Load Bruker AMIX Peaklist Files

Each Peaklist file is loaded and parsed such that one output row of the table contains the peaklist for 1 spectrum. Files may be a mix of 1D and 2D spectra

The output table contains:

  • The single spectrum peaklist file - ie the portion of the input file for a single spectrum
  • Title - Assigned by AMIX, not the spectrum title
  • Date - The date the peaklist was exported from AMIX, not the date the spectrum was obtained
  • User - The user on the machine AMIX was running on, not the user acquiring the spectrum
  • Host - The machine AMIX was running on, not the spectrometer
  • Spectrum - the path to the spectrum data loaded to AMIX
  • w1 - A list of the w1 frequencies ('w' in the case of 1D spectra are in this column)
  • w2 - A list of the w2 frequencies, for 2D spectra, or missing values
  • Intensity - A list of the peak intensities
  • Volume - A list of the peak volumes
  • Annotation - A list of the peak annotations (If there are no annotations, this will contain a missing value cell)

The lists can be correctly resolved using an Ungroup node

This node was developed by Vernalis Research . For feedback and more information, please contact knime@vernalis.com

Options

Select files
Use the 'Browse...' and 'Add from history' buttons to add all the files to be included in the table. Alternatively, a flow variable can be specified, containing one or more filenames separated by ';'. The latest added file(s) will be selected. If no files are highlighted in the 'Selected files' box, then the 'Browse...' button opens a new file browser window in the default location; otherwise, the file browser opens in the last highlighted file's location.
Select file encoding
Select the file encoding. 'Guess' will attempt to assign it based on the connectin property of the URL, the content-type, and the Byte-Order Mark (BOM). UTF-8 will be used if no other encoding is identified
Include paths in output table
Include the full file path and URLs as columns in the output table
Include filename in Row IDs
The filename will be included in the Row ID (duplicated will be suffixed with '_n', where n is an index starting at 0). Otherwise, the Row IDs will be in the format 'Row_n', with an an index starting at 0
Include filenames in output table
Include the filename as a column in the output table
Newline output
The newline character(s) to be used in the cell containing the full peaklist file for the individual spectrum. 'System' will dynamically use the the newline of the system the node is executed on (the current value for this is shown in the dialog, but on another system, the local value will be used). 'Preserve incoming' will look in the first 65535 characters of the file for the first linebreak ('\r\n' or '\n') and use that

Input Ports

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Optional flow variables containing file path(s)

Output Ports

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Parsed content of the loaded files

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Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes 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: Vernalis Research, UK
Plugin version: 1.36.5.v202312051850
On NodePit since: 2023-12-06
Last update: 2024-04-19
Tags: Streamable
KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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