MassNet

1. Introduction

MassNet is a web service to provide an automated pipeline for annotating the list of protein as the result of mass spectrometry analysis. MassNet can use a MASCOT result file or tab deliminated file. After you input your file, it then executes a analysis pipeline consisting of physico-chemical analysis, kegg pathway assignment, gene ontology mapping, and protein-protein interaction prediction.

The major advantage of MassNet is the exhaustive annotation of many proteins. MassNet now provides a comprehensive set of functional annotation tools for proteomic researchers to understand biological meaning behind list of proteins.

2. MassNet Analysis Pipeline

(1) If you want to use MassNet web server, you should input the result of mass spectrometry. You can use MASCOT's Peptide Mass Fingerprint result and MS/MS Ion Search result or TAB separated file.

(2) Physico-Chemical Properties

a. Sequence information - Length, Molecular Weight
b. Instability index - Half Life
c. Amino acid distribution
d. Amino acid distribution histogram
e. Count of hydrophobic and hydrophilic residues
f. Count of charged residues
g. Electrical charge as a function of pH - IEP
h. Hydropathy
i. Localization information (phobius)
g. signal peptide information (signalp)

(3) KEGG Pathway and Gene Ontology Assignment

a. Gene Ontology (GO) mapping
b. Pathway assignment (KEGG)

(4) Protein-Protein Interaction Prediction

a. Protein Experimental Interaction (BIND, DIP, HPRD, IntAct, MINT, CYGD, and BioGrid)
b. Protein Structural Interaction (PSIMAP)

3. Schematic of the MassNet workflow

4. Contact us

We welcome all the questions and comments about the MassNet web service.

Daeui Park (daeui@kribb.re.kr)
Seong-Woong Cho (sucho@kribb.re.kr)
Byoung-Chul Kim (chem1186@kribb.re.kr)
Seong-Jin Park (psj420@kribb.re.kr)
Sunghoon Lee (ishoon@kribb.re.kr) +
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Korean BioInformation Center (KOBIC)
Korea Research Institute of Bioscience and Biotechnology (KRIBB)
52 Eoeun-dong, Yusung-gu Daejeon 305-333, Korea.

5. Acknowledgment

We would like to deeply thank to Dr. Jong-Soon Choi and Dr. Seung-Il Kim at Korea Basic Science Institute.
Dr. Jong-Soon Choi (jschoi@kbsi.re.kr)
Dr. Seung-Il Kim (ksi@kbsi.re.kr)
- Proteomics Team
- Website : http://www.kbsi.re.kr