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Messages - Jan Stanstrup

1
XCMS / Re: File conversion for XCMS
To view raw files? No. To browse converted files you can use mzMine.

To do the centroiding? Yes, msconvert from Proteowizard can, but from the docs seems not well. msconvert cannot use the Waters' centroiding as it can for other vendor formats. So it has to use its own supposedly inferior implementation.
2
XCMS / Re: File conversion for XCMS
When you have files that are 1GB they are almost certainly in continuum mode.You need to first convert them to centroid mode in masslynx to be able to use XCMS. Typically centroid mode files are 50-100MB.
Masslynx --> tools --> accurate mass measure --> Automatic peak detection.
Then convert the resulting raw files.

As for the functions I am afraid also MSe is listed as TOF MS. So you probably have to ask the people that did the experiment what each are unless you can guess from that  _extern.inf file. But that probably requires comparison with something you know what is unless you are a really hardcore MS person.

For some info on XCMS I can plug my own tutorial here: https://github.com/stanstrup/XCMS-course
3
XCMS / Re: File conversion for XCMS
You need to figure out which of the 3 files you need. Mixing different functions will likely mess things up.
Since you have Databridge I guess you have masslynx. So open a chromatogram --> display --> TIC. Here you have the functions listed and you can get the TIC of each function.
If that doesn't clear it up either ask the people that did the experiment or try to decipher the _extern.inf in the raw folders. That contains all the experiment settings and have sections for each function. The format is not very consistent between versions but I just checked and it seems MSe functions will have things like
Transfer MS Collision Energy Low (eV)      10.0
Transfer MS Collision Energy High (eV)      40.0
listed at least in my files.

What do you mean by "load the files with XCMS"? Using xcmsSet? How heavy this is depends on the settings. What happens? You run out of memory? At which point? How large are the files? Maybe they are not centroided?
4
R / Re: DOUBT ABOUT MS^E
@cbroeckl doesn't it work if you use the scanEvent filter and not the msLevel filter?
5
XCMS / Re: File conversion for XCMS
You get one file per "function" with databridge. So you need to know how your experiment was set up to know which to use. Typically you might have a normal MS1 function and the lockmass function (not sure the latter is written as a file but might be). Then you might have added an MSe function. You can check what each are in masslynx.

What do you mean by clog up the system? XCMS doesn't load all raw data at the same time.
6
XCMS Online / Re: Agilent .d.zip file error
No idea. I think you will have better luck contacting the xcms online people directly (https://xcmsonline.scripps.edu/landing_page.php?pgcontent=contact). They don't seem to frequent these waters unfortunately.
7
XCMS Online / Re: Agilent .d.zip file error
https://xcmsonline.scripps.edu/docs/fileformats.html Doesn't seem like xcms online likes compressed files.
8
R / Re: MRM data
Info about the backend issues with this: https://github.com/sneumann/mzR/issues/73

From the discussion there it seems mzR at least should be able to read something from those files.
Maybe Msnbase can even read the files but I don't know.

XCMS issues:
https://github.com/sneumann/xcms/issues/57
https://github.com/sneumann/xcms/issues/169
9
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10
Tools / post-acquisition centroiding of Waters data
Hi,

I was wondering if anyone knows a way to get good centroiding of Waters data that was recorded in profile mode?
In MassLynx you can centroid a single spectrum and it looks like this as an example:



That seems reasonable by eye.
I tried then using the centroiding in msconvert (Proteowizard). Here is the result:




What it has done is not finding the center of the peak but has chosen the top scan for the m/z. This is not very accurate and is in this case a difference of 15 ppm.

So my question is if someone knows a better way to centroid data that was already acquired?
Msconvert can use vendor algorithms for centroiding for a lot of formats but apparently it is not available for waters data.
11
XCMS / Re: mz > 1000
In my dataset I get features > 1000 with no problems. Are you sure your data contains data above 1000 Da?
If you are sure your data has peaks > 1000 Da your best bet is to post a reproducible example with code and sample data.
12
XCMS / Re: xcms and BiocParallel issue
No clue. The first I would try is to install xcms (devel branch) and mzR from github. Your versions are a bit old and might not like each other.
13
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14
XCMS / Re: Howto re-integrate with new rtborders?
I haven't tried to manipulate it like that so I don't know.

But your peakwidth is too narrow I think if you want all in one. You have a max of 10 sec. If you want to merge all you need several minutes I assume. At least I'd try that.
15
XCMS / Re: Howto re-integrate with new rtborders?
One way to achieve this, I think, is to set mzdiff to something positive. That should make everything connected integrate as one. Of course this might have unwanted effects in other places.