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]> 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-2017-0 >>> 0005268/126/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]. > 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]. 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.
