[Markus Stoeckli]

The accuracy of the sample stage is just one thing to consider, but equally important are laser spot diameter and crystal size (see below). Also, smearing of analytes during wet matrix deposition will decrease spatial resolution. We use standards on the same plate to control the reproducibility of the matrix coating and for calibration.

markus

[img]http://www.maldi-msi.org/images/forum/DHB.jpg[/img]
Spray of DB in 70:30 methanol/water

[img]http://www.maldi-msi.org/images/forum/SA.jpg[/img]
Spray of SA in 50:50 ACN/water

[Markus Stoeckli]

We are typically not too concerned about the damage to the microstructure during the drying process since we image with a maximal resolution of 100 micron. Freeze-drying is commonly used in histology to preserve the tissue structure, but also here we observe some tissue shrinkage.

markus

[Markus Stoeckli]

At least twice the size of the image file.

Markus

[Markus Stoeckli]

Please refer to page 52 of the BioMap manual included with BioMap version 3.6.6. Let us know if that doesn’t help…

[Markus Stoeckli]

The behavior you are describing lets me assume that you are trying to acquire an image with the ‘Acquisition Mode’ in the 4700 acquisition method set to ‘automatic’. That works only if you defined a spotset matching your image raster. Otherwise, the instrument will always acquire a spectrum from the spot nearest to each image point.

markus

[Markus Stoeckli]

This short movie may get you started: [url=http://www.maldi-msi.org/download/BioMap-Browsing.wmv]BioMap-Browsing.wmv[/url]

Post edited by: net-climber, at: 2007/03/21 19:36

Post edited by: net-climber, at: 2007/03/21 19:36

[Markus Stoeckli]

That looks odd. Let me try to narrow things down…

The license generator works with the [b]MAC address[/b] of the first network interface in your computer. We had problems before when users would enable/disable a WLAN interface and the software would get a different MAC address. To see your current number, type ‘ipconfig /all’ in a DOS window.

Make sure that your licenserc file does not have an [b]extension[/b]. In Windows, the extension ‘.txt’ may be hidden. To overcome this problem, select the menu ‘Tools – Folder Option’ in the file manager. Switch to the ‘View’ tab and in there disable the option ‘Hide extensions for know file types’.

The [b]location[/b] of the licenserc file is critical. Simply copy it into the ‘..\BioMap\settings’ folder and execute ‘Install settings.bat’ located in the BioMap folder.

Hope that help – if not, please let us know…

markus

[Markus Stoeckli]

Yes, we had that in our lab before. Let me guess: Your mass spectra contain more than 32768 data points. This is a known limitation of BioMap which works internally with 16-bit signed integers.

markus

[Markus Stoeckli]

Thanks for reporting that bug. We’ll take care of it and it will be fixed in the upcoming release.

markus

[Markus Stoeckli]

To open a picture (e.g. jpg or tif): File-Import-Pixmap

To copy a ROI: Edit-Copy, Edit-Paste-ROI

markus

[Markus Stoeckli]

While there is no direct way to save files in DE format, they may be imported as ASCII. Here’s how:
[ul]Save spectra in BioMap as ‘List’. A text file will be created with a name similar to ‘your_file_plot.txt’.[/ul]
[ul]Localize this file and open it with a text editor. The content has this format:
[code:1] X L1
498.302 89.0408
498.555 87.3492
498.807 85.3810
499.059 85.1474
499.311 89.4717
499.563 88.5828
499.815 86.0317[/code:1][/ul]
[ul]Delete the first line and replace it with the following two lines:
[code:1]TITLE "Your Title"
TYPE MASSSPEC[/code:1][/ul]
[ul]Save the file.[/ul]
[ul]Open DE and open a random spectrum.[/ul]
[ul]Select the menu item File – Import – ASCII Spectrum…[/ul]
[ul]Localize the text file and load it.[/ul]

markus

[Markus Stoeckli]

This error occurs if you run BioMap version 3.6.2 or older on the IDL Virtual Machine. With BioMap version 3.6.3 this limitation was overcome and spectra may be exported with any IDL version.

markus

[Markus Stoeckli]

I checked it out on our sSTR and found nothing wrong with the MMSIT. For the mass range 2000-25000 with bin size 4 ns we end up with 40000 data points in reflector mode and 27000 in linear mode. 💡 Could you verify for me that the data file which you specified in the MMSIT was acquired with the appropriate number of data points (open it as instrument settings in the VC)? It is this file which defines the image settings, no the current settings of the VC.

Markus

[Markus Stoeckli]

voxel = vo(lume) + (pi)xel

Therefore we talk of pixels in 2d applications and voxels in 3d tools like BioMap.

[Markus Stoeckli]

The sofware ‘DataExplorer’ you are looking for is a product from Applied Biosystems. Contact them directly (http://www.appliedbiosystems.com) for more information.

markus

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