Disable Knime Node feature (unable to disable via configuration)

I'm new to knime, and I'm attempting to recreate this* OpenMS mass spectrometry workflow as an OpenMS-Knime workflow. The OpenMS workflow was originally performed manually at the OpenMS command line.

The bump I'm running into now is, the paper states ...

[OpenMS PeakPickerHiRes was used to calculate] centroids of peaks from profile mass spectra, with signal-to-noise filter disabled...

So, the Knime implementation of OpenMS has the correct PeakPickerRes node, with all the correct configuration parameters. However, the algorithm filter does not appear to have the option of simply being 'disabled'. It has configuration items that, perhaps, can be set to render it more-or-less non-functional, but I'm wondering if there's a way to manually edit the node (via code or another method) to entirely disable the feature


* Zhang et al. 2014 - DeMix Workflow for Efficient Identification of Co-fragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry



It is a bit hidden but have you tried a value of 0.0? The description states that this will disable the SNT estimation.

Let us know, if this is what you wanted to do. I can not speak for what the authors exactly did but I think this is what they mean.



Hi Julianus. 

Thanks for the reply. I did change the setting to 0.0 - but didn't get the identical output as the paper author (I used their original mzml data file as input).

However, I have subsequently discovered they changed some of the parameters with which their data set was run, so I WOULDN'T be getting the same result :D

I think your suggestion is probably the right one. 

So much for reproducible research these days ;-)

Indeed ;) Did they not provide the workflow? That is partly why we integrated our tools in KNIME. To share workflows that inherently include all the parameter settings.