Thanks! I'll let you know how it goes... Adam
On Friday, November 10, 2017 at 2:51:44 PM UTC-6, Luis wrote: > > Hi Adam, > > You can download the new version (1.2.1) from our Development folder at > Sourceforge: > > https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ > > I suggest you first make a backup of the current file you have, and then > copy this new one to the bin folder (usually c:/TPP/bin). Make sure you > also rename it to simply "StPeter.exe" so that Petunia will run it (no need > to if using the command-line). > > Hope this helps, > --Luis > > > On Fri, Nov 10, 2017 at 12:26 PM, Adam R <[email protected] <javascript:>> > wrote: > >> Hi Luis, >> >> Thanks for getting back on this. I realized also that I was searching >> using the wrong mod and should have used 229.16 and not the reporter ion >> mass! I will need a windows executable file please. >> >> Best, >> >> Adam >> >> On Friday, November 10, 2017 at 2:06:30 PM UTC-6, Luis wrote: >>> >>> Hi Adam, >>> >>> Thank you for your report. We have now modified how StPeter handles >>> modifications. If you build TPP from sources, you can see this in rev >>> 7675. Or let me know if you require a Windows executable, and we'll post >>> it on our files section. >>> >>> Cheers, >>> --Luis >>> >>> >>> On Thu, Nov 9, 2017 at 8:51 AM, Adam R <[email protected]> wrote: >>> >>>> Hi Everyone, >>>> >>>> I've tried to run StPeter on a prox.xml file from a sample that was >>>> labeled with TMT 126. This was not quantified with Libra, just trying to >>>> identify peptides, so I set the 126 mass as a fixed mass for lysine under >>>> fixed modifications and searched with comet. I have peptide IDs and may >>>> proteins identified with this approach, showing K[254] for the amino acid >>>> and the mod. I figured that setting up StPeter this way shouldn't an issue >>>> since this can be done with other fixed mods like with cysteine. Any >>>> thoughts? >>>> >>>> Best, >>>> >>>> Adam >>>> >>>> >>>> StPeter: MS2 intensity-based label-free quantification >>>> Copyright 2015-2017, Jason Winget, Michael Hoopmann, Institute for >>>> Systems Biology >>>> Version 1.2.0 October 11 2017 >>>> ****** BEGIN StPeter ANALYSIS ****** >>>> Time at start of analysis: Thu Nov 09 16:46:36 2017 >>>> >>>> Parameters: >>>> degenerate peptides = no >>>> fdr = 0.01 >>>> sample load = 0 >>>> tolerance = 0.4 >>>> intensities = no >>>> >>>> Reading protXML: >>>> c:/TPP/data/20171108_EL-2017-00005268/126/interact.ipro.prot.xml >>>> ERROR: Unknown modification: K[254] >>>> Please report to authors. >>>> >>>> -- >>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> 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 [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
