Of course, I am glad to help. The old and the new versions should run faster on the centroided data. There is no way to tell *a priori* with ASAPRatio how long it will take, but since it ran to completion on my machine and it generates one dot per ten PSMs it has processed; based on the dots you can see how much of the ASAPRatio processing has completed. Here are the dots from my run on your data:
[image: image.png] On Mon, Dec 4, 2023 at 2:57 PM sudarshan kumar <[email protected]> wrote: > 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. > 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/CALZrgHQ0OYG4op8rJ3NdcpidK1tJwdAGF3Jpb3YFcPc%3DnuW1GQ%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHQ0OYG4op8rJ3NdcpidK1tJwdAGF3Jpb3YFcPc%3DnuW1GQ%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-kC6avcheBE%3DCeCdGZLLnGZhObordqsf-vviUT%3D%2B-Fcg%40mail.gmail.com.
