Modification search in web version

[icheeseman]

I really like pepquery and have found this to be a valuable tool. However, I would also love to be able to search for specific modifications using the web version. Is there a way to input a peptide to indicate a modification on a specific amino acid?
Thank you!

[wenbostar]

What modifications do you want to search?

[icheeseman]

I particularly want to look at protein N-termini, which means it is very useful to include acetylation (either of methionine or the second residue) as an option as most mammalian N-termini are processed and modified. Thank you!

[wenbostar]

You can add these modifications by performing the search on local. All the online MS/MS data can be accessed through PepQuery command line on your local computer: http://pepquery.org/document.html#samul