Re: [Open-ms-general] MS1 quantification

[Peter W. <pwa...@gm...>]

Hi, Jorrit, Oliver,

Another option is to do the centroiding when creating the mzML file from
your raw file. I work with Thermo data, and I use ProteoWizard's excellent
msConvert tool for this.
My command line for creating an MS1-only mzML file for input to
FeatureFinderCentroided looks like this (proteoWizard's web site has more
details on filters, etc.):

msconvert <raw file> --mzML --filter "peakPicking true 1" --filter
"zeroSamples removeExtra 1"  --filter "msLevel 1"  -o <output directory>

The peakPicking filter does the centroiding. "true" means vendor-preferred,
which uses Thermo's DLLs, and does a very good job.

Best,
- Peter


On Tue, Dec 9, 2014 at 11:02 AM, Oliver Kohlbacher <
oli...@un...> wrote:

> Dear Jorrit,
>
> > On 09.12.2014, at 16:26, Jorrit Boekel <jor...@sc...>
> wrote:
> > Thank you for the explanations. I tried using FeatureFinderCentroided
> before after reading a comment from Oliver in another thread, but it gets
> killed by my system (exit code 137, ubuntu 14.04 inside a docker container)
> about a minute after ‘loading chromatogram list’. What I didn’t realise
> then is that my MS1 data is profile. Not sure if that is what kills the
> process, but if it is, maybe a warning should be issued by the program just
> to make it idiot proof.
> Yes, that is a know issue. Please use PeakPicker(Hires)
> on the data before handing it to PeakPickerCentroided.
> The issue is known and we are working on a warning for
> that.
>
> Cheers,
>   Oliver
>
>
>
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