Creating Pseudo-Gel Views - Revision history

Laschp at 08:46, 3 April 2025

2025-04-03T08:46:28Z

← Older revision		Revision as of 10:46, 3 April 2025
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	[[File:Gel-view.jpg\|600px\|thumb\|~~left~~\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]		[[File:Gel-view.jpg\|600px\|thumb\|right\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]

	When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated '''''pseudo-gel views''''' for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color or gray scales and plotted as a function of the m/z values. Gel views are usually generated from pre-processed and internally calibrated mass spectra.<br>		When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated '''''pseudo-gel views''''' for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color or gray scales and plotted as a function of the m/z values. Gel views are usually generated from pre-processed and internally calibrated mass spectra.<br>

Laschp at 08:46, 3 April 2025

2025-04-03T08:46:05Z

← Older revision		Revision as of 10:46, 3 April 2025
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	When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated pseudo-gel views for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color, or gray scales and plotted as a function of the m/z values. Gel views are usually generated from pre-processed and internally calibrated mass spectra.<br>
	The pseudo-gel view below displays pre-processed experimental mass spectra from the ~~''Escherichia coli'' database (see [http://www.wiki.microbe~~-~~ms.com/index.php?title=Download_MicrobeMS Download MicrobeMS])~~. The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a ~~color~~ code.<br>		[[File:Gel-view.jpg\|600px\|thumb\|left\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]

	~~[[File:Gel-view.jpg\|800px\|thumb\|center\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]~~		When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated '''''pseudo-gel views''''' for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color or gray scales and plotted as a function of the m/z values. Gel views are usually generated from pre-processed and internally calibrated mass spectra.<br>
			The pseudo-gel view below displays pre-processed experimental mass spectra from the an ESKAPE sample panel containing 212 MALDI-ToF mass spectra. The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a gray-scale code.<br>

	<br>		<br>
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	'''How to generate a pseudo-gel view?'''		'''How to generate a pseudo-gel view?'''

			1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.
	1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' ~~pulldown~~ menu.

	2. Perform [[Spectral Pre-processing\|spectral pre-processing]]		2. Perform [[Spectral Pre-processing\|spectral pre-processing]]

Laschp at 08:14, 2 April 2025

2025-04-02T08:14:07Z

← Older revision		Revision as of 10:14, 2 April 2025
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	:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.		1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

	:2. Perform [[Spectral Pre-processing\|spectral pre-processing]]		2. Perform [[Spectral Pre-processing\|spectral pre-processing]]

	:3. Select mass spectra to be displayed from the list box in the upper right corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS]. Hold the shift key while selecting multiple spectra.<br>		3. Select mass spectra to be displayed from the list box in the upper right corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS]. Hold the shift key while selecting multiple spectra.<br>

	:4. Select ''pseudo-gel view'' from the ''view'' pull down menu. Alternatively, press <ctrl><G>. A window entitled ''pseudo-gel view of MALDI-ToF mass spectra'' will come up.		4. Select ''pseudo-gel view'' from the ''view'' pull down menu. Alternatively, press <ctrl><G>. A window entitled ''pseudo-gel view of MALDI-ToF mass spectra'' will come up.

	:5. To modify the m/z range check the checkbox ''edit mass range manually'' and enter the respective m/z range values in the edit fields ''mass range''. Press then the button ''plot''		5. To modify the m/z range check the checkbox ''edit mass range manually'' and enter the respective m/z range values in the edit fields ''mass range''. Press then the button ''plot''

	6. The popup menu ''select color map'' allows to change the color map (the default color map is ''black'')		6. The popup menu ''select color map'' allows to change the color map (the default color map is ''black'')

	7. To modify the contrast of the pseudo-gel view modify the respective values in edit fields ''clim values''		7. To modify the contrast of the pseudo-gel view modify the respective values in edit fields ''clim values''

	8. The ''mouse over'' function of the gel view window shows the ID of the actual mass spectrum and the intensity - m/z pair (intensity of the pre-processed spectrum)		8. The ''mouse over'' function of the gel view window shows the ID of the actual mass spectrum and the intensity - m/z pair (intensity of the pre-processed spectrum)

	9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view (eps)'' from the context menu (right mouse button over the gel view)		9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view (eps)'' from the context menu (right mouse button over the gel view)

