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Messages - THBCCCU

1
XCMS Online / Re: Issue with .cdf files
Okay so i realise that I was being foolish, It suddenly dawned on me that its all MSe data with scan1 and scan2 representing low and high energy collision, Doh! But I am still confused about how to inform any would be preprocessing software that scan 1 is parent ions and scan 2 is fragment ions?
2
XCMS Online / Re: Issue with .cdf files
New update, I have checked my spectrums and scan numbers, i am confident they are correct. I am still not sure about a few thing and given that i am confident i am not alone i have a few questions.
So having used the scan filter on MSCovert to convert my APD.raw files to mzML as suggested, I now have a scan 1 and a scan2 files for each, to the best of my knowledge these represent MS1 in scan 1 and MSe in scan 2 (is this correct? if not can anyone point me in the direction of something to read to understand this better as the waters handbooks are pretty dry!)
Also I would like to use XCMS online, but does XCMS understand/ can i make it understand what each file represents so for example say i am uploading for a pairwise comparision of x vs y, 10 repeats of each, and a scan 1 and a scan 2 for each file. Should i have a stored data set of X, scan 1 (10 files) and compare that to Y, scan 1 (10 files) and then do the same for scan 2 OR should i use data set of X, scans 1 + 2 (20 files) and compare that to Y, scans 1 + 2 (20 files)? I hope that makes sense, or is there some intermediate step that i am not aware of
3
XCMS Online / Re: File check and TICs failed
If you click on the red error message it will give you more information about the error itself, Most likely it is an MD5sum error, on XCMS onlines FAQs it details what to check on your uploaded files.
4
XCMS Online / Re: Issue with .cdf files
Hi so I have followed all of your instructions but i think maybe i have an issue with the scan event function, my spectrum in Mzmine matches my 2nd TIC in Masslynx but the 1st is completely different, could someone explain what is going on here?

(blue = Mzmine, Helpfully the top green = 2nd TIC in masslynx and red = 1st TIC in Masslynx and the spectrum is the other way around in colour)

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5
XCMS Online / Re: Issue with .cdf files
Thank you for your reply, and please forgive my ignorance. But I want to be sure that I understand your instructions, so if I return to masslynx and compare that information with my .cdf files, you suggest I am likely to find discrepancies. That being the case how can I correct these and export data from masslynx that is centrioded?
6
XCMS Online / Issue with .cdf files
Hi all

I have been trying for a while now to make sense of all of the software etc. Available for use with metabolomics.

I have water .raw data run on a ULPC water synapt G2 which I converted using databridge, this gave me four files, I think one is lock spray and one is UV data...3.cdf and 4.cdf

Initially I tried using mzmine with my .raw files but it doesn't seem to like the scan filter and I have a lot to get through so moved onto my .cdf files. I have been trying to use xcms online but I am worried that the division of my mass spec info (ie. 1.cdf and 2.cdf) is meaning that I am losing information, is this concern valid?

I have seen some other threads suggesting that waters users need to go back to masslynx and make sure all their data is centrioded before they export and convert... but others suggest using proteowizard to convert .raw files to mzxml... I have tried a while ago to convert files using proteowizard but it doesn't or at least didn't seem to like waters files at the time... has this since been updated? As a return to masslynx would be a nightmare for me as I do not have a license and would need to travel to use it!

Anyways I am feeling very lost and due to the size of the files in question trying things to see if they work takes such a long time so if anyone has any suggestions it would be much appreciated. Thanks.