Proteomics

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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

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3506_AS_SiP_PRM_Uniprot_Mox_Phos_STY_ThreeTier_newname_PrSMs.txt Txt
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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]

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