PXD000192

PXD000192 is an original dataset announced via ProteomeXchange.

Title	Developing Soybean Seed Lysine-N-epsilon-acetylome
Description	Intact proteins, as well as Glu-C, and Lys-C/trypsin-derived peptides extracted from developing soybean seeds were immunoenriched using antibodies against acetyllysine residues. Enriched proteins were separated by SDS-PAGE prior to tryptic digestions and enriched peptides were analyzed directly, in both cases using a Thermo LTQ-Orbitrap XL. In separate LC-MS/MS runs fragmentation was achieved using CID, ETD, or a combination of the two mediated by a data-dependent decision tree. Individual RAW files were converted to mzXML format for mining with MS-GFDB (v2012.06.07) using default settings of the msconvert executable within the Trans-Proteomic Pipeline v4.6. Searches with MS-GFDB were performed with default methods and parameters, except as noted: number of allowed isotope errors was set at zero, and fully enzymatic peptides were specified, i.e. no non-enzymatic termini. Data mining was additionally performed with a local Mascot server, v2.3.1, and ZCore v1.17, both accessed through Proteome Discoverer v1.3 (Thermo Scientific), as well as Sequest HT v1.3, a reimplementation of SEQUEST within Proteome Discoverer v1.4. Tandem mass spectra were searched in Proteome Discoverer with allowed missed cleavages set to four. Prior to Mascot and Sequest searches, ETD spectra were further filtered to remove peaks resulting from precursors, charge-reduced precursors, and neutral losses thereof with mass windows of 4 Da, 2 Da, and 2 Da, respectively.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:01:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Colin Smith-Hammond
SpeciesList	scientific name: Glycine max (Soybean) (Glycine hispida); NCBI TaxID: 3847;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-03-25 02:56:36	ID requested
1	2013-12-02 01:27:59	announced
1	2013-12-02 01:28:33	announced
⏵ 2	2014-07-25 01:01:18	announced	Updated project metadata.

Smith-Hammond CL, Swatek KN, Johnston ML, Thelen JJ, Miernyk JA, )-acetylome. J Proteomics, 96():56-66(2014) [pubmed]

submitter keyword: soybean, seed, lysine acetylation, LC-MS/MS

Colin Smith-Hammond
contact affiliation	University of Missouri
contact email	clsppb@mail.missouri.edu
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/2013/12/PXD000192

PRIDE project URI

• PRIDE
  1. PXD000192
     1. Label: PRIDE project
     2. Name: Developing Soybean Seed Lysine-N-epsilon-acetylome