I think the SeeMS tool from ProteoWizard may be your best bet. If you have TPP installed, it may already be installed with TPP. Or otherwise, it is easy to download and install. Install all of ProteoWizard, and then from the Start menu under the ProteoWizard folder will be SeeMS.
Regards, Eric *From:* [email protected] <[email protected]> *On Behalf Of *ilya gertsman *Sent:* Friday, April 5, 2019 1:42 PM *To:* [email protected] *Subject:* Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Does anyone know of a good tool for viewing mzXML files, enabling one to look at total ion current, perform XIC's for m/z's of interest, and other basic functions (maybe something like AB Sciex's PeakView for .wiff files, but only generic ms files formats)? I saw a tool listed for TPP called mzXML viewer, but do not see how to access this through TPP. Any recommendations would be greatly appreciated! Many thanks! ilya On Fri, Apr 5, 2019 at 10:26 AM Ankit Balhara <[email protected]> wrote: Hi David, Thanks for your kind help. Actually I am estimating the FDR by using the Mayu tool, after combining the iprophet results of all the three datasets which I have, as this gives me single Posterior probability (PPs/IPs) that I am using in the SpectraST command line so as to generate the spectral library. Yes, I got the point which you have highlighted, but can I use Mayu for estimating the FDR at final stage and then filter the results below the threshold PP of FDR less than 1%, instead of filtering the results at each iProphet analyses? Thanks Ankit On Fri, 5 Apr 2019 at 20:03, David Shteynberg < [email protected]> wrote: Hello Ankit, If you computer has the resources to handle all files then running one iProphet job to combine the results will give you one analysis result with FDR rates that apply to all the data. If you do multiple iProphet runs then you have to be more careful about how you combine the results because your runs will overlap more in the correct result than the incorrect results so simply taking all results together above an FDR threshold will inflate your final FDR. One easy way to do this is to divide the FDR by the number of iProphet runs being combined. For example if you split the results into two iProphet analyses and you want the combined FDR to be less than 1% you would filter each iProphet analyses at 0.5% FDR and then take the total set. Does that make sense? Cheers, -David On Thu, Apr 4, 2019 at 8:57 AM Ankit Balhara <[email protected]> wrote: Thanks Felipe. I have posted this issue in the issues section of DIA-Umpire issue tracker. Ankit On Thu, 4 Apr 2019 at 19:21, Felipe da Veiga Leprevost < [email protected]> wrote: Hi Ankit; Please feel free to submit your DIA-Umpire questions and issues to our DIA-Umpire issue tracker: https://github.com/Nesvilab/DIA-Umpire Regards On Wednesday, April 3, 2019 at 7:05:59 AM UTC-4, Ankit Balhara wrote: Hi All, I am analyzing the SWATH-MS data using the DIA-Umpire. And I have 3 data files of same sample which lead to generation of 9 .mgf output files from DIA-Umpire, which were converted into 9 mzXML and then subjected to Comet and X! Tandem search, and subsequently to peptide prophet and hence total files generated during this process are 18 pep.xml files. My ultimate aim to build the assay library. So, I am confused how to combine the results of these 18 peptideprophet files. Should I combine the Comet search results of each data file separately and X! Tandem results separately and then combine these outputs again using iProphet? This should result in generation of 3 iprophet result files corresponding to each data file, which can again combined into one file by iProphet in final step? Or there is another way out of this problem? Thanks Ankit -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. 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For more options, visit https://groups.google.com/d/optout. -- *Clarus Analytical LLC. * *Ilya Gertsman, PhD* *Owner/manager* *7917 Ostrow St.* *San Diego, CA 92111* *www.clarusanalytical.com <http://www.clarusanalytical.com/>* *phone: 858-336-7693* -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. 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