Take a look at BatMass http://batmass.org/ BatMass: mass spectrometry data visualization
Best, Alexey Nesvizhskii On Friday, April 5, 2019 at 5:28:39 PM UTC-4, ilya gertsman wrote: > > 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] > <javascript:>> 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] <javascript:>> 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] >>> <javascript:>> 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] <javascript:>> 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] <javascript:>. >>>>> To post to this group, send email to [email protected] >>>>> <javascript:>. >>>>> 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] <javascript:>. >>>> To post to this group, send email to [email protected] >>>> <javascript:>. >>>> 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] <javascript:>. >>> To post to this group, send email to [email protected] >>> <javascript:>. >>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> 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.
