Normalizing baselines

[Tim Miller]

I am imaging kidney and I have variation in intensities between cortex and medulla- a lot of which is due not only to my protein signals, but also to a higher baseline in the shots from the medulla. Is there any way to correct all of my baselines in a given study without exporting the data to a spreadsheet and somehow normalizing all of my baselines so that BioMap is then able to interpret the points from scans starting from the same baseline values?. If data from scans must be exported, then how would I go about this? I use a Voyager DE STR. Any input would be greatly appreciated.
Tim Miller

[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

[Alia Schneider]

I’m still practicing with the demo rat in BioMap.
When I try to apply baseline correction
(scan from datamanager: Plot Tool > Config > Options > Filter Tab > Baseline correction > yes / or /
Plot Tool > Config > Baseline correction / or /
Tools > Calculation > Baseline Correction)
I always get the same error message window.
I add a screenshot.
Is it about the scan or do I miss sth.?

Thank you very much in advance.

Attachments:

• Error_BC.JPG
• Error_BC1.JPG

[Alia Schneider]

here the error window [img size=346]http://www.maldi-msi.org/images/fbfiles/images/Error_BC1.JPG[/img]

Attachments:

• Error_BC1.JPG

[Markus Stoeckli]

[b]schneial wrote:[/b]
[quote]When I try to apply baseline correction (scan from datamanager: Plot Tool > Config > Options > Filter Tab > Baseline correction > yes / or / Plot Tool > Config > Baseline correction / or / Tools > Calculation > Baseline Correction) I always get the same error message window. Is it about the scan? [/quote]

Uh, the demo data set does not have enough points… this is why it fails… I just tested it with 100 m/z points and it worked.

[Alia Schneider]

Ok thank you Markus. =)

[Author]

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