Thank you so much David for doing this for me. In fact I was running asapratio again on the centroid mzml file. But I see that though express completed easily but the asapratio is still running. Is there any way in tpp to see how much time will it take to complete.
But I will try with the version you have shared the link with me. Should I use centroid mzml for this ?. Regards, Sudarshan On Mon, Dec 4, 2023, 2:29 PM 'David Shteynberg' via spctools-discuss < [email protected]> wrote: > Hello Sudarshan, again! > > I was able to update the ASAPRatioPeptideParser.exe tool for your testing > purposes to see if it runs a bit faster after some optimization I was able > to implement. Please download the following version: > https://drive.google.com/file/d/1Pe1pBFZ9BOxrrYNY6O8rkrybKaGtDhZZ/view?usp=sharing > > And replace the copy you have in C:/TPP/bin/ > > When I ran it on my not very powerful desktop computer it completed on > your data in about 42,000 seconds using the new code (less than 12 hours) > > [image: image.png] > > > Notice that the interface still says that "This command is still > running..." even though the log says "job completed" > > This is because for very long jobs the webserver times-out before the job > completes. To solve this the user must click the link just above that is > next to the text: "If you commands have actually completed but the server > timed out, click here" > > I hope this helps you process your data given your current computational > resources in less than 1 day. > > Cheers! > -David > > On Mon, Dec 4, 2023 at 11:05 AM sudarshan kumar <[email protected]> > wrote: > >> one more query- >> I used same samples - for label free and SILAC express? >> Ideally I should get a similar conclusion from both the experiments. >> But the differentially expressed proteins are different in the two >> analyses. >> >> NOte: I have used only one run file of control and one run file of >> treatment for LFQ >> While for SILAC I have used 6 run files of same samples (technical >> replicates). >> >> Please let me know where I am wrong? In my point of view increasing the >> number of run files will improve PSM and hence quantification using >> express. What should i believe my SILAC express results or the same >> sample LFQ (st. peters results)? >> >> >> On Mon, Dec 4, 2023 at 10:58 AM sudarshan kumar <[email protected]> >> wrote: >> >>> Hi David, >>> I am using this tutorial for Expressan dASAPratio . can yuo please >>> comment on if I am using the right one.? >>> Regards, >>> Sud >>> >>> On Thu, Nov 30, 2023 at 10:53 AM sudarshan kumar < >>> [email protected]> wrote: >>> >>>> can i select all the three options? >>>> Will it impact Express analysis? >>>> Centroid all scans (MS1 and MS2) -- meaningful only if data was >>>> acquired in profile mode >>>> Compress peak lists for smaller output file >>>> Write the output as a gzipped file (other TPP tools can read gzipped >>>> files directly) >>>> >>>> On Wed, Nov 29, 2023 at 1:37 PM David Shteynberg < >>>> [email protected]> wrote: >>>> >>>>> Dear Sud, >>>>> >>>>> I was able to process your dataset! Although, I am still working on >>>>> getting a faster version of ASAPRatio compiled for your testing purposes. >>>>> Meanwhile you can help the process by filtering your files so that zero >>>>> intensity peaks in the MS1 data are removed and the MS1 data is >>>>> centroided. You can accomplish both of these things using the msconvert >>>>> tool. This will help reduce the time requirement to process this dataset. >>>>> I should have more to say about this particular case in the next few days. >>>>> >>>>> Cheers! >>>>> -David >>>>> >>>>> On Nov 29, 2023, at 10:17 AM, sudarshan kumar < >>>>> [email protected]> wrote: >>>>> >>>>> Hi David, >>>>> could you get time to see into my analysis? I need your advice. >>>>> Best regards, >>>>> Sud >>>>> >>>>> On Wed, Nov 22, 2023 at 3:51 PM 'David Shteynberg' via >>>>> spctools-discuss <[email protected]> wrote: >>>>> >>>>>> Hello Sudarshan, >>>>>> >>>>>> Please zip this directory on your system: >>>>>> c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param >>>>>> >>>>>> Then upload the zip file to your favorite cloud server and share the >>>>>> link with me. >>>>>> >>>>>> Thanks! >>>>>> -David >>>>>> >>>>>> On Wed, Nov 22, 2023 at 3:17 PM sudarshan kumar < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> *EXECUTING: cd c:/TPP/data/SILAC/Comet_SILAC/Comet_silac_param && c: >>>>>>> && C:/TPP/bin/xinteract -Ninteract_silaccomtwofiles.pep.xml -p0.0 -l6 >>>>>>> -THREADS=1 -PPM -OA -ipP -X-m0.1-c5-p1-L-nR,10.008269-nK,8.014199 >>>>>>> -A-lRK-F-C-Z-r0.05 110623_Silac_TEST_01.pep.xml >>>>>>> 110623_Sud_LH_TEST_02.pep.xml* >>>>>>> >>>>>>> On Wed, Nov 22, 2023 at 3:07 PM sudarshan kumar < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Thank you so much David, >>>>>>>> But can you tell me how can i compress? Do you mean this link? >>>>>>>> (6) ISB/SPC Trans Proteomic Pipeline :: jobs >>>>>>>> <http://localhost:10401/tpp/cgi-bin/tpp_gui.pl?Action=display&page=jobs&show_job=HGYB4F2HW2_20231120-150857> >>>>>>>> >>>>>>>> On Wed, Nov 22, 2023 at 2:31 PM 'David Shteynberg' via >>>>>>>> spctools-discuss <[email protected]> wrote: >>>>>>>> >>>>>>>>> Dear Sudarshan, >>>>>>>>> >>>>>>>>> It is hard to say why this particular execution resulted in >>>>>>>>> apparent failure, but if you are willing to compress the *whole >>>>>>>>> directory *of this analysis and send me a download link, I would >>>>>>>>> be happy to download this dataset and check why it failed. >>>>>>>>> >>>>>>>>> Cheers! >>>>>>>>> -David >>>>>>>>> >>>>>>>>> On Wed, Nov 22, 2023 at 12:04 PM sudarshan kumar < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> Can anyone please help me know, why when I am running express and >>>>>>>>>> ASAPratio it always takes more than two days time and though express >>>>>>>>>> is >>>>>>>>>> completed but after running for around 80% in asapratio it stucks >>>>>>>>>> and shows >>>>>>>>>> only the running status but nothing moves ahead. <Screenshot >>>>>>>>>> 2023-11-22 120242.png> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> 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/a1b10bac-e49a-429f-a255-500332721e7fn%40googlegroups.com >>>>>>>>>> <https://groups.google.com/d/msgid/spctools-discuss/a1b10bac-e49a-429f-a255-500332721e7fn%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/CAGJJY%3D8LhUKQ0CgKHSA55wddG9HwYASJNYKwXfvRYLCEXr0y2w%40mail.gmail.com >>>>>>>>> <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8LhUKQ0CgKHSA55wddG9HwYASJNYKwXfvRYLCEXr0y2w%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>>>> . >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------------------------------------------------- >>>>>>>> The real voyage of discovery consists not in seeking new lands but >>>>>>>> seeing with new eyes. — Marcel Proust >>>>>>>> >>>>>>>> Dr. Sudarshan Kumar >>>>>>>> (Fulbright-Nehru Fellow) >>>>>>>> (B.V.Sc.& A.H., M.V.Sc <http://m.v.sc/>., PhD.) >>>>>>>> Sr. Scientist >>>>>>>> Animal Biotechnology Center >>>>>>>> (Proteomics and Cell Biology Lab.) >>>>>>>> National Dairy Research Institute Karnal, 132001 >>>>>>>> Haryana, India >>>>>>>> Contact No 09254912456 >>>>>>>> URL www.ndri.res.in >>>>>>>> Orcid Id: https://orcid.org/0000-0002-9816-4307 >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ------------------------------------------------------------------- >>>>>>> The real voyage of discovery consists not in seeking new lands but >>>>>>> seeing with new eyes. — Marcel Proust >>>>>>> >>>>>>> Dr. Sudarshan Kumar >>>>>>> (Fulbright-Nehru Fellow) >>>>>>> (B.V.Sc.