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" 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