The latest ProteinProspector performs as well as pfind if used properly. See the 2011 abrf iprg study on etd analysis. Does pfind write pepxml?
-Matt On Jul 26, 2011 2:00 AM, "Amit Yadav" <[email protected]> wrote: > Thanks Kristian. > > I think you have summed up the situation well. I did use Tandem ETD in > previous just like you told, but CYCLONE release of X!Tandem says it has > incorporated rules found by pFind group. So, if I have to use it like the > way I did earlier, I am just curious how do they implement other rules(other > than c,z). > > pFind gives almost double/triple of what others can. Although it is evident > it was mean for ETD, some of the matches I have seen (manual interpretation) > are too poor to justify. Weak matches are undertandable but they were > outright poor (say 3-4 peaks in a 20mer peptide). Thats why I am confused. > > I am going to try MassMatrix for sure, thanks DD for pointing it out. > > > Regards, > > *Amit Kumar Yadav * > Senior Research Fellow (SRF-CSIR) > IGIB, New Delhi (India) > > *MassWiz Web server* <http://masswiz.igib.res.in> > * <http://masswiz.igib.res.in>**MassWiz sourceforge > project*<https://sourceforge.net/projects/masswiz> > * <https://sourceforge.net/projects/masswiz>**MassWiki*< https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=MassWiki> > > > > On Mon, Jul 25, 2011 at 11:23 PM, Kristian <[email protected] >wrote: > >> 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. >> >> > > -- > 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. > -- 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.
