Begin forwarded message:
> From: "Pudney Chris (ext) GBJH" <chris.pud...@syngenta.com>
> Date: March 21, 2011 5:59:13 PM GMT+09:00
> To: tomas Pluskal <plus...@oist.jp>
> Subject: Finished merging Syngenta code
>
> G'day,
>
> I've finished merging the Syngenta code into the main trunk of the MZmine 2
> repository.
>
> As well as the ChemSpider search there's now also:
> Raw data methods > Filtering > Baseline correction
> Peak list methods > Peak detection > Smoothing
> Peak list methods > Identification > NIST MS Search
> The baseline correction module uses R's ptw package to perform baseline
> correction on a raw data file. It relies on rJava/JRI to invoke R. As a
> consequence I've had to add some steps to the start-up scripts to make this
> possible. The user needs to have R, ptw and rJava installed if they want to
> make use of this module. However, if they don't then the start-up scripts
> and MZmine 2 will still run fine. I haven't modified the Mac start-up script
> as I don't have access to a Mac and am not very familiar with OS X.
>
> The smoothing module simply performs Savitzky-Golay smoothing on peak
> chromatograms. It's for use prior to deconvolution.
>
> The NIST MS Search module uses NIST MS Search to identify peaks. It's only
> available for Windows. I've had to add a couple of steps to the Windows
> start-up script to make this work. If the user doesn't have NIST MS Search
> installed then the script and MZmine 2 will still run fine.
>
> There's also an experimental module I've been working on to use XCMS to
> identify peaks. It's a work in progress and has not been merged. The code
> is on a feature branch.
>
> Please let me know if you have any questions about the above especially if it
> has caused any problems.
>
> Regards,
> Chris.
>
> Syngenta Limited, Registered in England No 2710846
> Registered Office : Syngenta Limited, European Regional Centre, Priestley
> Road, Surrey Research Park, Guildford, Surrey, GU2 7YH, United Kingdom
>
>
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