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-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] > <javascript:>> 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] <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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