Hi Alejandro, You can expect this feature for the next release of TPP (or you can get it now by compiling from our latest code tree).
Cheers, --Luis On Thu, Nov 23, 2017 at 4:12 AM, Alejandro <[email protected]> wrote: > Hi Luis, > > Thank you very much. I'm already testing it and for a few datasets that I > have tested it looks good and quite comparable to the Xpress based on > areas, although with much narrow standard deviation. Is it planned to use > this as an alternative for the Xpress quantitaion alos at the protein > level? Right now I'm exploring if I could get an intensity based ratio at > the protein level by using the peptide information (if it contribute with > evidence for the protein assembly) and then calculating the mean of the > peptide ratios of every protein. > > Cheers, > > Alejandro > > On Wednesday, November 22, 2017 at 8:28:12 PM UTC+1, Luis wrote: >> >> Hi Alejandro, >> >> You can download the updated Xpress and interfaces from our dev staging >> site: >> https://sourceforge.net/projects/sashimi/files/Trans-Proteom >> ic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/ >> >> Unzip XpressIntensityUpdate.zip, and place XPressPeptideParser.exe under >> the C:\TPP\bin\ directory, and the other 2 files under C:\TPP\cgi-bin\ (or >> wherever you installed TPP). I also recommend making backups of the >> original files in case you need them. >> >> Cheers, >> --Luis >> >> >> On Tue, Nov 21, 2017 at 1:01 PM, Alejandro <[email protected]> wrote: >> >>> 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]> 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]. >>>>> 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]. >>> 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]. > 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. 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