Hopefully, I am understanding your queries correctly, here goes. Centroiding the data will reduce the number of peaks in the spectra and reduce the running time of the analysis. Compressing the files to make them smaller will require that the tools reading the files uncompress the data (usually internally) prior to using it which will increase the running time. As far as affecting the results, compressing the files should not change the data while centroiding will. As far as how much this will affect the final ratios probably depends on the quality of centroiding algorithm and the quality of the data. Run some tests yourself and get a feel on some data you know well; testing should help you refine your approach. Hope that helps!
-David On Mon, Dec 4, 2023, 10:59 AM sudarshan kumar <kumarsuders...@gmail.com> 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 <kumarsuders...@gmail.com> > 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 < >> dshteynb...@systemsbiology.org> 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 <kumarsuders...@gmail.com> >>> 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 < >>> spctools-discuss@googlegroups.com> 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 < >>>> kumarsuders...@gmail.com> 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 < >>>>> kumarsuders...@gmail.com> 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 <spctools-discuss@googlegroups.com> 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 < >>>>>>> kumarsuders...@gmail.com> 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 spctools-discuss+unsubscr...@googlegroups.com. >>>>>>>> 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 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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 spctools-discuss+unsubscr...@googlegroups.com. >>>>> To view this discussion on the 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------------------------------------------------------------------- >>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>> 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 > 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