Nathan C Verberkmoes, et al., International Society for Microbial Ecology

This paper describes a newly approach for metagenomics data analysis, called metaproteomics. They take two individual samples from a pair of twins who have gastroenteritis. One is treated with anti-inflammatory drugs and the other one don’t have any treatment. [...]]]> Shotgun metaproteomics of the human distal gut microbiota

Nathan C Verberkmoes, et al., International Society for Microbial Ecology

This paper describes a newly approach for metagenomics data analysis, called metaproteomics. They take two individual samples from a pair of twins who have gastroenteritis. One is treated with anti-inflammatory drugs and the other one don’t have any treatment. The fecal samples were collected for this research study.

The microbial cells were extracted from fecal samples by using differential centrifugation. Each sample has a technical replicate to test the reproducibility of this approach. Then the LC-MS/MS is performed for the high-throughput data acquisition. The number of identify peptides are around 2,000 and 3,000 for sample 7 and 8 respectively against two human subject metagenome database. There are other three databases, which contain normal gut microbiota, human contamination and so on.

Those protein identification results are mapped to the COG database. The results show highly reproducible and consistent in COG categories, and several COG categories were more represented in the average microbial metagenomes which reported by previous study in the present study. The majority of detected proteins were involved in translation, carbohydrate metabolism or energy production.

The protein quantification results were derived from the normalized spectral abundance factors (NSAF) across all samples. The most abundance proteins are elastase, chymotrypsin C and salivary amylases, which are expected in the human gut microbial communality.

Those proteins which cannot be identified against with the databases are classified as hypothetical proteins. This class of proteins may belong to novel protein families, which are not being fully study and characterized by previous research. The majority of these proteins are highly representing in the human gut only.

This work is the first large-scale metaproteomics research. They take advantages of shotgun sequencing techniques to discovery new knowledge from a different aspect of view. Now the research can have information from before and after protein translation. For protein quantification, if the internal standard is used while data collecting stage, it will be more accurate in protein abundance estimation, and it is still a problem to detect those low detectable and abundance peptides.

Ref

After my Prof. Tang revise my abstract, it seem more clear than I wrote before.

I want to improve my English writing, any idea?

Original [...]]]> I world like to publish a poster in 2010. I wrote a abstract on my capstone project.

After my Prof. Tang revise my abstract, it seem more clear than I wrote before.

I want to improve my English writing, any idea?

Original Abstract

Revised Abstract

He wrote a R code which can deal with post-processing.

Remember to install rscproxy package. The error message will say you need to install rproxy.dll but it have been replace after [R] 2.8.

User can use [...]]]> For ASMS abstract Anoop and I want to incorporate our I690 class project(A Multi-PCA Approach to Glycan Biomarker Discovery using Mass Spectromtery Profile Data)  into my MultiNGlycan.

He wrote a R code which can deal with post-processing.

Remember to install rscproxy package. The error message will say you need to install rproxy.dll but it have been replace after [R] 2.8.

User can use DebugView to see what is needed.

Here is some Ref

The R Statistical Language and C#.NET: Foundations

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 from Tandem Mass Spectra

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and [...]]]> Complexities and algorithms for glycan structure sequencing using tandem mass spectrometry

Determination of Glycan Structure from Tandem Mass Spectra

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

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.