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.
