Hi Srikanth,
You shouldn’t need a spectrast usermods file for those common mods. Spectrast
is just reading your search results so if there are other modifications present
which it is reading, they are there because you’ve searched for them using
tandem/mascot/etc.
I suggest re-searching your
Hi Eric,
Thanks for the suggestion. I used iprophet and merged the files
successfully, followed by Mayu to calculate the proteinFDR. I also was able
to create a spectral library using spectraST.
The place where I get an error is when I create consensus library and try
to define the user modific
Hi Srikanth, I suggest after your step “I have convert the results
individually to pepxml using Mascot2XML, Tandem2XML and Idconvert and then
apply peptideprophet on each file” (which is good), the next step is merge
the 3 PeptideProphet outputs into a single PepXML file with iProphet. Then
build y
