Re: [proteowizard-developer] Missing Charge State when converting Sciex wiff to mzXML and mgf files

[Chambers, M. <mat...@gm...>]

Hi Moritz,

You can also add --filter "chargeStatePredictor maxMultipleCharge=3 
minMultipleCharge=2 singleChargeFractionTIC=0.9"

And it will consider fraction of intensity above and below the precursor 
in the MS2 to decide whether the spectrum is singly or multiply charged. 
If you specify a range of multiple charges, then that should be 
supported in both mzML and MGF, IIRC.

There's also turbocharger which will use the MS1 scans instead, but is 
somewhat more complicated to set up (and more finicky as a result):
--filter "turbocharger minCharge=1 maxCharge=4 precursorsBefore=2 
precursorsAfter=2 halfIsoWidth=1.5"

Hope this helps,
-Matt


On 3/7/2016 2:34 PM, Moritz Lassé wrote:
>
> Hi all,
>
>
> I'm using a TripleTof 5600 and tested the conversion of wiff to mzXML 
> or mgf using MSConvert and also qtofpeakpicker + MSConvert. The 
> resulting files do not contain a charge state which makes them 
> unusable for searches with X!tandem (vengeance).
>
>
> If I use the AB_SCIEX_MS_Converter, most (~80%) of the precursors have 
> associated charge states in the mgf file. X!tandem vengeance and 
> sledgehammer work with these mgf files.
>
> Has anyone had similar "issues"? Matt already sent a very helpful 
> reply in an email saying
>
> "This is simply because Sciex's API does not calculate the charge 
> state for us (and it's not stored in the file). Their standalone 
> converter does calculate it, and also uses the Protein Pilot peak 
> picker which is better than the one they give us in their API."
>
>
> This sounds like I am forced to use the Sciex converter even though I 
> would like to use qtofpeakpicker  because it is apparently better than 
> the sciex peak picker for centroiding Sciex TripleTof 5600 data 
> according to Schubert et al. 2015 
> (http://www.ncbi.nlm.nih.gov/pubmed/25675208)
>
>
>
> You can download my example files here (zipped wiff, wiff.scan, mzXML, 
> and the 3 different mgf files using 3 different conversion 
> strategies):https://drive.google.com/drive/folders/0BybCLLWRgDsUX2VTc0F1ZlpCMnM
>
> The commands I used for "manual" conversion with Pwiz were:
>
> Wiff to mzXML:
>
> "C:\Program Files\ProteoWizard\Pwiz\qtofpeakpicker.exe" -I 
> FILENAME.wiff -O FILENAME.mzXML --resolution=20000 --area=1 
> --threshold=1 --smoothwidth=1.1
>
> mzXML to mgf:
>
> "C:\Program Files\ProteoWizard\Pwiz\msconvert.exe" FILENAME.mzXML 
> --mgf --filter "threshold count 150 most-intense" --outfile FILENAME.mgf
>
>
> The commands I used for conversion with Sciex MS converter were:
>
> wiff to mgf:
>
> AB_SCIEX_MS_Converter WIFF "D:\Data\File A.wiff" -proteinpilot MGF 
> "D:\Data\File A.mgf"
>
> best wishes
>
> Moe
>
>