I have conducted protein analysis and functional determination using free online tools. Check out tiong, Steven, and muriana, 2016 Article at Article Comparison of Surface Proteomes of Adherence Variants of Lis...

Hi,

What do you mean by 'novel proteins'?

Given the 300 identified proteins you're referring to, I assume you used a database to retrieve these, but in theory, 'novel proteins' are not in any database.

So, that would mean you'd have to go through all your unassigned MS/MS spectra and do de novo sequencing to find potentially 'novel proteins', or are you referring to something else?

Thank you Eef Dirksen for your valuable response. Please tell me, how I can find these unassigned MS/MS spectra from my LCMS excel data? Is there specific remark to find out the unassigned MS/MS spectra?

It might be tricky (impossible) to obtain information about unassigned spectra from an Excel-based output, depending on the information that was extracted from the raw data.

Normally, the database search yields a list of unassigned queries that can then be interrogated together with the raw data: do you have those available too?

Please note that such a follow-up investigation usually is quite a labor-intensive, however, with no guarantee of finding 'new' proteins..

Nice to see you again very quickly Eef Dirksen. Yes, I have both raw data file and output Excel-based result. Again, I am tense about to find out exact proteins which represents antimicrobial potential among 300+ identified proteins. in addition to these, i filtered it out only cytosolic or secreted proteins from identified proteins. Beacuse, my protein of interest is cytosolic or secreted based. After this, i am looking for identify a particular new or novel protein from LCMS results which were not reported previously.

What software did you use to identify proteins from your raw data?

Maxquant software

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