Dear Sherry Bhalla,

You are right because the general format ie, the input data of MSGF+ was not applicable idPicker. if you try some small mass peptide means you will get.

after MSGF+ you need to check the specific requirement for idPicker means you may know the reason.

Good Luck & Regard

R.Selva....

Thank you R.Selva sir for replying.

But the output files i am getting from MSGF+ are in mzid format which is acceptable format for idPicker. Even the  idpDB sql files are forming for each input file ..but i am getting empty protein reports which means no validated peptide is being comming after validation.I need to optimize some parameters??

you can use format converters like idconvert (http://manpages.ubuntu.com/manpages/trusty/man1/idconvert.1.html) to convert mzID files to pepXML format. IDPicker should be easy to run with pepXML format.

Dear Sherry, You no need to optimize parameter. this because the IDPicker not read your peptide command because of unreadable format, so that you change pepXML format using online source means you will get response. if till you have confusion means just see some reference report from IDPicker of other possible sample, and same input format you follow means your problem will get resolve.

Yah MSGF+ are in mzID format it's acceptable format for IDPicker but you check your software support because it's may not get updated or some update file may getting hidden normally it happens.

Hope now you may got clear..

Good Luck & Regards again...

R.Selva...

Dear Sherry

Kindly Login to this URL

http://tools.proteomecenter.org/wiki/index.php?title=Software:MZIdentML 

Its an online freeware to validate files which are in "mzIdentML" format..

Hope it may be useful for you..

All the best

Regards

Sujay

Thanks every one for reply

I tried converting my mzid file using idconvert id proteowizard on linux system and got following error

Any suggestions I am attaching a sample input mzid file

Error writing analysis 1 in "kit 4 replicate 2 iTRAQ_4566_scaffold-pidres.scaffold-pidres.mzid":

[Serializer_pepXML::write] PepXML only supports a single search database.