[Markus Stoeckli]

Yes, BioMap allows to apply a baseline correction to a full data set, but no, I personally don’t think that it works well on MALDI TOF data. Here are the starting points if you want to explore it:

Open a data set, open a Plot Tool window, select Config – Baseline Correction. In there play with the parameter till you have a found optimal conditions. Note the parameters, close the Plot Tool window and select Tools – Calculation – Baseline Correction in the BioMap main app. Enter the parameters and apply.

Good luck! Please let us know in this forum if you are successful with your data.

Markus

[Markus Stoeckli]

Please excuse for the trouble you are having with BioMap installation. We realize that the install process is not very user-friendly, but we can confirm that BioMap runs with IDL 8.2. I assume that you tried to register using the splash-screen upon startup? Do you have write-access to the BioMap directory? If you are not sure, try to install it in a different directory like C:\Temp.

Please check also these posts for an answer:

http://www.maldi-msi.org/index.php?option=com_fireboard&Itemid=53&func=view&catid=2&id=721

http://www.maldi-msi.org/index.php?option=com_fireboard&Itemid=53&func=view&catid=2&id=633

Markus

[Markus Stoeckli]

With the slider you select the minimum and maximum intensity of your image which is them mapped to the color scale. As an example, if you select a greyscale and a max of 1000 and a min of 1, then all points with an intensity of 1000 and above are white and all points with an intensity of 1 or below are black.

Markus

[Markus Stoeckli]

When you click on Analyis – Plot – Global – Scan you are presented with a window where you enter a Maximum and Minimum intensity. So, in your case where you selected 100 and 0, all the spectra which fall into this intensity range are averaged. A typical use is to exclude low signal spectra and saturated spectra.

By selecting a m/z range in the spectrum you get multiple options on what the software should do: Mean, Max, Mean with BC, Max with BC and Peak Shift. Please be aware, that all these functions work with the raw data and that there is no peak fitting involved. The result is just the mathematics on the selected data points as indicated by the name. Do determine the baseline, we take the average of 3 points on either side of the selected range.

Markus

[Markus Stoeckli]

Hi Victoria

There is no such option. If you right-click on an image and open Properties, you may tick Crosshair under the Options tab to get a scale, or enter a Grid value to diplay a grid.

Markus

[Markus Stoeckli]

Dear peffs

If you are presented with a splash screen asking you to register upon start of BioMap, you don’t have an active registration. On this version of BioMap you don’t have to edit the license file. Please register, using copy/paste to transfer the Computer ID to the registration page. Once you receive the email (which should not take longer than a few seconds), copy the activation code directly to the box in the splash screen. This will then generate the license file for you. On a laptop, you might want to disable Wi-Fi and Bluetooth before you do this.

Hope this helps, please let us know

Markus

[Markus Stoeckli]

If you select a bin size other than 1, then this number of data points are average and imported as one data value. As an example, let’s say the data was acquired with 0.01 m/z mass resolution, but you want to analyze the data with 0.2 m/z resolution so that the whole mass range fits into memory. By selecting a bin size of 20, you achieve exactly this.

Markus

[Markus Stoeckli]

1. No, this must be an artifact from data acquisition and BioMap does not support correction.

2. All the data in the BioMap study database is stored under the selected directory in a file structure. Just copy the files to a new location and set the study database folder in the defaults to this location. Obviously, you can also manage the database by moving files around.

3. The ROI statistics also includes a pixel count. If you multiply this with the average value, you’ll get the integral.

Markus

[Markus Stoeckli]

Did you try to change the default folder to a place where you have write-access? Program Files and the folders below are protected in Windows 7.

markus

[Markus Stoeckli]

This is a known error and we will fix it in the next BioMap release.

Please excuse for this shortcoming of BioMap

Markus

[Markus Stoeckli]

This is how the MMSIT software works: The software interacts with VoyagerControl (VC) and the underlying Instrument Hardware Controller (IHC), but does not directly control the instrument. When an image is started, a call to the VC loads the data file you specified with the imaging method. A spectrum acquisition is then triggered to activate the method. Obviously, the method must be in manual mode and not automatic mode. After this initial step, the MMSIT software communicates exclusively with the IHC. It loads the new position, starts the laser, waits for completion and pulls the data directly from the IHC. One of the issues we had is that the VC is in parallel hooked up to the IHC, and for this reason it also displays the new data. This typically not an issue, except if there are other background processes running (e.g. virus scanners, windows update…) and resources get low. In this case, it helps to close the spectrum sub-window in the VC before you start the acquisition or you minimize the VC window.

Another issue might be hardware. The trigger diode for the laser pulse might get blind and the laser fires without triggering the acquisition. This can be solved either by moving the trigger board slightly to a different position, so that the blind spot is on the side. Or by replacing the diode (cost about 10 USD).

Good luck

Markus

[Markus Stoeckli]

Check out this post: http://www.maldi-msi.org/index.php?option=com_fireboard&Itemid=53&func=view&catid=11&id=759#762

[Markus Stoeckli]

Please excuse for this shortcoming of the software. We are aware of two issues with the imzML import functionality and will improve this part of the code with the next release.

Markus

[Markus Stoeckli]

Please click Edit – Defaults from the menu and select an appropriate Export folder. Once done, the export function should work.

Markus

[Markus Stoeckli]

Draw one or multiple regions of interest (ROI) on the image. Select Analysis – Plot – ROI to show the average spectrum. Select from this window File – Export – List to export the data.

Markus

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