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Calculate_​variable_​DIA_​windows

Calculate variable DIA windows from MS1

Calculates the sizes for DIA/SWATH windows depending on the intensity of MS1 data from DDA runs (AKA variable or dynamic DIA). The DDA files must be in mzML format (use ThermoRawFileParser or msConvert to convert vendor files). If the files are not peack-picked (controided), this will be performed by the workflow.

Calculate variable DIA windows from MS1 intensitiesCalculates the sizes for DIA/SWATH windows depending on the intensity of MS1 data from DDA runs. The DDA files must be inmzML format (use ThermoRawFileParser or msConvert to convert vendor files). If the files are not peak-picked (controided), this willbe performed by the workflow.Requirements:- OpenMS nodes must be installed into KNIMESettings:binned data minimum: the minimal m/z value for a windows (data below this is ignored)binned data maximum: the maximal m/z value for windows (data above this is ignored)final bins: the final number of bins (this should relect you possible cycle time!)calculation bins (optional): number of bins used for calculation (pre-binning of m/z values)intensity threshold (optional): the minimal intensity of a peak to take into account (quick noise filter)start and end RT: the retention time in seconds between which spectra are considered (to filter out column loading and increasing ofgradient at the end) 20191205 version 1.0 (by julianu) iterate over input filesselect the files(in mzML) for thecalculation of DIAwindows Chunk Loop Start read in mzMLspectra data settings get binned spectraintensities Loop End calculatefinal windows pre-process input Input Files Calculate variable DIA windows from MS1 intensitiesCalculates the sizes for DIA/SWATH windows depending on the intensity of MS1 data from DDA runs. The DDA files must be inmzML format (use ThermoRawFileParser or msConvert to convert vendor files). If the files are not peak-picked (controided), this willbe performed by the workflow.Requirements:- OpenMS nodes must be installed into KNIMESettings:binned data minimum: the minimal m/z value for a windows (data below this is ignored)binned data maximum: the maximal m/z value for windows (data above this is ignored)final bins: the final number of bins (this should relect you possible cycle time!)calculation bins (optional): number of bins used for calculation (pre-binning of m/z values)intensity threshold (optional): the minimal intensity of a peak to take into account (quick noise filter)start and end RT: the retention time in seconds between which spectra are considered (to filter out column loading and increasing ofgradient at the end) 20191205 version 1.0 (by julianu) iterate over input filesselect the files(in mzML) for thecalculation of DIAwindows Chunk Loop Start read in mzMLspectra data settings get binned spectraintensities Loop End calculatefinal windows pre-process input Input Files

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Created by: julian
Created at: 2018-02-19
On NodePit since: 2019-12-07
Last update: 2024-12-21
Created with KNIME version: v4.0.2
Tags: proteomicsDIA

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