FeedBack Needed

[Amit Kumar Yadav]

Dear Group members,

We had been busy validating and benchmarking the algorithms. Now we
need feedback.

Here I present a short overview of the results. Will be there to read
in detail in the paper (manuscript under preparation).

The PMF algorithm has been proved to work nicely with over 28000
simulation experiments.

The MassWiz MS/MS algorithm has been tested on about 30,000 spectra
from public repository (ISB standard 18 protein mix- refer to
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577160/?tool=pubmed ) and
has and identified the 18 proteins on top.

If you want to test, You can goto http://regis-web.systemsbiology.net/PublicDatasets/
and pick any mzXML file for any run. We have provided file converters
on tools page where you can convert the file to PKL format (our
default format for MS/MS search). Then you can search in "18_mix"
database(contains 180sequences).It has randomized + reversed sequences
to increase the database size just like the decoy strategy.

We have also benchmarked the algorithms with Mascot for PMF; and with
Mascot and X!tandem for MS/MS. The results are promising.

PLEASE use MassWiz and PLEASE provide us your valuable and critical
feedback.

Adieu for now. Will keep you all posted on latest developments !

Thanks