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 modifications. I only want Carbamidomethylation at C and Oxidation at M. I created a text file with the following lines:
# spectrast.usermods M|+16| C|+57| And I run the following command : spectrast -cAC -Mspectrast.usermods -cN/speclib_modfiltered -cICID_QTOF -cDUniprot_RRP_for_Spectrast.fasta -cd speclib.splib It created a library successfully but throws the following error: GENERAL: Illegal user-defined modification token: SpectraST . It must be of the form A[...], where ... does not start with a number. Ignored. And when I convert the results to text, I see other modifications as well (deamidation, acetylation, etc). Can you please tell me where I am going wrong. Srikanth On Wednesday, June 10, 2020 at 4:28:54 AM UTC+10, Eric Deutsch wrote: > > 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 your spectral library from that one file. > > > > Regards, > > Eric > > > > > > *From:* spctools...@googlegroups.com <javascript:> < > spctools...@googlegroups.com <javascript:>> *On Behalf Of *Srinivas > Srikanth > *Sent:* Monday, June 8, 2020 9:43 PM > *To:* spctools-discuss <spctools...@googlegroups.com <javascript:>> > *Subject:* [spctools-discuss] Spectral library generation > > > > Hi Phil, > > > > I have a 15 hek files searched with Mascot, X!Tandem and MSGF+ separately. > I am trying to create a library using TPP pipeline and SpectraST. > > I have convert the results individually to pepxml using Mascot2XML, > Tandem2XML and Idconvert and then apply peptideprophet on each file. My > question is about the next step, > > Should I be merging individual search engine results using iprophet and to > make three combined files and then merge them again using iprophet? > > Or I merge each run from three searches together using iprophet and then > merge the resulting 15 files together to apply ProteinProphet or Mayu ? > > > > > > Srikanth > > -- > 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...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/08ebe555-a53b-4c20-8ac8-14709b4f2d49o%40googlegroups.com > > <https://groups.google.com/d/msgid/spctools-discuss/08ebe555-a53b-4c20-8ac8-14709b4f2d49o%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/217c62c8-18ee-411f-a271-20300fe8ecffo%40googlegroups.com.
