Hi Luis, Yes, I would be really interested in testing it out as soon as you have a pre-release!
I haven't checked if thats also the case with an older version, I should have a computer running 4.8. I will check it out and see. Thanks for the info on the tag, I will try to then find the mod tag. BTW, great release with the 5.1, so far I have found it quite good to work with. Cheers, Alejandro On Saturday, November 18, 2017 at 4:07:04 AM UTC+1, Luis wrote: > > Hello Alejandro, > > We will add these columns to the PepXMLViewer for the next release; I can > let you know when we have a pre-release version if you would be interested > in testing it. > > I am not sure why the ratios are not being correctly calculated; we will > have a look and try to fix as well for the next release. Did you also have > trouble with this feature with the previous version of TPP? > > As you noted, modified peptide masses are rounded when reported in the > modified_peptide attribute of protXML in order save space and for making > the display simpler. You can find the full modification masses within the > mod_aminoacid_mas tags within modification_info. Or just round the pepXML > masses when comparing peptides. > > Cheers, > --Luis > > > > On Thu, Nov 16, 2017 at 6:04 AM, Alejandro <[email protected] > <javascript:>> wrote: > >> Dear all, >> >> I have been running since a while the 5.1 release candidate and since a >> week or so the new 5.1 release with great success thanks! >> >> Lately I have been running more the TPP tools from the command-line and >> came across the option in XPRESS to export intensities as well as intensity >> based ratios of labeled type of data. I have used it but I don't see the >> option in Petunia in the Pepxml viewer to add it to the table. By manual >> inspection of the Pepxml, file I see them reported within the xpress tag, >> although the ratio is always reported as 0.000, even though the intensities >> are reported, and by manually calculating in some peptides it seems quite >> close to the ratio calculated from the areas, as expected. Is there an >> option to parse those out when exporting the tsv file? Moreover have you >> have some experience on using the intensities as input for the protein >> ratio/abundance calculation? I tried to see if I could build it it up using >> the intensities but the peptides are annotated different in the Pepxml, >> than in the Protxml. All modifications are annotated either with the more >> precise mass shift or rounded. e.g CAM is reported as C[160.03] for the >> peptides in the Pepxml whereas as C[160] for in Protxml. >> >> Another question that I have related to xpress is if you have any >> experience on better settings for data analyzed on hi-res MS, ie. Q >> Exactive. Fixed elution peaks, number of chromatograms points, or number of >> 13C isotopic peaks. >> >> Any thoughts on this? >> >> Best, >> >> Alejandro >> >> -- >> 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.
