MSMS Spectrum Viewer

A node for displaying annotated MS/MS spectra of peptides based on the Lorikeet.js library (https://uwpr.github.io/lorikeet/). An input table could be generated by joining outputs from peptide search engines of the OpenMS plugin and the corresponding spectra from the input mzML file by the spectrum reference. MzML files can be converted to a KNIME table by the FileToTable node.

Options

Sequence
Select the (unmodified) sequence column.
Intensities
Select the intensities column.
MZ
Select the m/z column with the same size as intensities.
mods
Select the column with the modifications collection. Format: [POSITION-MASS,POSITION-MASS,...]
charge
Select the column with the precursor charge.
precursorMass
Select the column with the precursor mass.
Subscribe to selection events
If checked, the view reacts on notifications from other interactive views that the selection has been changed. See also "Publish selection events".

Input Ports

Icon
Data table containing the information for the sequence viewer. Check the config dialogue for the expected columns.

Output Ports

This node has no output ports

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Views

Interactive View: Spectrum Viewer
View single picked MS/MS spectrum with annotations.

Workflows

Links

Developers

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Installation

To use this node in KNIME, install the extension OpenMS JavaScript Views from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Zuse Institute Berlin
Plugin version: 1.0.0.202304261339
On NodePit since: 2023-12-06
Last update: 2024-04-29
KNIME versions: Since v4.4

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