Baseline correction for MALDI-TOF MS

[Mailaender]

Currently various algorithms are available to chromatograms. For MALDI MS spectra without chromatography none are available for now. As the application is slightly different, re-using existing algorithms may not be enough.

@sgibb proposed using

• an estimation by computing the median of the intensities in a moving window
• a computation of the convex hull of the spectrum via monotonic regression
• the PROcess algorithm
• the SNIP algorithm Bug 529410

in a 2011 conference publication.

Depends on https://bugs.eclipse.org/bugs/show_bug.cgi?id=496773 which has been resolved already.

[sgibb]

These algorithms are all implemented in my R package MALDIquant.

There are a lot of more algorithms in the baseline R package.

[eselmeister]

Hi Sebastian, using your project would be great. We already have a cooperation with KNIME. Our goal is to fully combine OpenChrom and KNIME. Our proof-of-concept already shows, that this is possible. They also offer a R-Node, so a connector to MALDIquant could be established: https://www.knime.org Furthermore, we are waiting for a release of StatET. This would give us direct access from within OpenChrom to R tools: https://projects.eclipse.org/proposals/statet-tooling-r-language Best, Philip Am 30.11.2016 um 20:53 schrieb Sebastian Gibb:

…

These algorithms are all implemented in my R package MALDIquant <https://github.com/sgibb/MALDIquant>. There are a lot of more algorithms in the baseline <https://cran.r-project.org/package=baseline> R package. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAp6T0n7TWvVdXbwiXhbkH1K_bmD8Kxnks5rDdQxgaJpZM4LAlfU>.

-- ~~~~~~~~~~~~~~~~~~~~~~~~ OpenChrom - the open source alternative for chromatography / mass spectrometry Dr. Philip Wenig » Founder » [email protected] » http://www.openchrom.net ~~~~~~~~~~~~~~~~~~~~~~~~

[Mailaender]

The feature was removed upstream. eclipse/chemclipse@125a391 It may need to be implemented here again.