Hi Alejandro, You can download the updated Xpress and interfaces from our dev staging site: https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%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.
