PXD000575

PXD000575 is an original dataset announced via ProteomeXchange.

Title	Mouse Acrosomal Matrix LC-MS/MS
Description	A critical step during fertilization is the sperm acrosome reaction in which the acrosome releases its contents allowing the spermatozoa to penetrate the egg investments. The sperm acrosomal contents are composed of both soluble material and an insoluble material called the acrosomal matrix (AM). The AM is thought to provide a stable structure from which associated proteins are differentially released during fertilization. Mouse acrosomal matrices were isolated from 2 different populations of epididymal spermatozoa: AM_caput from caput epididymal spermatozoa (2 replicates) and AM_cauda from cauda epididymal spermatozoa (3 replicates). Proteins were separated by SDS-PAGE on a 15% polyacrylamide gel. After electrophoresis, proteins were stained with Coomassie blue. Gel lanes were cut into 8–9 slices and each slice placed into a 0.5 ml microcentrifuge tube. The gel pieces were washed to destain the gels. Reduction was performed with dithiothreitol solution. After reduction, the proteins were alkylated. The gel pieces were washed, dehydrated and air-dried. The digestion was proceed with trypsin and peptides extracted. The peptides obtained from in-gel digestion were analyzed by nano-flow nano-LC-MS/MS using an LTQ-XL ion trap mass spectrometer. To get the maximum number of publicly available sequences for analyses, the mouse sequences from Ensembl were merged with those from NCBI. The database was built using BioPerl modules. Specifically, from Ensembl two files were downloaded and merged including Mus_musculus.NCBIM37.64.pep.all.fa.gz (containing the superset of all translations resulting from Ensembl known or novel gene predictions) and Mus_musculus.NCBIM37.64.pep.abinitio.fa.gz (containing translations resulting from “ab initio” gene prediction algorithms such as SNAP and GENSCAN). From NCBI, the nonredundant (nr) file (on 11/2011) was downloaded and mouse sequences extracted (Taxonomy ID = 10090). This file was merged with the Ensembl sequences to create a file containing 356,881 sequences of which some were redundant. Duplicates were removed based on identical amino acid sequences to get 203,220 unique sequences used to build our blast database. Spectra obtained from the trypsin digestion products using the LTQ Orbitrap XL mass spectrometer were identified by the Proteome Discoverer (version 1.3) program, based on SEQUEST cluster as a search engine (University of Washington, licensed to Thermo Electron Corp., San Jose, CA) against our mouse database (203,220 nonredundant protein sequences). The search engine used the following parameters: precursor ion mass tolerance, 2.5 Da; fragment ion mass tolerance, 0.8 Da; fully tryptic enzyme specificity; two missed cleavages; dynamic modifications of cysteine carbamidomethylation and of methionine oxidation. The proportion of false positive assignations among the tentative peptide identifications, also called false discovery rate (FDR), has been estimated by using decoy databases constructed from the target database and was set at 1%.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:46:05.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dr Gail A Cornwall
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ XL

Revision	Datetime	Status	ChangeLog Entry
0	2013-11-11 02:22:11	ID requested
1	2013-11-14 02:40:54	announced
1	2013-11-14 02:42:44	announced
⏵ 2	2014-07-25 01:46:06	announced	Updated project metadata.

Guyonnet B, Zabet-Moghaddam M, SanFrancisco S, Cornwall GA, Isolation and proteomic characterization of the mouse sperm acrosomal matrix. Mol Cell Proteomics, 11(9):758-74(2012) [pubmed]

submitter keyword: Mouse, Spermatozoa, Acrosome, Acrosomal matrix, Proteome

Dr Gail A Cornwall
contact affiliation	Texas Tech University Health Sciences Center, Cell Biology & Biochemistry Department
contact email	benoit.guyonnet@live.fr
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/2013/11/PXD000575

PRIDE project URI

• PRIDE
  1. PXD000575
     1. Label: PRIDE project
     2. Name: Mouse Acrosomal Matrix LC-MS/MS