To whom ETD concerns:
Vagisha Sharma and Jimmy Eng's etdz charge prediction tool (http://pubs.acs.org/doi/full/10.1021/pr1006685) has been embedded in the latest snapshots of
ProteoWizard. If you want to use it, add a filter on the msconvert command-line like so:
msconvert data-with-etd.RAW --filter "chargeStatePredictor true 4 2 0.9"
It synergizes well with the existing ETDFilter (which removes the precursor, charge-reduced precursors, and neutral losses); just make sure to run ETDFilter
AFTER chargeStatePredictor (filters are applied in the order they are found on the command-line):
msconvert data-with-etd.RAW --filter "chargeStatePredictor true 4 2 0.9" --filter
"ETDFilter true true true false 3.1 mz"
The new chargeStatePredictor is available in pwiz 2.1.2385 and later:
http://teamcity.labkey.org:8080/repository/download/bt77/22680:id/pwiz-bin-windows-x86-vc90-release-shared-2_1_2385.tar.bz2?guest=1
The charge state prediction is most important for MSn spectra triggered by low resolution precursors, but there might be some gain in the high resolution world
as well (especially for low intensity peptides).
The ETD filtering is a critical preprocessing step for any analysis engine that
doesn't do its own ETD filtering.
-Matt
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