Laschp at 08:05, 2 April 2025

2025-04-02T08:05:11Z

← Older revision		Revision as of 10:05, 2 April 2025
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	1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.		:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

	2. Perform [[Spectral Pre-processing\|spectral pre-processing]]		:2. Perform [[Spectral Pre-processing\|spectral pre-processing]]

	3. Select mass spectra to be displayed from the list box in the upper right corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS]. Hold the shift key while selecting multiple spectra.<br>		:3. Select mass spectra to be displayed from the list box in the upper right corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS]. Hold the shift key while selecting multiple spectra.<br>

	4. Select ''pseudo-gel view'' from the ''view'' pull down menu. Alternatively, press <ctrl><G>. A window entitled ''pseudo-gel view of MALDI-ToF mass spectra'' will		:4. Select ''pseudo-gel view'' from the ''view'' pull down menu. Alternatively, press <ctrl><G>. A window entitled ''pseudo-gel view of MALDI-ToF mass spectra'' will come up.
	come up.

	5. To modify the m/z range check the checkbox ''edit mass range manually'' and enter the respective m/z range values in the edit fields ''mass range''. Press then the button ''plot''		:5. To modify the m/z range check the checkbox ''edit mass range manually'' and enter the respective m/z range values in the edit fields ''mass range''. Press then the button ''plot''

	6. The popup menu ''select color map'' allows to change the color map (the default color map is ''black'')		6. The popup menu ''select color map'' allows to change the color map (the default color map is ''black'')
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	7. To modify the contrast of the pseudo-gel view modify the respective values in edit fields ''clim values''		7. To modify the contrast of the pseudo-gel view modify the respective values in edit fields ''clim values''

	8. The ''mouse over'' function of the gel view window shows the ID of the actual mass spectrum and the intensity - m/z pair (intensity of the pre-processed		8. The ''mouse over'' function of the gel view window shows the ID of the actual mass spectrum and the intensity - m/z pair (intensity of the pre-processed spectrum)
	spectrum)

	9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view (eps)'' from the context menu (right mouse button over the gel view)		9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view (eps)'' from the context menu (right mouse button over the gel view)

Laschp at 08:03, 2 April 2025

2025-04-02T08:03:47Z

← Older revision		Revision as of 10:03, 2 April 2025
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	1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format),		1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.
	[[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

	2. Perform [[Spectral Pre-processing\|spectral pre-processing]]		2. Perform [[Spectral Pre-processing\|spectral pre-processing]]

	3. Select mass spectra to be displayed from the ~~listbox~~ in the upper right		3. Select mass spectra to be displayed from the list box in the upper right corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS]. Hold the shift key while selecting multiple spectra.<br>
	corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS].
	Hold the shift key while selecting multiple spectra<br>

	4. Select ''pseudo-gel view'' from the ''view'' ~~pulldown~~ menu. Alternatively, press		4. Select ''pseudo-gel view'' from the ''view'' pull down menu. Alternatively, press <ctrl><G>. A window entitled ''pseudo-gel view of MALDI-ToF mass spectra'' will
	<ctrl><G>. A window entitled ''pseudo-gel view of MALDI ~~TOF~~ mass spectra'' will
	come up.		come up.

	5. To modify the m/z range check the checkbox ''edit mass range manually'' and		5. To modify the m/z range check the checkbox ''edit mass range manually'' and enter the respective m/z range values in the edit fields ''mass range''. Press then the button ''plot''
	enter the respective m/z range values in the edit fields ''mass range''.
	Press then the button ''plot''

	6. The popup menu ''select color map'' allows to change the color map (the default		6. The popup menu ''select color map'' allows to change the color map (the default color map is ''black'')
	color map is ''black'')

	7. To modify the contrast of the pseudo-gel view modify the respective values		7. To modify the contrast of the pseudo-gel view modify the respective values in edit fields ''clim values''
	in edit fields ''clim values''

	8. The ''mouse over'' function of the gel view window shows the ID of the actual		8. The ''mouse over'' function of the gel view window shows the ID of the actual mass spectrum and the intensity - m/z pair (intensity of the pre-processed
	mass spectrum and the intensity - m/z pair (intensity of the pre-processed
	spectrum)		spectrum)

	9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view''		9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view (eps)'' from the context menu (right mouse button over the gel view)
	''(eps)'' from the context menu (right mouse button over the gel view)

