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

Sample Analysis Fees Schedule for Analyzing Proteins and Small Molecules

 

Services

Analytical methods

price

(RMB) /sample

1. Identification of proteins (post-translational modifications)

Accurate mass determination of a purified protein or peptide

High-resolution MS/ MALDI-TOF-TOF

300 RMB

Sequencing of peptides

High-resolution MS/ MALDI-TOF-TOF

4000 RMB

Identification of purified  proteins OR for IP samples (phosphorylation, acetylation, ubiquitination, etc)

In-solution digestion(*)-Peptide desalting- LC MS/MS- Database searching

1800 RMB

Identification of proteins in gel (phosphorylation, acetylation, ubiquitination, etc)

In-gel digestion(*)-Peptide desalting- LC MS/MS- Database searching

2000 RMB

Identification of digested peptides (phosphorylation, acetylation, ubiquitination, etc)

Peptide desalting- LC MS/MS- Database searching

1500 RMB

Identification of phosphorylation sites of IP samples (enrichment of phosphorylated peptides)

In-solution digestion(*)-enrichment of phosphorylated peptides-

Peptide desalting- LC MS/MS- Database searching

2500 RMB

Database searching

MascotPD or Maxquant

100 RMB

Note: * Double digestion will increase the fee

2. Analysis of High - throughput proteomics

Label-free quantification of proteome

 

Protein extraction- Protein desalting- In-solution digestion(double digestions)- Peptide desalting-( Peptides fractionation- Peptide desalting)- quantification of peptides- LC MS/MS- Database searching and analysis

4000RMB

 (Fractionation will increase the fee according to machine-hour)

TMT quantification of proteome

 

Protein extraction- Protein desalting- In-solution digestion(double digestions)- Peptide desalting and quantification - TMT labeling and desalting -(Peptides fractionation- Peptide desalting)- quantification of peptides- LC MS/MS- Database searching and analysis

5000RMB

 (Fractionation will increase the fee according to machine-hour)

Label-free quantification of Phosphoproteome

Protein extraction- Protein desalting- In-solution digestion(double digestions)- Peptide desalting and quantification-enrichment of phosphorylated peptides-

Peptide desalting -(Peptides fractionation- Peptide desalting)- quantification of peptides- LC MS/MS- Database searching and analysis

6000 RMB

 (Fractionation will increase the fee according to machine-hour)

TMT quantification of Phosphoproteome

Protein extraction- Protein desalting- In-solution digestion(double digestions)- Peptide desalting and quantification - TMT labeling and desalting- enrichment of phosphorylated peptides- Peptide desalting and quantification

-( Peptides fractionation- Peptide desalting)- LC MS/MS- Database searching and analysis

7000 RMB

 (Fractionation will increase the fee according to machine-hour)

TMT quantification of ubiquitproteome

Protein extraction- Protein desalting- In-solution digestion(double digestions)- Peptide desalting and quantification - TMT labeling and desalting- enrichment of ubiquited peptides- Peptide desalting and quantification

-( Peptides fractionation- Peptide desalting)- LC MS/MS- Database searching and analysis

10000 RMB (Fractionation will increase the fee according to machine-hour)

PRM

First, the PRM uses the quadruple to select the precursor ion with the selection window m/z≤2; the precursor ion is fragmented, and then all product ions are detected by Orbitrap with high resolution and high accuracy.

2500RMB/protein

MRM

First, the MRM uses the quadruple (Q1) to select the precursor ion; then, the precursor ion is fragmented in the collision cell (Q2); finally, Q3 scans targeted product ions with high sensitivity.

2500RMB/protein

Orbitrap Fusion,

Q Exactive HF-X 

machine-hour (no more than two hours)

800RMB/sample

Q Exactive, Q Exactive plus, QTRAP 6500+

machine-hour (no more than two hours)

600RMB/sample

Database searching

MascotPD or Maxquant

100 RMB

3. Metabolomics

3.1 GC-MS (A)

GC-MS

 

Without any treatment (A1)

GC-MS- Database searching

500 RMB

Complex samples (A2)

sample purification or derivatization- GC-MS- Database searching

800 RMB

Complex samples (A3)

sample purification and derivatization- GC-MS- Database searching

1000 RMB

Absolut quantification (A4)

GC-MS-data analysis

600 RMB

3.2 LC-UV (B)

 

 

Without any treatment (B1)

UPLC-UV

300 RMB

Complex samples (B2)

sample purification or derivatization- UPLC-UV-data analysis

500 RMB

Complex samples (B3)

sample purification and derivatization- UPLC-UV-data analysis

700 RMB

Absolut quantification (B4)

UPLC-UV-data analysis

500 RMB

3.3 Plant hormone quantification (ABA/JA/SA/IAA/GA/SLs)(C)

UPLC-MS

 

1 plant hormone

plant hormones extraction- UPLC-MS- data analysis

600 RMB

( If multiple hormones are measured at the same time, the cost will increase according to 200 RMB/ hormone)

3.4 Plant metabolites quantification (L-Glu/GABA/ O-Acetyl-Serine etal.) (D)

UPLC-MS

 

1 plant metabolite

plant metabolites extraction- UPLC-MS- data analysis

600 RMB

( If multiple metabolites are measured at the same time, the cost will increase according to 200 RMB/metabolite )

4. Other instruments

High Speed Centrifuge

 

20 RMB/hour

Super High Speed Centrifuge

 

50RMB/hour

Freeze-dryer

 

20 RMB/hour

AKTA Protein purification system

 

300 RMB/ 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

Core Facility Manager: 
Pengcheng Wang

Assistant: Xiaomei Chen
Tel: 021- 57078238
Email: proteomics@psc.ac.cn