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 -- 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/CALZrgHS%3DWXiK7ma%2BtwA9pYKtQL6uzWk%3DxW66QZ1A6T5fAtHb2A%40mail.gmail.com.
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