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]. 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.
