Biomarker discovery by automatic annotation of N-glycan species in MALDI-TOF-TOF spectra

Mass Spectrometry has high-throughput and high accuracy characteristic. These features make it become a major tool for analysis complex chemical composition and biological sample. The glycoprotein has diverse structure and complex composition; therefore it is more difficult to decompose the conformation of glycoprotein than regular protein. [...]]]> 2010-04-08

Biomarker discovery by automatic annotation of N-glycan species in MALDI-TOF-TOF spectra

Mass Spectrometry has high-throughput and high accuracy characteristic. These features make it become a major tool for analysis complex chemical composition and biological sample. The glycoprotein has diverse structure and complex composition; therefore it is more difficult to decompose the conformation of glycoprotein than regular protein. We combine machine learning, statistic and signal processing techniques to automatically annotate the MS spectra with glycan composition. We can detect not only single glycan composition but also overlap glycan composition in one spectrum. We also can report significant glycan across multiple spectra. This feature can be use as potential biomarker discovery procedure across two different groups.

2010.04.08.Capstone

2010.04.22.Capstone

2010.04.25.Capstone

2010.05.13 Capstone

2010.05.25 Capstone Report

Software Link

2009-12-08

Determination of N-Glycan structure use tendem mass

There are more than 50% of all eukaryotic proteins are glycosylated.[1] Glycoslyated modification is one of the important post-translational modifications. We cannot fully understand the proteomics field without knowing this PTM.Glycan is the carbohydrate portion of a glycoconjugate. There are two common classes of glycan found in eukaryotes which are O- and N-linked glycans. Glycans can be linear or branched and there are five linkage sites. Due to these reasons, the structure of glycans is diverse. The goal is using Tandem MS spectra to construct possible N-linked glycans composition and topology. This problem can be divided by two steps, candidate generation and candidate evaluation. In candidate generation step, it is important to generate small and high accuracy set. In candidate evaluation step, scoring the glycans topology will be the major problem need to be solved. The goal is to find out all the possible topology and report score to user in an acceptable time. The program will be evaluated by using annotated spectra and compare to other software.

Reference

[1]Apweiler, R., Hermjakob, H., Sharon, N.: On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim. Biophys.Acta 1473(1), 4–8 (1999) Link

[2]Böcker, S., Kehr, B., Rasche, F.: Determination of Glycan Structure from Tandem Mass Spectra.  Link

[3]Tang, H., Mechref, Y., Novotny, M.V.: Automated interpretation of MS/MS spectra of oligosaccharides. Bioinformatics 21(suppl. 1), i431–i439 (2005); Proc. of Intelligent Systems for Molecular Biology (ISMB 2005) Link

[4]Cooper, C.A., Gasteiger, E., Packer, N.H.: GlycoMod – a software tool for determining glycosylation compositions from mass spectrometric data. Proteomics 1(2), 340–349 (2001) Link

Determination of Glycan structure use MS

Determination of Glycan structure use MS

After presentation, Prof. Memo give me some advise. I will modify and upload it.

Title: Determination of N-Glycan structure use MS/MS

isomeric molecules isoform

De novo De novo

biology biological

Why my problem is NP-Hard?

Because the glycan structures is diverse, the number of candidate glycan structures is huge.

Paper for [...]]]> Unlocking the secrets of the genome

Paper for Capstone assignment