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bioconductor-msnbase smooth chromatogram (version 2.32.0+galaxy0)

Input mzML File:

The input mzML file containing the MSnbase data.

Half window size:

The half window size for the moving window smoothing method. This determines the number of data points on either side of the center point to include in the smoothing calculation.

Weighted:

Specify whether to apply a weighted moving average, where the weights depend on the distance from the center of the window.

QTOF:

Indicate if the data was acquired using a QTOF (Quadrupole Time-of-Flight) instrument, which affects the time domain processing.

ppm tolerance:

The parts-per-million (ppm) tolerance for considering mz values as belonging to the same ion. A higher value allows for more variation in mz values.

Function to combine intensities:

Choose the function to combine the intensity values of the same m/z value within the moving window. Options include mean, median, min, max, and sum.

What it does

This tool performs chromatogram smoothing on mass spectrometry data using the MSnbase package in R. It applies a moving window smoothing method to the input mzML file, which helps in reducing noise and improving the signal quality.

Usage

Input: Provide the input mzML file containing the mass spectrometry data to be smoothed.
Parameters:
- Half window size: The number of data points on either side of the center point to include in the smoothing calculation.
- Weighted: Whether to apply a weighted moving average.
- QTOF: Indicate if the data was acquired using a QTOF instrument.
- ppm tolerance: The parts-per-million tolerance for considering mz values as belonging to the same ion.
- Function to combine intensities: Choose the function to combine the intensity values within the moving window.
Output: The smoothed mzML file.

Input

Input mzML File: The input mzML file containing the MSnbase data to be smoothed.

Output

Output mzML File: The resulting mzML file after applying the smoothing algorithm.