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Core Facilities

Plant Proteomics and Metabolomics

Plant Cell Biology




Homepage > Core Facilities > Plant Proteomics and Metabolomics

 Introduction  Equipment  Service and fee  Technical resources  Contact
Introduction Top

Plant Proteomics and Metabolomics utilize the state-of-the-art instrumentation of chromatography and mass spectrometry, and multi-dimensional omics strategies to conduct simultaneous qualification and quantification of the entire proteome and metabolome in plant cells and tissues. Large-scale analysis of protein population, abundance changes and molecular interactions allows us to understand the environmental impacts on plant physiology, and therefore to decipher cellular signaling transduction pathways. Structural characterization of organic metabolites and protein post-translational modifications could gain in-depth insights into the stress adaptation of plants in harsh environmental conditions, as well as the diversity of metabolic pathways and other cellular mechanisms which are involved in plant growth and development, regulation, molecular cross-talk, stress response and defense. As plant proteome and metabolome are highly dynamic in living systems, the integrated strategy, using both proteomic and metabolomic analyses, thus provides a global and reliable approach to investigate unknown biological pathway events related to the survival of plants, and the interaction of multiple pathways in response to environmental stimuli and stresses.

Research in the laboratory focuses on developing newly advanced techniques for high-resolution separation, high-throughput identification and accurate quantification of proteins, peptides and small molecules, together with a wide range of scientific resources to meet the needs of cutting-edge research in the research institute. Efforts are undertaken to establish world-leading research programs in differential proteomics, phosphoproteomics, glycoproteomics, degradomics, structural proteomics, interaction proteomics and metabolomics of plants. The laboratory is also dedicated to construct in-house databases of protein sequences, modifications, natural products and metabolites of plants for proteomic and metabolic data mining with the aid of bioinformatics tools, and to ultimately help discover novel metabolic networks and signaling transduction pathways, and further validate the structural function of specific protein targets and biomarkers in the plant physiological processes.

Equipment Top
Agilent 7000C Triple Quadrupole GC/MS
PerkinElmer NexION 300D ICP-MS
AB SciexTripleTOF 5600 Plus
Thermo Q ExactiveOrbitrap
ThermoOrbitrap Fusion TribridTM
Service and fee Top


The core facility of Plant Proteomics and Metabolomics provides a comprehensive set of mass spectrometry service to academic researchers and industry users including accurate mass determination and structural analyses of large biomolecules (proteins and peptides) and small organic compounds, and identification of post-translational modifications as well as quantification of proteome, metabolites and inorganic metal ions.

MS service fees schedule:

Sample submission form:
Sample Submission form for Analyzing Small Molecules [WORD] [PDF]
Sample Submission Guidelines for Analyzing Small Molecules [WORD] [PDF]
Sample submission form and Guidelines for proteins and peptides [WORD] [PDF]
Sample submission form and Guidelines for Elemental Analysis [WORD] [PDF]

Mail address:
Proteomics and Metabolomics, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences
Room 319, Research Building, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
Contact phone: (021) 5707 8238; (021) 5707 8239 Contact E-mail:

Service Fees Schedule for Analyzing Proteins and Small Molecules

ServicesAnalytical methodsInternal price
(US dollars)
IPPE price
(US dollars)
External price
(US dollars)
1. Protein identification and quantification
Accurate mass determination of a purified protein or peptidesHigh-resolution MS$20/sample$25/sample$30/sample
High-through protein identificationNanoLC MS/MS$100/sample$130/sample$160/sample
De novo sequencing of peptidesHigh-resolution MS/MS$25/peptide$35/peptide$50/peptide
Identification of protein post-translational modifications (phosphorylation, acetylation, glycosylation, etc)NanoLC MS/MS$100/sample$150/sample$200/sample
Strutural identification of glycans of glycoproteinsNanoLC MS/MS$200/protein$300/protein$400/protein
Quantification of proteome in a complex biological systemStable isotope labeling and nanoLC MS/MSTBDTBDTBD
2. Organic compounds and metabolomic analysis
Structural identification of organic compoundsHigh-resolution MS/MS$20/compound$30/compound$40/compound
Quantification of amino acidsChemical derivatization and UPLC$20/sample$30/sample$40/sample
Quantification of oligosaccharidesChemical derivatization and UPLC$30/sample$35/sample$40/sample
Quantification of known metabolitesUPLC-MS & MS/MS$40/sample$50/sample$70/sample
Quantification of plant hormonesUPLC-MS & MS/MS$40/sample$50/sample$70/sample
3. Elements analysis
Quantification of trace elementsICP-MS & MS/MS$50/sample
4. Sample pretreatments
In-solution digestion of proteinsTryptic digestion$20/sample$30/sample$40/sample
In-gel digestion of proteinsTryptic digestion$30/sample$50/sample$70/sample
Protein desaltingDialysis$20/sample$30/sample$40/sample
Peptide desaltingC18/SCX ZipTip$20/sample$30/sample$40/sample
Purification of organic compoundsExtraction, SPE desalting$20/sample$30/sample$40/sample
Technical resources Top
Arabidopsis ProteinDatabase Downloads
1.       Public databases
National Center for Biotechnology Information(NCBI)
The UniProt Knowledgebase (UniProtKB)
The Arabidopsis Information Resource (TAIR)
The Plant Proteome Database (PPDB)
2.       Phosphoprotein databases
Plant protein phosphorylation database (P3DB)
The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 4.0)
3.       N-Glycoprotein Databases
N-Glycoprotein database was constructed by refining amino acid sequences of the Arabidopsis proteins or peptides containing the Asn-X-Ser/Thr/Cyr motif (X, not proline) from TAIR10 (downloaded on January 6th, 2014; 35,386 sequences) or NCBI non-redundant database (downloaded on January 6th, 2014; 226,526 sequences) to exclude non-N-glycosylated proteins and redundant peptides, where the generated glycopeptide sequences containing 2 missed trypsin cleavage sites away from the N-glycosylation motif in each putative glycoprotein were collected.
Ma J, Wang D, She J, Li J, Zhu JK, She YM.Endoplasmic reticulum - associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis. New Phytologist 2016.
Potential Arabidopsisglycoproteins containing NxS/T/C motifs in the NCBI database
Potential Arabidopsis glycoproteins containing NxS/T/C motifs in the Tair10 database
Potential Arabidopsisglycopeptides containing NxS/T/C motifs in the NCBI database
Potential Arabidopsisglycopeptides containing NxS/T/C motifs in the Tair10 database
Contact Top
Dr. Yi-Min She
Room 319, The Core Facility of Proteomics and Metabolomics
Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences
3888 Chenhua Road, Shanghai 201602, China
Tel: 011+86+21 5707 8239
Copyright 2012-2016 Shanghai Center for Plant Stress Biology (PSC) All Rights Reserved
Address: No. 3888 Chenhua Road, Shanghai 201602, P. R. China
Shanghai ICP #05033115