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Messages - AmelieV

1
XCMS - FAQ / Re: XCMS - MS1 scans empty
Thank you to both of you, that is very helpful!
I'm actually currently digging both of your leads : Jan I have been able to import my datas thanks to a package described in the links you provided! But at some point I'm stuck with one command, I'll have to figure out how to skirt this but I'm sure it's feasible.
CorgeyG your method works thank you!! The program runs well for now, even if some extra warnings comes up, I'll see if it can lead to something without any conflict.

Sorry for my late answer..
2
XCMS - FAQ / Re: XCMS - MS1 scans empty
I misspoke what I meant, I am indeed doing a parent ion scan so I do have MS2 data. But when I am importing my data into the xcms program in R, an error message comes up because my "MS1 scans are empty". The xcms program seems to need something in these MS1 scans that I can't provide with my data, or at least with the conversion settings I am using.
I tried with the SIM as Spectra / SRM as Spectra like you suggested but it gives rise to the same error.
3
XCMS - FAQ / Re: XCMS - MS1 scans empty
Hi Jan Stanstrup,

I'm actually not running my samples through a Q-TOF but I'm doing LC-MS with a QQQ. It should explain why I would need a different conversion settings? Do you know more about these settings I should use?
I'm using QQQ in scan mode with parent = 350-600, product = 97. I have a great peak separation and found all the parent ion peaks I was looking for in the MassHunter software.
I opened my converted data in seeMS ans the only scan that appear is a MS level 2, not the MS1 I'm expecting.

Thank you!
4
XCMS - FAQ / Re: XCMS - MS1 scans empty
Hi CoreyG,
After a look to your indications and the links you provided, it seems that I was using to good settings on the MSConvert for a classic Q-TOF analysis but maybe not for a QQQ like Jan Stanstrup mentionned.
Thank you for these indications
5
XCMS - FAQ / XCMS - MS1 scans empty
Hi,

I'm completely new to MS analysis and to the use of xcms program.
I'm trying to import my LC-MS datas to the xcms program, after conversion of my .d files into mzXML files via MSConvert (ProteoWizard).
An R message tell me that my MS1 scans are empty, I wonder if the problem would be with the conversion settings on MSConvert, does anyone know exactly what settings I should use? Or otherwise what could be the issue leading to some MS1 empty scans?

Thank you!!
Amélie