Hi Luis, Oh good to hear that it is already solved. If I could have a windows binary would be really useful.
Thanks. Cheers, Alejandro On Tuesday, November 21, 2017 at 8:06:25 PM UTC+1, Luis wrote: > > Hi Alejandro, > > The misreported intensity ratios was a bug when using the -L or -H options > in XPRESS. We have fixed this, as well as added support for those fields > in PepXMLViewer and Petunia. If you are building from sources, simply > build revision 7683, or let us know if you would like Windows binaries. > This will also be in the next official release of TPP. > > Thanks for reporting this, and for the positive feedback on 5.1! > --Luis > > > On Sun, Nov 19, 2017 at 11:36 AM, Alejandro <[email protected] > <javascript:>> wrote: > >> 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]> 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]. >>>> 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. 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