PXD006773

PXD006773 is an original dataset announced via ProteomeXchange.

Title	A new method for differential proteomic analysis utilizing native MS-electropherograms: a comparison between plasma and serum proteins by combining native PAGE, whole-gel slicing and quantitative LC-MS/MS
Description	MS identification has long been used for PAGE-separated protein bands, but global and systematic quantitation utilizing MS after PAGE has remained rare and not been reported for native PAGE. Here we reported on a new method combining native PAGE, whole-gel slicing and quantitative LC-MS/MS aiming comparative analysis on not only protein abundance, but structures and interactions in different samples. A pair of human plasma and serum samples were used as test samples and separated on a native PAGE gel. Six lanes of each sample were cut, each lane was further sliced into thirty-five 1.1 mm x 1.1 mm squares and each square was subjected to standardized procedures of in-gel digestion and quantitative LC-MS/MS. The results, comprising 958 data rows that each contains the abundance information of a protein in one square in eleven gel lanes (one plasma lane excluded), showed satisfactory reproducibility of assignment and quantitation. A total of 315 proteins were assigned and for each protein, the abundance distributions in the plasma and serum gel lanes were reconstructed, respectively (named as ‘native MS-electropherograms’). Comparison of the electropherograms revealed significant plasma-vs-serum differences in 33 proteins (fold difference > 2 or < 0.5, p < 0.05), among which 18 showed differences in more than one squares. Many of the differences matched with accumulated knowledge on protein interactions and proteolysis involved in blood coagulation, complement and wound healing processes. We expect this method would be used to analyze changes or differences between proteomic samples, providing information on both protein abundance and structures.
HostingRepository	PRIDE
AnnounceDate	2017-09-08
AnnouncementXML	Submission_2017-09-08_00:57:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ya Jin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-22 01:05:37	ID requested
⏵ 1	2017-09-08 00:57:40	announced

Wen M, Jin Y, Manabe T, Chen S, Tan W, A comparative analysis of human plasma and serum proteins by combining native PAGE, whole-gel slicing and quantitative LC-MS/MS: Utilizing native MS-electropherograms in proteomic analysis for discovering structure and interaction-correlated differences. Electrophoresis, 38(24):3111-3123(2017) [pubmed]

curator keyword: Technical

submitter keyword: Differential proteomic analysis, Gel slicing, Native MS-electropherogram, Native 1D-PAGE, Human plasma and serum, Quantitative LC-MS/MS

Ya Jin
contact affiliation	Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology
contact email	yajin@gdut.edu.cn
lab head
Ya Jin
contact affiliation	Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology
contact email	ya.jin@ymail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006773
     1. Label: PRIDE project
     2. Name: A new method for differential proteomic analysis utilizing native MS-electropherograms: a comparison between plasma and serum proteins by combining native PAGE, whole-gel slicing and quantitative LC-MS/MS