Hello,

Use MassTRIX first: http://masstrix3.helmholtz-muenchen.de/masstrix3/ .

For extensive ID annotations, use MZMine (http://mzmine.github.io/) which is free and can integrate HMDB, PubChem, Metlin, ChemSpider, BioCyc, KEGG) into the software and do data processing and annotations simultaneously, XCMS (locally or XCMSOnline (https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage) which are also free and can be useful in searching the same DBs as above, meta-P does fine (free), or you can do one-by-one at mzCloud (free, https://www.mzcloud.org/), at METLIN DB (also free: https://metlin.scripps.edu/). Use Mass++ (v, also free) to analyze the spectra and do simultaneous searches for the spectra at MassBank http://www.massbank.jp/?lang=en, free) too. You can also search against MoNA:http://mona.fiehnlab.ucdavis.edu/spectra/browse, also free!

Takes a while to get used to and do analysis, but GNPS (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp) is free can be extremely useful.

However, Progenesis from Water's integrates a lot of these DBs for annotations (commercial), Sciex's XCMSPlus (does similar integration of DBs) (these later two can be expensive!), while the third commercial tool for these annotations would be "Elements for Metabolomics" from ProteomeSoftware, though commercial would be cheapest.

Also, please have a look at our review which would be useful to pick up some open source tools and softwares for data analysis and interpretation/ visualization, which is an update for 2014-2015: http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/pdf

Actually a lot of "free" resources to use!

Thanks,

Biswa

Thank you very much sir. This information is of great help.

Try METLIN Metabolomics Database. This  is a repository of metabolite information as well as tandem mass spectrometry data. The library is free. https://metlin.scripps.edu

Vishal Gupta, 

The list Biswa gave you is really a good start. and I also recommend the review he mentioned (Updates in metabolomics tools and resources: 2014-2015), you will find more info. 

All the best.

http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/pdf

Thank you Prof. Ghosh