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

[Witold E W. <wew...@gm...>]

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