We are using TPP 5.1.0. As for the version of StPeter, I am not sure. I am not able to verify which version right now. We updated to TPP 5.1.0 about a month ago. Thank you for your help!
On Friday, May 25, 2018 at 2:57:55 PM UTC-7, Michael Hoopmann wrote: > > This is indeed unintended. I will try to figure out what the problem is. > What version of TPP and StPeter are you using? > > > > *From:* [email protected] <javascript:> [mailto: > [email protected] <javascript:>] *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:* [email protected] [mailto:[email protected]] > *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 [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.
