Re: [proteowizard-support] msconvert --filter "MS2Denoise ... usage?

[Brian P. <bri...@in...>]

I've improved the documentation for that (in the usage statement, and the
online docs):

MS2Denoise [<peaks_in_window> [<window_width_Da>
[multicharge_fragment_relaxation]]]
Noise peak removal for spectra with precursor ions.
<peaks_in_window> - the number peaks to select in window, default is 6.
<window_width_Da> - the width of the window in Da, default is 30.
<multicharge_fragment_relaxation> - if "true" (the default), allows more
data below multiply charged precursors.
The filter first removes any m/z values above the precursor mass minus the
mass of glycine.
It then removes any m/z values within .5 Da of the unfragmented precursor
mass.
Finally it retains only the<peaks_in_window> most intense ions within a
sliding window of<window_width_Da> Da.
If<multicharge_fragment_relaxation> is true, allows more peaks at lower
mass (i.e. below precursor).
If<window_width_Da> is set to 0, the window size defaults to the highest
observed mass in the spectrum (this leaving only<peaks_in_window> ions in
the output spectrum).
Reference: "When less can yield more - Computational preprocessing of MS/MS
spectra for peptide identification", Bernhard Y. Renard, Marc Kirchner,
Flavio Monigatti, Alexander R. Ivanov, Juri Rappsilber, Dominic Winter,
Judith A. J. Steen, Fred A. Hamprecht and Hanno Steen Proteomics, 9,
4978-4984, 2009.


On Wed, May 29, 2013 at 9:32 AM, Witold E Wolski <wew...@gm...> wrote:

> Hi,
>
> I am trying to use MS2Denoise to smooth data? At least this is my first
> guess that this filter is doing this.
>
> I am running it on an mzML file containing profile spectra at ms 2 level.
>
>
> msconvert  --filter "MS2Denoise 2000 20" --mzML -z --outfile smooth.mzML
> prep.mzML
>
> This is the command I am using.
>
> the only difference between input and output is:
>
> <         <spectrum index="0" id="scan=1" defaultArrayLength="4420"
> dataProcessingRef="dp_sp_0">
> ---
> >         <spectrum index="0" id="scan=1" defaultArrayLength="4420"
> dataProcessingRef="pwiz_Reader_conversion">
> 127c132
> <         <spectrum index="1" id="scan=2" defaultArrayLength="4367">
> ---
> >         <spectrum index="1" id="scan=2" defaultArrayLength="4367"
> dataProcessingRef="pwiz_Reader_conversion">
> 173c178
> <         <spectrum index="2" id="scan=3" defaultArrayLength="4303">
> ---
>
> I am using msvoncert:
>
> ProteoWizard release: 3.0.4585 (2013-5-24)
> ProteoWizard MSData: 3.0.4585 (2013-5-24)
> ProteoWizard Analysis: 3.0.4584 (2013-5-24)
> Build date: May 29 2013 18:00:05
>
>
>
> Help highly appreciated.
>
> Witold
>
>
>
>
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