Hi David Will do so, thank you! That makes a lot of sense. I have also added the mzXML files but this might be the cause of the discrepancy I see!
Thanks Shagun On Friday, March 25, 2022 at 4:42:46 PM UTC-4 David Shteynberg wrote: > Hello Shagun, > > I noticed in your condition file you are using TMT10 with the following > masses: > <reagent mz="126.127726" /> > <reagent mz="127.124761" /> > <reagent mz="127.131081" /> > <reagent mz="128.128116" /> > <reagent mz="128.134436" /> > <reagent mz="129.131471" /> > <reagent mz="129.137790" /> > <reagent mz="130.134825" /> > <reagent mz="130.141145" /> > <reagent mz="131.138180" /> > > > The difference between neighboring channels is <0.01 at the lowest and yet > you are using tolerance of 0.2: > > <massTolerance value="0.2" /> > > > I think the appropriate mass tolerance for this type of labeling should be > ~0.001. > > Does that make sense? Please try running Libra with the mass tolerance > appropriate for this type of label. > > Cheers, > -David > > On Fri, Mar 25, 2022 at 10:34 AM Shagun Gupta <[email protected]> wrote: > >> Hi David >> >> Could you suggest a good email to reach you with? I can share the >> pep.xml's and Libra condition file that way? >> >> -Shagun >> >> On Friday, March 25, 2022 at 11:00:38 AM UTC-4 David Shteynberg wrote: >> >>> Hello Shagun, >>> >>> Thank you for your email and interest in the TPP. I have recently been >>> comparing TMTPro analysis by ProteomeDiscoverer and Byonic to that produced >>> by TPP's Libra. As far as I can tell, when I run and compare the >>> quantities (intensities) they are mostly the same between Libra (without >>> isotopic impurity correction and 0 pseudocounts) and the >>> ProteomeDiscoverer/Byonic. Execution of Libra is defined in the >>> conditions.xml file that has to be defined for each Libra run. I would be >>> happy to take a look at your data and analysis to see if it can be placed >>> on the right path for the Libra analysis to work. Please post your results >>> somewhere I can download and test. >>> >>> Cheers, >>> -David >>> >>> On Fri, Mar 25, 2022 at 6:36 AM Shagun Gupta <[email protected]> wrote: >>> >>>> Hello >>>> >>>> Our lab has been trying to use Libra to quantify MS2 (Ion-trap) >>>> identification and MS3-based quantification of TMT datasets and we were >>>> trying to benchmark with an artificial yeast and mammalian spiked dataset >>>> with known fold-change (FC) values. However we observe drastically >>>> different values than expected, something we don't observe with other >>>> search engines for the same dataset. >>>> >>>> Has this issue been encountered before/ is there something obviously >>>> wrong when running with TPP that might cause this? Happy to provide >>>> further >>>> details on the dataset and parameters used to run with (most of them >>>> default apart from additions like static modification for TMT and >>>> specification of MS3 for quantification among others). >>>> >>>> Thank you, >>>> Shagun >>>> >>>> -- >>>> 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 view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/7a0b1188-7c5f-4528-9e90-282b860e7627n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/7a0b1188-7c5f-4528-9e90-282b860e7627n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/9f9b5ee4-bfd0-4279-8ea6-dffb3932b7een%40googlegroups.com.
