ETD Search

[Amit Kumar Yadav]

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. 

[DD]

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 <amit007thech...@gmail.com>
wrote:

[Kristian]

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.

[Amit Yadav]

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

MassWiz sourceforge project

MassWiki

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[Matt Chambers]

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" <amit007...@gmail.com> 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>