Metabolomics is a marrige between hardcore chemistry and informatics to study the complexe behavio of biological system on the level of metabolite. You can find tons of literature on google about metabolomics. Here we only emphasie only the practical aspects of this branch like techniques, tools, protocols, data analysis. If you never heard about this branch here is a brief introduction.

Inside the cell there are complex factories and machines are workign together to execute some definate functions. These active entities may includes gene, rna, enzyme,metabolites etc.  Due the advacnement of science and technology humans designed many plateform and developed strategies to study the biological systems on these levels. They are utilizing maths, chemistry, physics and statistics to understand the biology. These plateform can be called as genomics, transcriptomics, proteomics and metabolomics. On each level  guys want to analyze some stuffs by quantitative and qualitative approach. On each level there are particualr techniques are utilizing to get the data. And there are extensive and powerful software are available in front of our eyes to analyzed this masive amount of data and get some conclusions. (Whenever you see some "omics" it means there is lots of software (tons of data) are working, a layman definition).  For example on the level of genomics you have powerfull and also beutiful sequencers to sequence the genome, for protemics various types of mass spectrometry. There are lots of refforts are ongoing to integrate these heterogenous data to build a systems level understanding of biological system. And this advancement of highthroughput technologies (wet labs work of large scale and very repidly) and experts software pave the way towards emergence of systems biology.

For the metabolomics we can use all the analytical chemistry tools, like GC, HPLC, UV, IR, MS, NMR or hyphenated GCMS or LCMS. Currently GCMS and LCMS are the most utilized techniques for meatbolomics. What we do with these technologies.

Well, answer is simple, we want to measure the metabolite in a biological matrix(Microbes, Plants, Human, Algae, Fungi and Mammals etc. ). So before going onward we should talk something about the metabolite, our targets.

Their are million of metabolites are exist in the nature. For example Plant possess a estimated value of 200,000 metabolites with different nice properties to increase our curicity. Nature evolved this metabolite by the million years of hardwork and screeing so they are the fittest candidate on darwin principles.( Thats why most of the drugs are simply natural compunds or their Analougs.)

So we have million of targets in our metabolomics field. But due to the limitation of analytical chemistry only few of them are characterized, majority of compounds are stills in the blackbox. They can be highly useful in the field of drug discovery or related stuffs. So one of our task will be indentified this compound by high throughput technologies. On the other hand we have plenty of identified compounds with various properities and role in the biological systems. These compounds interact with gene, enzyme or whatever they wants and make some resaons fot study them. These all are involved in to the complexity of metabolic pathways and they interact with each other by the add of enzymes. So it is a complex scene of netwroks in where these compunds play some rols. And in the metabolomics approach we tried to quantitaviely analyze the measurable level by our analytical tools. For example present days we can measure apprx 300-400 compounds in a single GCMS experiment. GCMS based approch have an advantage over the LCMS as we have spectral library of 2-3 million compound so we dont need to run the standard compounds but in the case of LCMS we are lacking comprehensive library but still it is a powerful tool than GCMS.

So we understnd that what is our targets (metabolite). Now We needs protocols to extract these guys from our biological matrix as they are buried in to the complexity of cellular organization. If we are intrested in a group of compound like amines or amino acid or fatty acid than we need optimized protocols  and we could not be include in to the matabolomics. In metabolomics we trying to extract whole metabolism by our extraction protocols (optimization) so we can get a pictur of active metabolism. Like if we can see metabolite X and  then we can say that there is definately a enzyme which is working to produce this metabolite and if we got a unknown huge signal then we need to studied that which enzyme is synthesizing this unkwon guy.  So we want to anylze the metabolism on a global level without any prior bias.

Now we have a extract of some biological matrix and we need some machines to throw it in. Selection of machines is depend on what you wants beacause of our analytical limits we wont be able to see all the compund by a single machine. If we are interested in volatile compounds then GCMS will be the choice. and if we are interested in Nonvolatile and heavy compound then we can go to LCMS (but some limitations). So after selection of machine we need some operational training to play with it. So you guys are need some training on these machine, try to figure out which machine is near to you.

Machine has many parameter for operations and you can find nice manuals with it. Go throuth that manual, they explained everything.