& A.H., M.V.Sc <http://m.v.sc/>., PhD.) >>>>>>> Sr. Scientist >>>>>>> Animal Biotechnology Center >>>>>>> (Proteomics and Cell Biology Lab.) >>>>>>> National Dairy Research Institute Karnal, 132001 >>>>>>> Haryana, India >>>>>>> Contact No 09254912456 >>>>>>> URL www.ndri.res.in >>>>>>> Orcid Id: https://orcid.org/0000-0002-9816-4307 >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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/CALZrgHT-jhN6BGkYap6epaK-QjKmZ83ErBsvxmb%2BFR-TQs%3DpMA%40mail.gmail.com >>>>>>> <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHT-jhN6BGkYap6epaK-QjKmZ83ErBsvxmb%2BFR-TQs%3DpMA%40mail.gmail.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/CAGJJY%3D_med6%3D2YdYkgF1XQ_vMTLRxd5AbNzHe4tnWQj%3D3uMZpg%40mail.gmail.com >>>>>> <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D_med6%3D2YdYkgF1XQ_vMTLRxd5AbNzHe4tnWQj%3D3uMZpg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>> . >>>>>> >>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------- >>>>> The real voyage of discovery consists not in seeking new lands but >>>>> seeing with new eyes. — Marcel Proust >>>>> >>>>> Dr. Sudarshan Kumar >>>>> (Fulbright-Nehru Fellow) >>>>> (B.V.Sc.& A.H., M.V.Sc <http://m.v.sc/>., PhD.) >>>>> Sr. Scientist >>>>> Animal Biotechnology Center >>>>> (Proteomics and Cell Biology Lab.) >>>>> National Dairy Research Institute Karnal, 132001 >>>>> Haryana, India >>>>> Contact No 09254912456 >>>>> URL www.ndri.res.in >>>>> Orcid Id: https://orcid.org/0000-0002-9816-4307 >>>>> >>>>> >>>>> -- >>>>> 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/CALZrgHTCU_6N7XeTffeoRm64ztPYX_PA2N-2JtCAu45yB6xiEA%40mail.gmail.com >>>>> <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHTCU_6N7XeTffeoRm64ztPYX_PA2N-2JtCAu45yB6xiEA%40mail.gmail.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/512A0D1D-8CF0-4C63-A9D3-214A5FA5748B%40systemsbiology.org >>>>> <https://groups.google.com/d/msgid/spctools-discuss/512A0D1D-8CF0-4C63-A9D3-214A5FA5748B%40systemsbiology.org?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------- >>>> The real voyage of discovery consists not in seeking new lands but >>>> seeing with new eyes. — Marcel Proust >>>> >>>> Dr. Sudarshan Kumar >>>> (Fulbright-Nehru Fellow) >>>> (B.V.Sc.& A.H., M.V.Sc., PhD.) >>>> Sr. Scientist >>>> Animal Biotechnology Center >>>> (Proteomics and Cell Biology Lab.) >>>> National Dairy Research Institute Karnal, 132001 >>>> Haryana, India >>>> Contact No 09254912456 >>>> URL www.ndri.res.in >>>> Orcid Id: https://orcid.org/0000-0002-9816-4307 >>>> >>>> >>> >>> -- >>> ------------------------------------------------------------------- >>> The real voyage of discovery consists not in seeking new lands but >>> seeing with new eyes. — Marcel Proust >>> >>> Dr. Sudarshan Kumar >>> (Fulbright-Nehru Fellow) >>> (B.V.Sc.& A.H., M.V.Sc., PhD.) >>> Sr. Scientist >>> Animal Biotechnology Center >>> (Proteomics and Cell Biology Lab.) >>> National Dairy Research Institute Karnal, 132001 >>> Haryana, India >>> Contact No 09254912456 >>> URL www.ndri.res.in >>> Orcid Id: https://orcid.org/0000-0002-9816-4307 >>> >>> >> >> -- >> ------------------------------------------------------------------- >> The real voyage of discovery consists not in seeking new lands but seeing >> with new eyes. — Marcel Proust >> >> Dr. Sudarshan Kumar >> (Fulbright-Nehru Fellow) >> (B.V.Sc.& A.H., M.V.Sc., PhD.) >> Sr. Scientist >> Animal Biotechnology Center >> (Proteomics and Cell Biology Lab.) >> National Dairy Research Institute Karnal, 132001 >> Haryana, India >> Contact No 09254912456 >> URL www.ndri.res.in >> Orcid Id: https://orcid.org/0000-0002-9816-4307 >> >> -- >> 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/CALZrgHSmLvSAME3twFJBy4gf8z0r6AGEqEkQtR8ALGL4psGceQ%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHSmLvSAME3twFJBy4gf8z0r6AGEqEkQtR8ALGL4psGceQ%40mail.gmail.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/CAGJJY%3D9hY7jwBN9h-m-ZSDnuJ-QFpq4AExw6HJ0YbHXFN33SaQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D9hY7jwBN9h-m-ZSDnuJ-QFpq4AExw6HJ0YbHXFN33SaQ%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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