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

[Moritz L. <mor...@gm...>]

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