It depends on your analytical setup which in term is guided by what you are looking for. You will use differently optimized extraction methods for general metabolites vs lipids and yet different methods to extract proteins.

For untargeted metabolomics many researchers use Compound Discoverer by Thermo Fisher, which could be combined with targeted approaches for better results [1]. I also recommend using the SIRIUS suite of programs [2] which can give you great insights into which compound classes to focus on.

For lipidomics I´d suggest using LipidMatch [3] in combination with LDA [4].

[1] Züllig T, Zandl-Lang M, Trötzmüller M, Hartler J, Plecko B, Köfeler HC. A Metabolomics Workflow for Analyzing Complex Biological Samples Using a Combined Method of Untargeted and Target-List Based Approaches. Metabolites. 2020 Aug 25;10(9):E342

[2] Dührkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, Dorrestein PC, Rousu J, Böcker S. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat Methods. 2019;16(4):299-302

[3] Koelmel JP, Kroeger NM, Ulmer CZ, Bowden JA, Patterson RE, Cochran JA, Beecher CWW, Garrett TJ, Yost RA. LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. BMC Bioinformatics. 2017 Jul;18(1):331

[4] Hartler J, Triebl A, Ziegl A, Trötzmüller M, Rechberger GN, Zeleznik OA, Zierler KA, Torta F, Cazenave-Gassiot A, Wenk MR, Fauland A, Wheelock CE, Armando AM, Quehenberger O, Zhang Q, Wakelam MJO, Haemmerle G, Spener F, Köfeler HC, Thallinger GG. Deciphering lipid structures based on platform-independent decision rules. Nat Methods. 2017 Dec;14(12):1171-1174

We have plant samples and we want to identify unknown compounds present in the methanolic plant extracts. We got peaks after LC - MS/MS but those peaks tell nothing about the compounds. How to identify them.

Complete unknown ID by LC/MS is fairly difficult. LC/MS/MS data is good if you are experienced with interpretation, but typically you'd want high-resolution data as well to try and narrow down to a formula. Even then you may only be able to get a class of compound. What are you looking for, exactly?

It should be HR-MS data and compound discoverer software platforms should be provided for small molecule identification. What are your analytical tools for the experiment (the type of the instrument, software, etc)?

There are online tools and libraries to identify the compounds in case of supplying the appropriate data. It depends on how your acquisition method and instrument capability but also your supplemental software that can deconvolute the mass spectrum.

LC - MS/MS is not suitable techniques for analthe ysis of unknown compounds. You can easily identify unknown by GCMS and LCMS single Quard. With LCMSMS you can only confirm the known compounds. You can use LCMSMS only for tracing the unknown if you have respective database alongwith your LCMSMS. Kindly share information about the instrument and software you use???

Noel W Davies I am seeking for a collaborator who can help me in Identifying the compounds and can collaborate in Publication.

Dear Sajjad Hyder ,

Thanks for your interest. For the interpretation of data derived from LC-MS/MS, you have to earn knowledge about liquid chromatography tandem mass spectrometry and for the interpretation of data, I suggest you to read the article based on LC-MS/MS, and you have to discuss with the persons who have knowledge about LC-MS/MS. I am giving you the link of few articles based on LC-MS/MS, I hope these will be helpful for you.

Besides this, you have to select the analytes and the matrix as well. Based on your desired analytes and matrix, I suggest you to search such type of articles. Thanking you very much....

Link:

1. DOI 10.1007/s12161-014-9898-3

2. DOI: 10.1080/03067319.2015.1025227

3. DOI: 10.1080/03601234.2016.1181922

4. DOI 10.1007/s12161-016-0537-z