Import Mass Spectra in a mzXML Data Format - Revision history

Laschp at 06:16, 14 December 2024

2024-12-14T06:16:06Z

← Older revision		Revision as of 08:16, 14 December 2024
Line 2:		Line 2:
	This function allows loading of spectral data files stored in a [https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzXML mzXML data format] which in principle allows analyzing also data obtained by the [http://www.biomerieux-diagnostics.com/vitek-ms VITEK® MS solution from bioMérieux].		This function allows loading of spectral data files stored in a [https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzXML mzXML data format] which in principle allows analyzing also data obtained by the [http://www.biomerieux-diagnostics.com/vitek-ms VITEK® MS solution from bioMérieux].

	The mzXML import function of MicrobeMS is based on the Matlab routine [https://www.mathworks.com/help/bioinfo/ref/mzxmlread.html readmzxml] and is available either from the ''File'' menu bar or by the shortcut combination <Ctrl>+<X>. Select the spectral data files and press the button ''open'' to import ~~the selected~~ spectra.		The mzXML import function of MicrobeMS is based on the Matlab routine [https://www.mathworks.com/help/bioinfo/ref/mzxmlread.html readmzxml] (requires the Bioinformatics Toolbox of Matlab!) and is available either from the ''File'' menu bar or by the shortcut combination <Ctrl>+<X>. Select the spectral data files and press the button ''open'' to select and import mzXML formatted MALDI-ToF mass spectra.

	In some cases it has been noted that unprocessed mass spectra acquired by Shimadzu systems may exhibit only low spectral signal-to-noise (S/N) levels, possible because online smooth (aka hardware smooth) has not been carried out. In this instances, it might be useful to apply the Savitzky-Golay smoothing procedure with more than 30 smoothing points after data import.		In some cases it has been noted that unprocessed mass spectra acquired by Shimadzu MS systems may exhibit only low spectral signal-to-noise (S/N) levels, possible because online smooth (aka hardware smooth) has not been carried out. In this instances, it might be useful to apply the Savitzky-Golay smoothing procedure with more than 30 smoothing points after data import.

Laschp at 06:14, 14 December 2024

2024-12-14T06:14:07Z

← Older revision		Revision as of 08:14, 14 December 2024
Line 4:		Line 4:
	The mzXML import function of MicrobeMS is based on the Matlab routine [https://www.mathworks.com/help/bioinfo/ref/mzxmlread.html readmzxml] and is available either from the ''File'' menu bar or by the shortcut combination <Ctrl>+<X>. Select the spectral data files and press the button ''open'' to import the selected spectra.		The mzXML import function of MicrobeMS is based on the Matlab routine [https://www.mathworks.com/help/bioinfo/ref/mzxmlread.html readmzxml] and is available either from the ''File'' menu bar or by the shortcut combination <Ctrl>+<X>. Select the spectral data files and press the button ''open'' to import the selected spectra.

	In ~~many~~ cases ~~we have~~ noted that unprocessed mass spectra acquired by Shimadzu systems ~~often~~ exhibit only low signal-to-noise (S/N) levels, possible because online smooth (aka hardware smooth) has not been carried out. ~~Therefore~~, it ~~is strongly recommended~~ to apply the Savitzky-Golay smoothing procedure with more than 30 smoothing points after data import.		In some cases it has been noted that unprocessed mass spectra acquired by Shimadzu systems may exhibit only low spectral signal-to-noise (S/N) levels, possible because online smooth (aka hardware smooth) has not been carried out. In this instances, it might be useful to apply the Savitzky-Golay smoothing procedure with more than 30 smoothing points after data import.

Laschp: Created page with "Import of mass spectral data files in the mzXML format This function allows loading of spectral data files stored in a [https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzXML mzXML data format] which in principle allows analyzing also data obtained by the [http://www.biomerieux-diagnostics.com/vitek-ms VITEK® MS solution from bioMérieux]. The mzXML import function of MicrobeMS is based on the Matlab routine [htt..."

2023-03-18T09:35:37Z

Created page with "400px|thumb|right|Import of mass spectral data files in the mzXML format This function allows loading of spectral data files stored in a [https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzXML mzXML data format] which in principle allows analyzing also data obtained by the [http://www.biomerieux-diagnostics.com/vitek-ms VITEK® MS solution from bioMérieux]. The mzXML import function of MicrobeMS is based on the Matlab routine [htt..."

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[[File:Load-mzXML.jpg|400px|thumb|right|Import of mass spectral data files in the mzXML format]]
This function allows loading of spectral data files stored in a [https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#mzXML mzXML data format] which in principle allows analyzing also data obtained by the [http://www.biomerieux-diagnostics.com/vitek-ms VITEK® MS solution from bioMérieux].

The mzXML import function of MicrobeMS is based on the Matlab routine [https://www.mathworks.com/help/bioinfo/ref/mzxmlread.html readmzxml] and is available either from the ''File'' menu bar or by the shortcut combination <Ctrl>+<X>. Select the spectral data files and press the button ''open'' to import the selected spectra.

In many cases we have noted that unprocessed mass spectra acquired by Shimadzu systems often exhibit only low signal-to-noise (S/N) levels, possible because online smooth (aka hardware smooth) has not been carried out. Therefore, it is strongly recommended to apply the Savitzky-Golay smoothing procedure with more than 30 smoothing points after data import.