[spctools-discuss] Mascot automatic decoy xinteract
Dear all, I was wondering about the automatic decoy search in recent Mascot versions: Is there a way to use this in defining the negative entries while using xinteract? Or shall I rather use a concatenated manually reverted database in the search to assess the negative distribution? Any input appreciated! best Andreas Dr. Andreas Otto Institute for Microbiology Department of Microbial Proteomics Ernst-Moritz-Arndt-University Greifswald F.- Hausdorff-Str. 8 17489 Greifswald phone: +49 3834 420 5920 fax:+49 3834 420 5902 -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] TPP for large databases/ metaproteomics
Dear all, We are currently trying to set up the TPP for large databases (>4GB) and would like to know if there is anyone who could propose the best setup for the software? Is there any way of allocating kernels/ memory to the TPP to let it run faster? I appreciate your help! best Andreas Dr. Andreas Otto Institute for Microbiology Department of Microbial Proteomics Ernst-Moritz-Arndt-University Greifswald F.- Hausdorff-Str. 8 17489 Greifswald phone: +49 3834 420 5920 fax:+49 3834 420 5902 -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] TPP for large databases/ metaproteomics
Dear all, We are currently trying to set up the TPP for large databases (>4GB) and would like to know if there is anyone who could propose the best setup for the software? Is there any way of allocating kernels/ memory to the TPP to let it run faster? I appreciate your help! best Andreas Dr. Andreas Otto Institute for Microbiology Department of Microbial Proteomics Ernst-Moritz-Arndt-University Greifswald F.- Hausdorff-Str. 8 17489 Greifswald phone: +49 3834 420 5920 fax:+49 3834 420 5902 -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] ProteoGrapher
Dear all - Does anyone know what ProteoGrapher is about? I was not able to find anything apart from the release notes. best Andreas -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
Re: [spctools-discuss] xcorr (sequest) and charge filtering for pep.xml files
Dear David, I guess that refers to the viewer? This possibility was apparent to us - I am sorry for being imprecise: We would like to filter our pep.xml prior to spectrast for specific PTM as we have done previously with our data to keep up with our workflows and therefore we would need an output as pep.xml again. Is that possible somehow? best Andreas Am Freitag, 5. Dezember 2014 19:29:13 UTC+1 schrieb David Shteynberg: PepXMLViewer.cgi should be able to do it. Using Petunia open the Files link at the top. Navigate to the directory containing your file and click on the link in the View? column. -David On Thu, Dec 4, 2014 at 11:06 PM, andrea...@uni-greifswald.de javascript: wrote: Dear all, Is there any possibility to filter pep.xml files according to charge state and/ or XCorr? We would like to do it either in the GUI or at the command line. best, Andreas -- 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 javascript:. To post to this group, send email to spctools...@googlegroups.com javascript:. Visit this group at http://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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
[spctools-discuss] xcorr (sequest) and charge filtering for pep.xml files
Dear all, Is there any possibility to filter pep.xml files according to charge state and/ or XCorr? We would like to do it either in the GUI or at the command line. best, Andreas -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
