Peptide identification from Mass spec data

Question

[atharvakarkare14]

I have long non coding RNAs extracted from RNA-seq data. Now I want to predict the peptides and filter them. Is using MS/MS peptide data is feasible?

How can I go further in predicting peptides from my ncRNAs.

[Michael]

You are talking about non-coding RNA, thus - by default - they are not expected to be translated, so no peptides. Do you have any evidence that they are coding for protein anyway?

[atharvakarkare14]

They dont code for protein but, lncRNAs translate into peptides of short length, around 8 aa to 90 aa. Many studies are going on. see here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8649637/

[Michael]

Thank you for the link. I looked at the NAR paper they are citing (Lu et al. 2019). In the methods there it is stated that they generated a database from all the ORFs in the coding-non-codingRNA candidates plus the 'normal' human proteome. This DB can then be used as database for peptide mass fingerprinting and blasting. The only bioinformatics step in that was the ORF detection for which they used MATLAB. But I am assuming you can also use any other orfFinder like getOrf for that. So, if you have the raw data you should be able to run the peptide identification again using that DB.