PXD006177

PXD006177 is an original dataset announced via ProteomeXchange.

Title	Establishment of dimethyl labeling-based quantitative acetylproteomics in Arabidopsis
Description	Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both CsCl density gradient (CDG) centrifugation-based protein fractionation and a dimethyl-labelling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl chemical labelling with chromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based computational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named Stable isotope-based Quantitation-Dimethyl labelling (SQUA-D), and finally the confirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7,456 unambiguous acetylation sites were found from 2,638 different acetylproteins, and 5,250 acetylation sites, including 5,233 sites on lysine side chain and 17 sites on protein N-terminus, were identified repetitively. Out of these repetitively discovered acetylation sites, 4,228 sites on lysine side chain (i.e., 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signalling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and 31 hormone-suppressed acetylpeptide groups or called unique PTM peptide arrays (UPAs) that share the identical unique PTM site pattern (UPSP). This CDG centrifugation protein fractionation in combination with dimethyl labelling-based quantitative PTM proteomics, and SQUA-D may be applied in the quantitation of any PTM proteins in any model eukaryotes and agricultural crops as well as tissue samples of animals and human beings.
HostingRepository	PRIDE
AnnounceDate	2018-03-16
AnnouncementXML	Submission_2018-03-16_01:30:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fengchao Yu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive; TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-27 03:28:50	ID requested
1	2018-02-21 01:53:17	announced
⏵ 2	2018-03-16 01:30:16	announced	Updated project metadata.

Liu S, Yu F, Yang Z, Wang T, Xiong H, Chang C, Yu W, Li N, Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis. Mol Cell Proteomics, 17(5):1010-1027(2018) [pubmed]

curator keyword: Biological

submitter keyword: Arabidopsis, 4C proteomic workflow, CsCl density gradient (CDG) centrifugation, Stable isotope dimethyl labelling, Acetylproteomics, Quantitative PTM proteomics, SQUA-D

Ning Li
contact affiliation	Division of Life Science, The Hong Kong University of Science and Technology
contact email	boningli@ust.hk
lab head
Fengchao Yu
contact affiliation	The Hong Kong University of Science and Technology
contact email	fyuab@connect.ust.hk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006177
     1. Label: PRIDE project
     2. Name: Establishment of dimethyl labeling-based quantitative acetylproteomics in Arabidopsis