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I am having an issue where the MS for my antibody (intact/nonreduced, deglycosylated by PNGase) shows multiple clusters of what appear to be ghost peaks after deconvolution, and the main peak is extremely broad and appears to show a ton of different adducts.

I'm reasonably confident this shouldn't be the case, as the reduced chains are extremely sharp and homogeneous and show the exact expected mass consistently.

Has anyone else observed this phenemenon? Any idea what causes it and/or how to abrogate it?

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  • $\begingroup$ Your images don't work. Also mention what deconvolution technique is being used? Is it an LC-MS experiment? $\endgroup$ – M. Farooq Jun 7 at 23:38
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    $\begingroup$ Yes it is an LCMS experiment. I'm using maximum entropy deconvolution. $\endgroup$ – oryza Jun 7 at 23:45
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    $\begingroup$ Okay, I am not familiar with maximum entropy deconvolution. Keep in mind that deconvolution can very easily generate plenty of artifacts. Secondly, poor plumbing in chromatography can also generate broad peaks. As as an analytical chemist I can tell you one thing. Whenever you see an odd behavior in any instrument, it is time to go back and repeat an experiment with known results. Can you repeat an experiment under standard conditions? $\endgroup$ – M. Farooq Jun 7 at 23:52
  • $\begingroup$ For other readers, if this is an LC-MS experiment, one should see time on the x-axis. Please clarify that you have focused on a single chromatographic peak, which after "clicking" is showing the MS spectrum of the peak. Is this assumption correct? $\endgroup$ – M. Farooq Jun 8 at 3:29
  • $\begingroup$ Yes its the deconvolution of a single peak. I have run other samples with the same method that look fine, it is only certain proteins that end up with this kind of unusual broadness, but I have no idea what is causing it - whether it has to do with the sample or the machine, and I haven't found a single instance of similar phenomenon being reported in the literature. $\endgroup$ – oryza Jun 8 at 7:30

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