From: Matthew C. <mat...@gm...> - 2012-02-23 16:08:31
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I meant that AB Sciex's MS Data Converter will always deisotope the spectra when you choose -proteinpilot peak picking, and will also deconvolute the multiply charged fragments when MGF output is selected. If you you want raw peak lists, your best option now is Mascot Distiller. -Matt On 2/23/2012 4:53 AM, Gavin Blackburn wrote: > Hi Matt, > > Could you elaborate on "both formats deisotope the spectra"? It may be a silly question but I'm interested as we are beginning to do C13 studies (using mzXML) and I was wondering if the peaks we are interested in would be removed? > > Cheers, > > Gavin. > > -----Original Message----- > From: Matthew Chambers [mailto:mat...@gm...] > Sent: 22 February 2012 16:38 > To: Cappadona, S.; proteowizard-support > Subject: Re: [proteowizard-support] wiff ->centroided mzXML > > The index option is only to speed up random access to spectra. If you're passing it to msconvert, > it'll start converting a little bit faster (because it always has to have random access, so it will > make an index in memory if one doesn't already exist). > > The fragments in the mzML output are not charge-state deconvoluted. In the MGF, they are. Both > formats deisotope the spectra. > > -Matt > > > On 2/22/2012 4:45 AM, Cappadona, S. wrote: >> Hi Matthew, >> Thanks for your prompt answer. >> Actually the empty mzML is the centroided one. The -proteinpilot one look OK. >> >> I would just ask you two more questions, if possible: >> - shall I use the /index option? (I think I read wiff files have a problem in the way scans are saved in the mzXML file... does indexing help?) >> >> - do you have an idea if the ms2 information in the mzML is deconvoluted? >> I mean, if I simply create the mzML, and then export an mgf from it, will I get the same optimized mgf as if I use msdataconverter directly on the wiff? >> I ask because many programs out there can use mzXML alone, and extract all information from it, or they can be forced to use an external search, in the form of pepXML, for instance. >> >> I am sure it takes more time to write the questions, than to answer (-: >> >> Thanks again for your help. >> >> Salvo >> >> >> Salvatore Cappadona, PhD >> Hecklab - Biomolecular Mass Spectrometry and Proteomics Group - Bioinformatics | Utrecht University >> H.R. Kruytbuilding | Padualaan 8 | room O.609 |3584 CH, Utrecht | The Netherlands >> T. +31 (0)30 - 253 6149 | F. +31 (0)30 - 253 6919 | S.C...@uu... >> >> >> -----Original Message----- >> From: Matthew Chambers [mailto:mat...@gm...] >> Sent: Tuesday, February 21, 2012 8:36 PM >> To: Cappadona, S. >> Cc: su...@pr... >> Subject: Re: [proteowizard-support] wiff ->centroided mzXML >> >> Hi Salvo, >> >> I recommend using MSDataConverter with the -proteinpilot option and mzML output. Then you can use >> msconvert to go from mzML to mzXML if you need to. You said you tried this, and the mzML contained >> no peaks. You didn't say whether you used -centroid or -proteinpilot. If you see no peaks with >> -proteinpilot, there is probably something wrong with the data (is it peptides?). Pwiz is not a good >> choice at the moment for peak picking on WIFF data. >> >> -Matt >> >> >> On 2/21/2012 12:50 PM, Cappadona, S. wrote: >>> Dear Support, >>> >>> Can you suggest me the best option to create a */_centroided mzXML_/* from a TT5600 wiff file? >>> >>> I have been struggling with this problem for quite some time, and I had given up. >>> >>> But now I see that new releases of msconvert and MS_Data_Converter are out, so I would give it a new >>> try. >>> >>> I have tried many options and combinations, but without success. >>> >>> -I thought I could use ABSciex MS_Data_Converter to create an mzML file, followed by mscoverter to >>> create an mzXML. But centroided mzML from MS_Data_Converter look 'almost' empty (no peak information) >>> >>> -I see that I can also create mzML files with the option -profile or -proteinpilot. >>> >>> -Do you think I can then convert them by your msconvert? shal I use the peakpicking option? And >>> prefer vendor algorithm? (I think ABSciex explicitly state that centroiding has problem, in the >>> MS-Data_Converter manual) >>> >>> -Shall I better use msconvert straight away from wiff files? >>> >>> I mady many trial, with different operating systems, with vendor software installed or not . >>> >>> I already made new trials, but I still have many combinations to test . >>> >>> So I would really appreciate if you (or someone which I didn't find in your mailing list) have >>> already worked out a solution to my problem. >>> >>> Thanks a lot, >>> >>> Salvo > > ------------------------------------------------------------------------------ > Virtualization& Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |