Re: [proteowizard-support] msconvert wiff files chargeStatePredictor problems

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Hi Achim,

chargeStatePredictor works by looking at the intensity above and below the precursor m/z in the MS2+ scan and determining whether it's 
likely to be singly or multiply charged. If it's multiply charged, it will assign multiple probable charge states (according to the filter's 
settings). There is another filter, turbocharger, which uses isotopic distributions in the MS1s to predict charge, and it was specifically 
designed to work on Sciex data, but it can be a bit tricky to use:

Don't apply peak picking (to MS1s) before using this filter, it will do the peak picking itself. Here's the usage info:

turbocharger [minCharge=<minCharge>] [maxCharge=<maxCharge>] [precursorsBefore=<before>] [precursorsAfter=<after>] [halfIsoWidth=<half-width 
of isolation window>] [defaultMinCharge=<defaultMinCharge>] [defaultMaxCharge=<defaultMaxCharge>] [useVendorPeaks=<useVendorPeaks>]
Predicts MSn spectrum precursor charge based on the isotopic distribution associated with the survey scan(s) of the selected precursor
   <maxCharge> (default: 8) and <minCharge> (default 1): defines range of possible precursor charge states.
   <before> (default: 2) and <after> (default 0): number of survey (MS1) scans to check for precursor isotopes, before and after a MS/MS in 
retention time.
   <half-width of isolation window> (default: 1.25): half-width of the isolation window (in Th.) from which precursor is derived. Window is 
centered at target m/z with a total size of +/- the value entered.
   <defaultMinCharge> (default: 0) and <defaultMaxCharge> (default: 0): in the event that no isotope is found in the isolation window, a 
range of charges between these two values will be assigned to the spectrum. If both values are left at zero, no charge will be assigned to 
the spectrum.

Hope this helps,
-Matt

On 6/13/2017 12:00 PM, Achim Treumann wrote:
>
> Hi Brian,
>
>
> when I wrote 'ruin through', I meant 'run through', of course 😊
>
>
> However, when I look at the mgf file, there are still no correct charges in the header... Do I misunderstand the use of 
> chargeStatePredictor? The 'Title' line that I am trying to build should have the charge sitting as the second last bit of information, 
> prior to the 'HCD'.
>
>
> Achim
>
>
> ================== from mgf file ================
>
> BEGIN IONS
> TITLE=170411_26_test;630;3.123733333333;;HCD
> RTINSECONDS=187.424
> PEPMASS=721.689696805151
> CHARGE=2+ and 3+
> 229.1193747 0.0584093988
> 234.1468104 0.0751502665
> 305.1810434 0.0772159607
> ...
>
> ================== end mgf file ================
>
>
> Achim Treumann
> http://www.ncl.ac.uk/nuppa
> email: ach...@ne...
> phone: 0191 2084804
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------
> *From:* Achim Treumann
> *Sent:* 13 June 2017 17:54
> *To:* Brian Pratt
> *Cc:* su...@pr...; Andrew Porter
> *Subject:* Re: [proteowizard-support] msconvert wiff files chargeStatePredictor problems
>
> Hi Brian,
>
>
> it does now ruin through without an error! Thanks a lot.
>
> As the file is a bit big, it will take a short while to check, if it has really guessed charges and put them into the mgf file, I will 
> feed back, if I cannot find them.
>
>
> Thanks again,
>
> Achim
>
>
> Achim Treumann
> Director, NUPPA
> Newcastle University Protein and Proteome Analysis and
> Newcastle University Institute of Ageing
> Devonshire Building
> Devonshire Terrace
> Newcastle upon Tyne NE1 7RU
>
> http://www.ncl.ac.uk/nuppa
> email: ach...@ne...
> phone: 0191 2084804
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------
> *From:* Brian Pratt <bs...@pr...>
> *Sent:* 13 June 2017 17:21
> *To:* Achim Treumann
> *Cc:* su...@pr...; Andrew Porter
> *Subject:* Re: [proteowizard-support] msconvert wiff files chargeStatePredictor problems
> OK, this time actually looking at the code I think you might try using 0 and 1 instead of false and true.
>
> Let me know it that works, and hopefully the author of that code will make an adjustment. I suspect it's a platform/compiler dependent thing.
>
> Cheers
>
> Brian
>
> On Tue, Jun 13, 2017 at 9:10 AM, Achim Treumann <ach...@ne... <mailto:ach...@ne...>> wrote:
>
>     Hi Brian,
>
>     Many thanks for your fast response.
>
>     I have already done it with and without quotation marks on all different lines. Does not make a difference.
>
>     Achim
>
>     Email: ach...@ne... <mailto:ach...@ne...>
>
>     Phone: +44 191 2084804 <tel:+44%20191%20208%204804>
>
>     URL: http://www.ncl.ac.uk/nuppa
>
>     *From:*Brian Pratt [mailto:bs...@pr... <mailto:bs...@pr...>]
>     *Sent:* Tuesday, June 13, 2017 5:08 PM
>     *To:* Achim Treumann <ach...@ne... <mailto:ach...@ne...>>
>     *Cc:* su...@pr... <mailto:su...@pr...>; Andrew Porter <And...@ne...
>     <mailto:And...@ne...>>
>     *Subject:* Re: [proteowizard-support] msconvert wiff files chargeStatePredictor problems
>
>     Without really investigating,I'm guessing it's that you haven't got quotes around that filter as you have with the others. Give that a
>     go and let us know how it works.
>
>     Cheers
>
>     Brian
>
>     On Tue, Jun 13, 2017 at 8:07 AM, Achim Treumann <ach...@ne... <mailto:ach...@ne...>> wrote:
>
>         Dear all,
>
>         I am running proteowizard 3.0.10922 on a Windows 8.1 computer, trying to extract a peaklist in *.mgf format from Sciex TT6600
>         data. I am trying to do this with a config file (at the bottom of this email.
>
>         One issue with the conversion of Sciex TT6600 data is that it appears to be tricky to extract the precursor ion charges, which is
>         why I was trying to make msconvert caluclate them - however, I failed miserably (see output below). I am a bit conused by the last
>         two lines of the output.
>
>         Anybody can tell me where I am going wrong?
>
>         Many thanks,
>         Achim
>
>         ====================== output of msconvert beginning ================
>         E:\data\1704 test>msconvert ".\170411_26_test.wiff"
>          -c .\mgfconfig_wiff.txt
>         Reading configuration file .\mgfconfig_wiff.txt
>
>         format: MGF
>         outputPath: E:\data\1704 test\
>         extension: .mgf
>         contactFilename:
>
>         filters:
>           "peakPicking true 1-"
>           "threshold count 80 most-intense"
>           "MS2Denoise 12 100 true"
>           chargeStatePredictor makeMS2=true
>           "titleMaker <RunId>;<ScanNumber>;<ScanStartTimeInMinutes>;<ChargeState>;<ActivationType>"
>
>         filenames:
>           .\test.wiff
>
>         processing file: .\test.wiff
>         Error writing run 1 in "test.wiff":
>         [parseKeyValuePair] error parsing "true" as value for "makeMS2=";
>         expected true or false
>
>         ====================== output of msconvert end ================
>
>         ====================== config file beginning ================
>
>         mgf=true
>         verbose=true
>         filter="peakPicking true 1-"
>         filter="threshold count 80 most-intense"
>         filter="MS2Denoise 12 100 true"
>         filter=chargeStatePredictor makeMS2=true
>         filter="titleMaker <RunId>;<ScanNumber>;<ScanStartTimeInMinutes>;<ChargeState>;<ActivationType>"
>         outdir=E:\data\1704 Linda Brochhausen\
>
>         ====================== config file end ================
>
>         Achim Treumann
>         Director, NUPPA
>         Newcastle University Protein and Proteome Analysis and
>         Newcastle University Institute of Ageing
>         Devonshire Building
>         Devonshire Terrace
>         Newcastle upon Tyne NE1 7RU
>
>         http://www.ncl.ac.uk/nuppa
>         email: ach...@ne... <mailto:ach...@ne...>
>         phone: 0191 2084804
>
>
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