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.
