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Messages - hwhitwell

1
Mass spectrometers / LQT Convectron gauge pressure too high.
Hello,

I am running an LTQ-Orbitrap XL and have high pressure (2.4 and should be 1) on the convectron gauge for the LTQ. I removed the ion tube to block the ion inlet to the front of the API stack, the vacuum should drop to zero, but only achieves 0.2, therefore I think there must be a leak somewhere between the API stack and the vacuum pumps.

I have tried dripping some methanol around to API stack whilst watching the vacuum levels on the convectron gauge, however I couldn't find anywhere...

If I put my ear to the the panel below the API stack I can hear a small hiss, but I don't know if it is related or not...!

Has anyone had any similar problems or can anyone suggest something to check?

Thanks!
2
XCMS / Re: m/z value off by 0.1~0.2 Da
Hi,

I have a similar problem when using LC-MS/MS orbi data. I have used MSConvert to export centroided values, but the output m/z from xcms are around 0.1m/z out.

I am trying to use XCMS to perform peak alignment of proteomics samples. I want to use this to assign peptide ID's in samples where no MS/MS was performed on the same parent.

It may be the way I am approaching the problem with xcms - I'm not really sure on how to use the package very well...! I have essentially followed the instructions in the vignette for LC-MS preprocessing and analysis.

Any help/suggestions would be appreciated!

Thanks
Harry