Laschp at 06:54, 14 December 2024

2024-12-14T06:54:26Z

← Older revision		Revision as of 08:54, 14 December 2024
Line 2:		Line 2:
	The pseudo-gel view below displays pre-processed experimental mass spectra from the ''Escherichia coli'' database (see [http://www.wiki.microbe-ms.com/index.php?title=Download_MicrobeMS Download MicrobeMS]). The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a color code.<br>		The pseudo-gel view below displays pre-processed experimental mass spectra from the ''Escherichia coli'' database (see [http://www.wiki.microbe-ms.com/index.php?title=Download_MicrobeMS Download MicrobeMS]). The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a color code.<br>

	[[File:Gel-view.jpg\|800px\|thumb\|~~left~~\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]		[[File:Gel-view.jpg\|800px\|thumb\|center\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]

	<br>		<br>

Laschp at 06:53, 14 December 2024

2024-12-14T06:53:40Z

← Older revision		Revision as of 08:53, 14 December 2024
Line 2:		Line 2:
	The pseudo-gel view below displays pre-processed experimental mass spectra from the ''Escherichia coli'' database (see [http://www.wiki.microbe-ms.com/index.php?title=Download_MicrobeMS Download MicrobeMS]). The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a color code.<br>		The pseudo-gel view below displays pre-processed experimental mass spectra from the ''Escherichia coli'' database (see [http://www.wiki.microbe-ms.com/index.php?title=Download_MicrobeMS Download MicrobeMS]). The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a color code.<br>

	[[File:Gel-view.jpg\|800px\|thumb\|~~center~~\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]		[[File:Gel-view.jpg\|800px\|thumb\|left\|Screenshot of the "pseudo-gel view" window of MicrobeMS]]

	<br>		<br>

Laschp: Created page with "When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated pseudo-gel views for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color, or gray scales and plotted as a function of the m/z values. Gel views are usually gene..."

2023-03-18T09:31:26Z

Created page with "When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated pseudo-gel views for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color, or gray scales and plotted as a function of the m/z values. Gel views are usually gene..."

New page

When dealing with large spectral databases which sometimes comprise hundreds of individual mass spectra, data inspection and data assessment cannot be done by manual screening of the individual spectra alone. In these instances simulated pseudo-gel views for visual analysis of the data set are popular means. In gel view representations, spectral peak intensities are converted to color, or gray scales and plotted as a function of the m/z values. Gel views are usually generated from pre-processed and internally calibrated mass spectra.<br>
The pseudo-gel view below displays pre-processed experimental mass spectra from the ''Escherichia coli'' database (see [http://www.wiki.microbe-ms.com/index.php?title=Download_MicrobeMS Download MicrobeMS]). The x-axis records the m/z values while the y-axis displays the running spectrum number. Log-scaled spectral intensities are expressed by a color code.<br>

[[File:Gel-view.jpg|800px|thumb|center|Screenshot of the "pseudo-gel view" window of MicrobeMS]]

  <br>

'''How to generate a pseudo-gel view?'''

1. Load the mass spectral data files via the [[Load spectra (Bruker format)|load spectra]] (Bruker data file format),
[[Import Mass Spectra in a mzXML Data Format|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

2. Perform [[Spectral Pre-processing|spectral pre-processing]]

3. Select mass spectra to be displayed from the listbox in the upper right
corner of the main window of MicrobeMS (see [http://www.wiki.microbe-ms.com/index.php?title=Screenshot_of_MicrobeMS screenshot MicrobeMS].
Hold the shift key while selecting multiple spectra<br>

4. Select ''pseudo-gel view'' from the ''view'' pulldown menu. Alternatively, press
<ctrl><G>. A window entitled ''pseudo-gel view of MALDI TOF mass spectra'' will
come up.

5. To modify the m/z range check the checkbox ''edit mass range manually'' and
enter the respective m/z range values in the edit fields ''mass range''.
Press then the button ''plot''

6. The popup menu ''select color map'' allows to change the color map (the default
color map is ''black'')

7. To modify the contrast of the pseudo-gel view modify the respective values
in edit fields ''clim values''

8. The ''mouse over'' function of the gel view window shows the ID of the actual
mass spectrum and the intensity - m/z pair (intensity of the pre-processed
spectrum)

9. To export the gel view select ''capture gel view (jpg)'' or ''plot gel view''
''(eps)'' from the context menu (right mouse button over the gel view)