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Missing mass ions jessica fairhall  2018-07-20 14:18
 

Hi there,

I was wondering if anyone has had any issues skyline completely dropping chromatographs for certain ionization masses? and if you know how to fix it?

Attached is a screenshot of replicate runs for the same compound, you can see that in the first run the M+H does not show at all, however it does in the second run. I have spot checked my data using Agilent's MassHunter and the M+H definitively is there +/- 0.0003 m/z. I have my mass accuracy set to 20ppm, so I don't see a reason why Skyline would not include it. Some samples are completely missing both M+H and +Na with zero background.

Thanks in advance for your help,

Jess
 
 
Brendan MacLean responded:  2018-07-20 15:07

Hi Jess,
I take it that these are extracted from MS1 spectra, then? From an Agilent Q-TOF? Without any ion mobility? Can you fill in a bit more detail and give us a screenshot of the MassHunter view that makes you confident what you are seeing in Skyline is incorrect?

After that, we may need a copy of your document (using File > Share - Complete to create a .sky.zip) and a raw data file (also zipped) that you feel is imported incorrectly for us to take a closer look.

You can upload these files to:

http://skyline.ms/files.url

Hopefully, we can get the issue sorted out quickly once we have the necessary information.

--Brendan
 
jessica fairhall responded:  2018-07-23 13:39

Hi Brendan,

Yes that is all correct, the model is an Agilent 1290 UPLC coupled to an Agilent 6550 ESI-QTOF.

Attached is screen shots from MassHunter and I have upload the raw data and sky document into the share folder.

Data for F1 is missing M+H and F6 is missing both M+H and M+Na, both show up in F2.

Thanks for your help!

Jess