Dear Pratic,

To answer your qutation, It is important to know about the parent compound that you are goin to be analysed. Because, Sometime, LC method may not suitable for the analysi of metabolites which are not soluble in aquos phasees. So, such occations you can use GC/MS method.

However, you can analysis some metabolites which has the aquos compatible properties.

You have to identify all peaks of you LC/MS. Sometime, you have to compare spectrum of peak with libraris alredy avilable.

Futher, to understand, metabolic pathways, you have to use radio label parent compound (only for the qutationanable locations).

Let me know about the parent compound that you are going to analyse.

Piyal Aravinna

Hello, which software is on your LCMsMs may be you already have database or database CD like NIST.

https://chemdata.nist.gov

Unless you are following a known database LC protocol, your only recourse is to work with the masses. You can lookup the monoisotopic masses of known metabolites in one of several public databases, like NIST. The isotopic pattern can be used to select the most likely metabolites that a given monoisotopic peak represents using isotopic vector angle analysis. [Method Isotopic Vector Angle Analysis in Mass Spectrometry v2

HI all.

If I attach my file, can you guys help me in finding some metabolites. I am principally looking metabolites of glycolysis, TCA cycle, nucletoide metabolism, Pentose phosphate pathway and hexosamine biosynthesis pathway.

Hi Pratik,

Hope you are doing pretty well. As you mentioned in your question that you got a file of m/z, RT, fragments etc.. So, now use these informations to find out the metabolites form online databases (HMDB, MassBank, Metlin, etc) or your lab database (if they have). From the database, match the m/z and fragments of metabolites. Hope this would help you anyway.

Best of luck.

You can take a look the presentation "From Features to Compounds: How To Get Started and Move Forward" here: http://metabolomicssociety.org/site-map/articles/88-videos/218-2016-emn-webinars-public

Pathway analysis requires some bioinformatics skills. It is not just feeding data in to some magic box. If this is not your core business I would suggest finding a collaborator that can do it. Otherwise you probably need a course or really dig yourself into the literature. For example the papers related to the tools available at https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp

Hi Pratik

You can find some useful references that I add to you

Ref.1 = Software Tools and Approaches for Compound Identification of LC-MS

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjAAegQIChAB&url=https%3A%2F%2Fwww.mdpi.com%2F2218-1989%2F8%2F2%2F31&usg=AOvVaw1IDbAfFINe2jd_iHY7eKqk

About software Ref.2 = Software Tools and Approaches for Compound Identification of LC-MS

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjABegQIAhAC&url=https%3A%2F%2Fres.mdpi.com%2Fmetabolites%2Fmetabolites-08-00031%2Farticle_deploy%2Fmetabolites-08-00031.pdf%3Ffilename%3D%26attachment%3D1&usg=AOvVaw3XJvlHz7wpQD17g-NTro7j

Ref.3 = Metabolite identification and quantitation in LC-MS/MS

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjACegQICBAB&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3278153%2F&usg=AOvVaw2Yu_wLDZzgQ5fYCe96fcrO

Ref.4 = Metabolite identification and quantitation in LC-MS

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=4&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjADegQIBhAB&url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F221843264_Metabolite_identification_and_quantitation_in_LC-MSMS-based_metabolomics&usg=AOvVaw2FitM7QsGUAAiJ8i22fuPg

Ref.5 = Identification of Metabolites through GC/LC–MS Processed Data using

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjAEegQIBRAB&url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F305407454_Identification_of_Metabolites_through_GCLC-MS_Processed_Data_using_Different_Reference_Libraries_and_Their_Comparison&usg=AOvVaw3kpcg9On5CNr2qVz6sQuTq

Ref.6 = Metabolite Identification and Characterization

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=6&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjAFegQICRAC&url=http%3A%2F%2Fweb2.uconn.edu%2Frusling%2FPrakash%2520CP.pdf&usg=AOvVaw0CAenGL_CD2zrsdfLrbEM1

Ref.7 = Enhanced MS/MS coverage for metabolite identification in LC-MS

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjAGegQIARAB&url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS0003267017310450&usg=AOvVaw0PXG4MCamlMrGABD6RtdZM

Ref.8 = A ROUGH GUIDE TO METABOLITE IDENTIFICATION USING HIGH:

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=8&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjAHegQIAxAB&url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2001037014600489&usg=AOvVaw3NYXARouZ50qWjzOSeV-Yp

Ref.9 = Computational Analysis of LC-MS/MS Data for Metabolite Identification

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=2ahUKEwiljsCi7ubgAhWP6aQKHdxFAp4QFjAIegQIBBAB&url=https%3A%2F%2Fvtechworks.lib.vt.edu%2Fhandle%2F10919%2F36109&usg=AOvVaw2wQYi38QHsZaDkiAiBOe9o

Ref.10 = MyCompound ID MS/MS Search: Metabolite Identification Using

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&cad=rja&uact=8&ved=2ahUKEwiGrc-B9ObgAhXM-KQKHWlcCIg4ChAWMAB6BAgKEAE&url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Facs.analchem.5b03126&usg=AOvVaw3avgHYU74yi9g14QqeeyMF

Thanks all of you. I have figured out how to perform LC-MS and use XCMS/metaboanalyst to identify the pathways.