I've used OMSSA and X!Tandem with ETD data. I get slightly different results, but that's to be expected from different search engines. I haven't tried X!Tandem Tornado yet, but in previous versions all you had to do to search ETD data was specify c and z ions and exclude a,b,x,y ions. See http://www.thegpm.org/TANDEM/api/index.html for help on formatting X!Tandem params files.
Of the search engines you mentioned, I believe pFind is the only one that was designed to specifically deal with ETD data, especially the neutral losses from charge reduced (a.k.a. ET no D) species. Optimizing searching of ETD data is still a work in progress in the proteomics community, so there isn't really an established best way to do it. But others may have a different opinion on that. On Jul 25, 8:08 am, DD <[email protected]> wrote: > I know Massmatrix (free/open-source) accepts ETD, ECD and CID/ETD. It > is easy to install. It is a nice piece of software. > DD > > On Jul 25, 5:45 am, Amit Kumar Yadav <[email protected]> > wrote: > > > > > > > > > Dear All, > > > I want to know about some ETD search tools, preferably free/open-source. > > > I tried Mascot, OMSSA and pFIND but getting drastically different > > results.Don't know what to believe. X!Tandem TORNADO download page says that > > they have incorporated ETD search citing pFind's latest paper (JPR,2010). > > But, I could not find any help on how to use the function. > > > I am confused. Can anyone lead me to some good ETD search algorithm. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
