1 Topic by Katz

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Topic: Peak picking not working?

I'm having trouble picking peaks with the automatic tool.

I'm analyzing ESI data that was converted with compassXport.

(Also, just so you know, I don't even run the MS myself...  I just give my sample to someone and get the file back.)

So when I open my file, I already have all peaks picked. Even tiny little ones. If I want to delete labels, it deletes the whole peak.
If I use the automatic peak picking tool, it doesn't change anything, whatever threshold I set. Is it supposed to delete labels for peaks under the threshold? Right now, whether I set a random high S/N ratio, an mid-height a.i. or a 50% relative intensity, it doesn't seem to do anything.

I run my laptop under Ubuntu, and mMass is the only way I can analyze my MS data from there, so I'd really like to be able to only label the peaks I want.

Thank you for any help!

2 Reply by Martin

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Re: Peak picking not working?

Hi,

to delete peak labels below threshold:
- on the peaklist panel bottombar click the "-" button and select Delete by Threshold...

to perform automatic peak picking
- open Processing panel and select Peak Picking tool
- open the ESI-ICR Peptides presets
- in the spectrum viewer check the red line indicating current threshold approximation
- play with the threshold numbers to set it as you want
- for the first try, turn off all the checkboxes bellow the Picking height slider
- press Apply button and check the results
- now you can play with the checkboxes and corresponding panel settings

Please note that to perform peak picking, you must have profile data, not just centroides! Since you said that you see the labels immediately after opening converted data, I think this is the problem - you have centroided data, therefore there is nothing to label.

Martin

3 Reply by Katz

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Re: Peak picking not working?

[quote=Martin]Please note that to perform peak picking, you must have profile data, not just centroides! Since you said that you see the labels immediately after opening converted data, I think this is the problem - you have centroided data, therefore there is nothing to label.[/quote]

That may be my problem, indeed. That would probably also explain why if I delete labels, it actually deletes the whole peak. I'll look into this. Thank you!

4 Reply by Katz

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Re: Peak picking not working?

Hum, it looks like I can't edit my posts... Sorry for the double post, then.

As I said, I'll look into getting profile data instead of centroid. Still, is there no way to have labels only for some peaks in centroid data in mMass?
I don't mind all the peaks showing up on my spectrum, but if they're all labeled, it gets quite messy and hard to work with. As I said, I can delete the peaks under a certain threshold, but I'd rather just delete the labels, not the whole peaks, as it changes the way the spectrum looks...

5 Reply by Martin

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Re: Peak picking not working?

Actually, centroides are just the labels of the real profile peaks.
Centroid=Label, therefore you cannot remove label without centroid.

6 Reply by Katz

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Re: Peak picking not working?

Bleah...

OK, thanks !

7 Reply by Katz

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Re: Peak picking not working?

And... another double post.

So it's a simple matter of exporting the raw data with compassXport rather than the line spectrum. Easy enough once you know what you're looking for. Thanks a lot for your help!