This is indeed unintended. I will try to figure out what the problem is. What version of TPP and StPeter are you using?
From: spctools-discuss@googlegroups.com [mailto:spctools-discuss@googlegroups.com] On Behalf Of Alexander Pelletier Sent: Friday, May 25, 2018 12:59 PM To: spctools-discuss Subject: Re: [spctools-discuss] StPeter blank values Hello Mike. That makes sense. It would not make sense to include these values in our analysis afterall. However, I re-ran the quantification to see if it is indeed possible, allowing for degenerate peptides and it doesn't seem to work. The entire SIn column appears as blank for all values (including the ones which were previously shown). I'm not sure if this is the intended output for the software or not. Thank you for your help! On Wednesday, May 16, 2018 at 5:36:33 PM UTC-4, Michael Hoopmann wrote: Hi Alexander, It looks like the blanks belong to proteins in a group, possibly where there are no non-degenerate peptides for those proteins. It might be possible to perform the quantification if you allow degenerate peptides in the analysis with the –d option when you run StPeter. Cheers, Mike From: spctools...@googlegroups.com <javascript:> [mailto:spctools...@googlegroups.com <javascript:> ] On Behalf Of Alexander Pelletier Sent: Wednesday, May 16, 2018 2:15 PM To: spctools-discuss Subject: [spctools-discuss] StPeter blank values Hi. I am using StPeter for label free quantification and the tool works well! However, I have a question about the blank values in the SIn column (see attached). Occasionally, there appear blank values. My interpretation is that these proteins were identified, but are unable to be quantified, or the quantification value does not pass some sort of threshold or noise filter. What are these blank values, and how should we be handling these? Thank you! -- 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 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 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. -- 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.
