Thanks for your prompt answers. I have substituted all charges with 0s
and it worked well with both X!Tandem and TPP. It appears to be the
simplest fix so I will stick to it. Again - thanks!
On Apr 27, 11:08 am, Matthew Chambers
wrote:
> The chargeStatePredictor filter in msconvert can override
Try re-generating the index at the end of the mzXML file after you
edit out the charge state. The TPP tools are failing to parse your
mzXML because the scan index is no longer valid. You can re-generate
the index using "indexmzXML" which is distributed with the TPP
(c:\inetpub\tpp-bin\indexmzXML.
The chargeStatePredictor filter in msconvert can override existing charge states and put in multiple
possible charge states for multiply charged spectra and charge=1 for singly charged spectra (based
on %TIC below the precursor m/z). It works fine with mzML but I'm not sure how X!T would handle i
Is there a suggested way to interpret the site probability score
calculated by PTMProphet. Is 0.9 consider a reasonable score like the
other Prophets, and does it map on to an FDR somehow?
Many thanks for any advice,
Ben
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Hi,
I am analyzing some old data from Velos that was acquired with charge
state screening during acquisition, i.e. charge state is determined
and stored in .raw file. However, we now want to search this data
without pre-determined charge state since it is often not accurately
assigned (this is just
