PXD019155

PXD019155 is an original dataset announced via ProteomeXchange.

Title	In-depth investigation of low-abundant proteins in matured and filling stages seeds of Glycine max by a combination of protamine sulfate precipitation and TMT-based quantitative proteomic analysis
Description	The presence of seed storage proteins is a major bottleneck in soybean seed proteome analysis despite the significant technical advancements in mass spectrometry and data analysis software. Our previous studies have shown that effective ways to improve the detection of low-abundance proteins in soybean seeds using protamine sulfate (PS) with 2-DGE analysis. Besides, verification of the PS precipitation method revealed broad application to other leguminous plants like pea, broad bean, and peanut. Nonetheless, it is difficult to overcome the poor reproducibility and limitation of the dynamic range of identification during 2-DGE analysis. Thus, to elucidate the suitability and efficacy of protamine sulfate precipitation method for shotgun proteome approach, we performed TMT-based quantitative analysis using matured and filling stages seeds by application of two-way pre-fractionation using PS and chromatographic methods. Interestingly, this approach led to the identification of 2,200 and 924 differential proteins in the matured and filling stage of soybean seeds, respectively. These results revealed enrichment of various proteins related to major metabolism in soybean seeds including amino acid, major carbohydrate, lipid metabolism, and among others. Taken together, results provided the new insight into current complexity and limitation of soybean seed proteomics through two-way pre-fractionation combined with TMT-based quantitative analysis.
HostingRepository	PRIDE
AnnounceDate	2020-06-28
AnnouncementXML	Submission_2020-06-27_17:11:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sun Tae Kim
SpeciesList	scientific name: Glycine max; NCBI TaxID: 3847;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-12 22:52:47	ID requested
⏵ 1	2020-06-27 17:11:33	announced

Min CW, Park J, Bae JW, Agrawal GK, Rakwal R, Kim Y, Yang P, Kim ST, Gupta R, Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis. Cells, 9(6):(2020) [pubmed]

submitter keyword: Glycine max, Basic pH Reversed Phase, Filter-Aided Sample Preparation, Low-abundant proteins, MaxQuant, Protamine sulfate precipitation, Perseus, Tandem mass tags

Sun Tae Kim
contact affiliation	Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
contact email	stkim71@pusan.ac.kr
lab head
Sun Tae Kim
contact affiliation	Pusan National University
contact email	stkim5505@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD019155
     1. Label: PRIDE project
     2. Name: In-depth investigation of low-abundant proteins in matured and filling stages seeds of Glycine max by a combination of protamine sulfate precipitation and TMT-based quantitative proteomic analysis