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Messages - RaphBil

1
XCMS / Re: Lockmass gap correction
Jan,

The script works now. Everything seems to be fine !
I'll double check the output and keep you updated if there are some errors.

Thanks a lot.
Best,

Raphaël
3
XCMS / Re: Lockmass gap correction
Hello Jan,

Thanks for your fast answer.
You're right. The screenshot is from masswolf. Here is the one from R :

Error in writeLines(unlist(log_convert_warning), fileConn) :
  invalid 'text' argument
Then the script stops : close(fileConn)
The only created file is a mzXML one.

How would you like me to send you an exemple file ? (approximately 80 Mo)
If we cannot read the MSE file, how could I edit the script in order to read only the MS1 trace and the lockmass trace ?

Best,

Raphaël
4
XCMS / Lockmass gap correction : MSE data conversion
Hello Jan,

The script worked very well with MS1 data, but I tried it with MSE data (also from a Synapt Waters) and here is the error statement :

First function is not of type MS, is this MS^E data? Continuing anyway.
Second function is not of type MS, is this MS^E data? Continuing anyway.
(got computer name: C-TAC)
Calculating sha1-sum of mzXML
--done (mzXML sha1):8160c2c3905aba20aeb020ca843c7e61bd71c8df


Only one file is created and then the script stop at the second one, probably the MSE one ?

Thanks a lot for your help.
Best,
Raphaël
5
Mass spectrometers / Loss of sensitivity
Hello,

I'm currently working on a Waters Synapt (ESI + source) and I encounter an important loss of sensitivity over time, probably due to the source clogging (I'm working with intact proteins).
Which normalisation method would you recommend to fix this quasilinear "drift" ? Could we assume that this drift is similar to a dilution effect and correct it using PQN or Median normalisation ?

Thanks for your help.
8
XCMS / Re: Lockmass gap correction
Hello everybody,

I encountered the same issue as you Asun, and tried to fix it according to Paul's answer, but I still get the following error message trying to apply the lockMassFreq correction...

Warning in AutoLockMass(xRaw) :
  Lock mass frequency wasn't detected correctly

Any idea to fix it ?

Thanks for your help

Raphaël
9
Mass spectrometers / Deconvoluted mass spectrum
Hello everybody,

Does anyone know how to save a deconvoluted mass spectrum processed by MaxEnt1 (Waters MassLynx deconvolution software) in order to process it on XCMS ?

Thank you for your help !

Raphael Bilgraer