay Marina M  

Proteomes 20210430 2

Protamines replace histones as the main nuclear protein in the sperm cells of many species and play a crucial role in compacting the paternal genome. Human spermatozoa contain protamine 1 (P1) and the family of protamine 2 (P2) proteins. Alterations in protamine PTMs or the P1/P2 ratio may be associated with male infertility. Top-down proteomics enables large-scale analysis of intact proteoforms derived from alternative splicing, missense or nonsense genetic variants or PTMs. In contrast to curr  ...[more]

Similar Datasets

Proteomics Characterization of human sperm protamine proteoforms through a combination of top-down and bottom-up mass spectrometry approaches
2019-11-11 | PXD014618 | Pride
Proteomics Revealing Corynebacterium glutamicum proteoforms through top-down proteomics
2022-12-10 | PXD038038 | Pride
Proteomics Capillary Zone Electrophoresis-High Field Asymmetric Ion Mobility Spectrometry-Tandem Mass Spectrometry for Top-down Characterization of Histone Proteoforms
2023-12-07 | PXD041357 | Pride
Proteomics Predicting electrophoretic mobility of proteoforms for large-scale top-down proteomics
2020-02-17 | PXD017265 | Pride
Proteomics Capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics of mouse brain integral membrane proteins
2023-12-07 | PXD042298 | Pride
Genomics Developmentally regulated isoform of HNF4α reprograms the adult liver
2023-05-10 | GSE231538 | GEO
Proteomics Large-scale Top-down Proteomics of the Arabidopsis thaliana Leaf and Chloroplast Proteomes
2023-01-05 | PXD034368 | Pride
Proteomics Capillary zone electrophoresis-tandem mass spectrometry with activated ion electron transfer dissociation for large-scale top-down proteomics
2019-06-11 | PXD012247 | Pride
Transcriptomics Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamine 1 [scRNA-Seq]
2023-05-09 | GSE225270 | GEO
Methylation profiling Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse Protamine 1 [MNase-Seq]
2023-05-09 | GSE225268 | GEO