Hi RG community
I'm analyzing some proteomics datasets acquired by LC-MSMS on a VelosPro Orbitrap. I'm wondering if anyone knows of a free program to search the files for unknown/unexpected and unbiased modifications on peptides (ie, not found in the PTM options).
Basically, I need an output of peptides where a mass gap/tag of the unexpected modification is annotated at its location in sequence.
I know there are a few commercial options (Peaks, Byonic) but I've already used there trial versions. At this time I want a quick solution as I have no budget to purchase these programs. I've used Modi before, but I cant seem to find it in its original URL. Not sure whether InsPecT will work.
Any ideas?
Alex
You might try PMOD. This is open source and modifiable, but as with most open source stuff you are left to your own devices to get it to work.
Thanks Luke, I'll give PMOD a try. I also stumbled upon two tools which could provide me with similar outputs: MODa from https://prix.hanyang.ac.kr/ and MSFragger from the Nesvizhskii lab. Let's see wich does the trick :-)
Hi Alejandro,
I would recommend using Morpheus. Wide tolerance (1000 Da) based searches are described here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5387672/.
Thanks Ilian, I'll give that a try. However, I understand Morpheus will only search on previously annotated PTM on the Uniprot... this might not be the best suited algorithm for my case. I stumbled on MSFragger, which I think is 'similar' than Morpheus but does not operate on a predetermined list of PTMs... I'll follow up!
Cheers
Alejandro