iprophet is search showing blank page

[sudarshan kumar]

I have analyzed a data file using peptide prophet. I got results.

But when I am analyzing by iprophet i see a blank page . can anyone tell me what does it mean.

Where is the problem? 

Regards,

Sudarshan

[David Shteynberg]

Hello Sudarshan,

Did the program report any messages when it ran?  Are you certain that the PeptideProphet input going to iProphet contains PSMs with non-zero probabilities?

Thanks,

-David

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/26849cc4-1680-40b5-861d-a1517cbc992en%40googlegroups.com.

[sudarshan kumar]

Thank you David,

I tried with another file. It worked. But can you please tell me about the relationship between Xcorr and probabilities. I read in the tutorial, that this relationship is good to determine MPT (Minimum Probability Threshold). 

My data 

When I see my data, I conclude that at almost every Xcorr above 1 the iprobability is near to zero (i. e. least error) image below). 

Now what should I infer from probability of 0 (for one peptide with high Xcorr) and .9 (for another peptide again with high Xcorr)? 

Please guide me. 

Regards,

Sudarshan

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-xjWM9naw0x%3DTTj9d7iyzGsiJZgw-2xiHzmB95gdU-SA%40mail.gmail.com.

--

-------------------------------------------------------------------
The real voyage of discovery consists not in seeking new lands but seeing with new eyes. — Marcel Proust

Dr. Sudarshan Kumar
(B.V.Sc.& A.H., M.V.Sc., PhD.)
Scientist
Animal Biotechnology Center
(Proteomics and Cell Biology Lab.)
National Dairy Research Institute Karnal, 132001
Haryana, India
Contact No 09254912456
URL www.ndri.res.in

Orcid Id: https://orcid.org/0000-0002-9816-4307