PXD015649

PXD015649 is an original dataset announced via ProteomeXchange.

Title	Towards a better understanding the testicular proteome of domestic pig
Description	For gaining additional insights into the composition of the testicular proteome of the domestic pig (Sus scrofa domestica), we conducted 2DE-MS. Two-dimensional SDS PAGE was run on testicular lysates of three boars, with three gels per boar. Upon matching across gels, we arbitrarily selected protein spots for mass spectrometry analysis. Excised slices were vacuum dried and soaked with digestion buffer containing trypsin (0.01 μg/μl), followed by overnight incubation at 37°C in the same buffer without trypsin. Subsequently, peptides were extracted in solvents of increasing acetonitrile content, by sonication. Upon vacuum-centrifugation, peptides were reconstituted in 0.1% formic acid (FA). Following this, peptides were fractionated by reversed phase liquid chromatography (C18; buffer A: 0.1% FA dissolved in HPLC-H2O; buffer B: 0.1% FA, dissolved in CAN; flow-rate: 0.4 µL/min; gradient: 2-30% in 30 minutes). Eluted peptides were injected via an electrospray ionization interface into a Q-TOF mass spectrometer (one boar, Q TOF Ultima, Micromass/Waters, Manchester, UK) and an ion-trap mass spectrometer (two other boars, XCT ion-trap, Agilent Technologies, Waldbronn, Germany). We used ProteomeDiscoverer 2.4 (Thermo Fisher Scientific, San Jose, USA) for peptide and protein identification. Using Sequest HT, we searched peak lists (*.mgf) against the Sus scrofa reference proteome database (UniProt Proteome ID: UP000008227, 49,793 proteins).
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-12_00:00:50.626.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marcel Kwiatkowski
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue
Instrument	6340 Ion Trap LC/MS; Q-Tof Ultima

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-01 00:23:52	ID requested
⏵ 1	2022-08-12 00:00:52	announced

Kwiatkowski M, Hotze M, Schumacher J, Asif AR, Pittol JMR, Brenig B, Ramljak S, Zischler H, Herlyn H, Protein speciation is likely to increase the chance of proteins to be determined in 2-DE/MS. Electrophoresis, 43(11):1203-1214(2022) [pubmed]

submitter keyword: sus srofa, 2DE-MS, proteomics

Holger Herlyn,
contact affiliation	Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Germany
contact email	hherlyn@uni-mainz.de
lab head
Marcel Kwiatkowski
contact affiliation	University of Innsbruck
contact email	marcel.kwiatkowski@uibk.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015649
     1. Label: PRIDE project
     2. Name: Towards a better understanding the testicular proteome of domestic pig