Hello,
I recently got results from LC-MS analysis of my nodule samples. The results came in a form of an excel sheet with the Accession number (uniprot) of the protein and some other (for me unimportant) information. I'm looking for a recommendation for a simple bioinformatic tool that would help me sort all the information according to the biological process they belong or their function.
You are also free to give me any recommendation on ways i can process this data. I'm MSc student so I'm still a noobie and I want to learn as much as possible.
Thanks
Hi
will u pl.read the imp article in link for clues of your question---ajit
Article LC–MS Based Detection of Differential Protein Expression
You can have services from the site also
https://www.embl.it/research/interdisciplinary_research/bioinformatics/services/list-of-services/
Hello Natasha, for LCMS data analysis you can use openms softwares which is available on www.openms.de its a very good software can produce the data related to proteomics, metabolomics and it also provides workflow softwares. Try it for best results.
Check here. I found it very useful: https://compomics.com/bioinformatics-for-proteomics/
But it seems that you already (somehow) have the final output, including the Uniprot hits, then, you would need to get the amino acid sequences of those proteins and use for example blast2go and or Argot
There is a database for MS fragments that are generated from various organic and biomolecules. All you have to do is compare your fragments to the fragments in the database and, voila, the parent compound is automatically identified for you, making your life easier. I forgot the name of the database, but of course you can google it yourself. I knew the dbase by heart when I was teaching bioinformatics.
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