PXD000247

PXD000247 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of the testa from developing soybean seeds
Description	Soybean (Glycine max (L.) Merr. cv Jack) seed development was separated into nine defined stages (S1 to S9). Testa (seed coats) were removed from developing seeds at stages S2, 4, 6, 8, and 9, and subjected to shotgun proteomic profiling. For each stage "total proteins" were isolated from 150mg dry weight of seed coat using a phenol-based method, then reduced, alkylated, and digested with trypsin. The tryptic peptides were separated using a C18-reversed phase matrix, then analyzed using an LTQ Orbitrap Mass Spectrometer. Spectra were searched against the Phytozome G. max DB using the Sorcerer 2 IDA Sequest-based search algorithm. Identities were verified using Scaffold 3. A total of 306 (S2), 328 (S4), 273 (S6), 193 (S8), and 272 (S9) proteins were identified in three out of three biological replicates, and sorted into 11 functional groups: Primary Metabolism, Secondary Metabolism, Cellular Structure, Stress Responses, Nucleic Acid metabolism, Protein Synthesis, Protein Folding, Protein Targeting, Hormones and Signaling, Seed Storage Proteins, and Proteins of Unknown Function. In selected instances, individual seed coat proteins were quantified by spectral counting. The number of proteins involved in intermediary metabolism, flavonoid biosynthesis, protein folding and degradation are discussed as they relate to seed coat function. A database was constructed using the open reading frames of Phytozome G. max DB (updated August 8, 2009), plus a decoy DB generated by reversing the target sequences. Spectra were searched against the combined target-decoy DB using the Sorcerer 2 IDA Sequest-based search algorithm. Identities were verified using the Scaffold 3 program, and the false discovery rate (FDR) was estimated as (Ndecoy/Ntarget). For 186,364 peptide spectra examined, the FDR was between 5.18 and 5.26%. Samples were analyzed in biological triplicate; proteins were included in the results only if they were identified in all three biological replicates. Relative protein abundance was quantified by spectral counting ; data presented are the mean of three independent determinations. The coefficient of variation values calculated for each developmental stage are < 0.0516.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_08:55:57.024.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000247
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jan Miernyk
SpeciesList	scientific name: Glycine max; NCBI TaxID: 3847;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-05-08 03:44:57	ID requested
1	2013-08-09 06:43:28	announced
1	2014-07-28 00:36:41	announced
2	2013-08-09 07:02:51	announced	Add reference
⏵ 3	2024-10-07 08:55:57	announced	2024-10-07: Updated project metadata.

Miernyk JA, Johnston ML, Proteomic analysis of the testa from developing soybean seeds. J Proteomics, 89():265-72(2013) [pubmed]

10.1016/j.jprot.2013.05.013;

10.6019/PXD000247;

submitter keyword: seed coat,Soybean, LC-MS/MS

Jan Miernyk
contact affiliation	USDA Agriculture Research Service
contact email	jan.miernyk@ars.usda.gov
lab head
Jan Miernyk
contact affiliation	USDA Agriculture Research Service
contact email	jan.miernyk@ars.usda.gov
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/2013/08/PXD000247

PRIDE project URI

• PRIDE
  1. PXD000247
     1. Label: PRIDE project
     2. Name: Proteomic analysis of the testa from developing soybean seeds