For your basic information you can find some links for operation part of some instruments.

Now we run samples on a machine. I would suggest here to design your experiment with all the contorl and blanks. (Method Blank, Negetive Control, Positive Control, Intrenal Standrad, External Standard,Reagent Blank, Quality Control Mixtures, Minimum 6  Replicate. ) This will help you interprate the  data.

Now after runnign the sample we get some data. The structure of that data are complex and information itensive. We need some computer software to process this data and analyze that. We have some good software to do that. You need to get training on that, which you can do on your home with your computer. A list can be find at the end of the page.

So we did some software job and get some tables for statistical treatments. The end of every scienctific experiment will be the numbers which we need to analyze by stat so you guys supposed to be experts on the math and stats if you want to work in this field.

So after statistical treatment (basic and multivariate statistics) we get some some predction about meabolites and their working behavior.

This is a simple work pipline of the metabolimics. We can target various ideas and application by this techniques. Need to study the biochemistry and metabolism and to get some goos problem based on metabolits. If you guys have any problem in your mind send us we can discuss on it and can figure out how to deal with it.

There are many group are working in this field. Dr Fiehn is the prioneer worker who give the initial Start to this branch.

Hope I was able to give you a sip of metabolomics. If you have some confusion  these websites.

Inetrested in metabolomics

If a student of undergraduate students want a job in this field or wants higher education, following practical skill needed.

1. Sample Preparation :- Weighing on electronic balance, Liquid hanlding with micropipettes, Use of Centrifuges, Sonicaters, Thermomoxers,Vortexers, Vacum Evaporater, Lyophilzer, Liquid Nitrogen and dry ice handling, autocalving, Eppendorf tube Labeling, Work under clean bench and chemical hood, Proper lab safety (Goggles, Gloves, Apperal, Shoes etc), Notebook writing.

2. Design of Experiments. :- Number of replicates, controls, standards, refrences, quality controls, Variables and parameters, metadata

3. Operation of Equipment: - Instrumental Parameters, What not to do and what to do, Data file Naming, Sequence tables and methods, Gas pressures. There are separate paramters for GC/LC and Mass spectrometry.

Agilent :- GCMS (Quadrapole)

Leco:-GCTOFMS (Time of flight)

Thermo

4. Data processing:- Depend of the equipment, most utilized are

1. Agilent Chemstation

2. Leco Chroma TOF :-  one of the powerful (According to Dr. Fiehn)

3. NIST AMDIS :- Free You can download.

4. NIST MS Search

5. Mass Frontier.

6. ACDLABs MS Manager

7. LIB2NIST: -Free

8. MS Interpreter.:-Free

9. XCalibur:-

5.  Statistical Analysis:-

1. Mircrosoft Excel:- Find some tutorials. HERE

2. Statistica:- Very powerful software.

3. Rapidminer :- Free

4. R-project :- Free.

6. Molecule and structure file modeling and Handling: - For working on this tools you should have advance knowledge of organic chemistry. Otherwise it will just like to play without getting the rules.

1. Chemaxon Softwares. Marvins, Instant Jchem, molconvert etc. Free  for academics

2. ACDLAbs Software. Chem Folder, Spectral Database etc.

3. Openbabel

4. EPI Suite

Databse :- Now the real thing comes.

1. Pubchem

2. KEGG

3. Chebi

4. CAS

5. ZINC

6. Drugbank

7. DNP

8. Metacyc.

9. Brenda

10. Protein Data Bank

A good list can be find here.

Beside all this knowledge you need  Good Biochemistry to find out what to study in this pipeline. So go to this link and understand the biochemistry

Here are some links which is useful to understand some more in-depth knowledge. I would upload many links in next two days (Now it is too midnight so i want to go  bed).

Basic Introduction

Gas Chromatography -Mass spectrometry:-

There are millions of links which you can find on the interent to undersatnd this techniques but we are compling some good one accoring to us. If you find something, please mail us.

Liquid Chromatography-Mass Spctrometry

FT-MS

Basic of Mass spectrometry

Basic of Chromatography

http://www.chem.neu.edu/Courses/1221PAM/chromatogr/ppframe.htm