[proteomics] Background Ions (Contaminants) in Ionizing Solvents for ESI-MS

  • From: Mavi Gozler <mavigozler@xxxxxxxxx>
  • To: proteomics@xxxxxxxxxxxxx
  • Date: Mon, 15 Jan 2007 00:03:52 -0800 (PST)

I do not have much in terms of years of experience with ESI-MS.

I suppose that the many of you who have checked first to see your background 
spectra (collecting scans of just the solvent) have seen high counts of certain 

The typical solvent we use is 50% MeCN + 0.1% formic acid for positive mode 
work.  Our water is MilliQ Gradient, our acetonitrile is LC grade stuff that is 
either Riedel de Haen Chromasolv or Merck.  Our formic acid is Fluka "LC-MS" 
grade with an expiration date.  I should add that I pass the water additionally 
through a SepPak C18 cartridge prior to mixing it with MeCN and FA;  I haven't 
tried doing after mixing.

There is one ion (+1) at m/z 355 that generates a high number of counts, 
something like 60 counts or more in a 2-second scan.

As a curiosity, I set up the quadrupole to filter it (MS/MS mode) so that I 
could get a few scans by adjusting the collision energy (CE).  The normal CE is 
10V, and when I increase the CE to 15V, ions at 5-10% intensity relative to 
parent appear at m/z 285 and 303.  At CE=20V there is an appearance of ions at 
m/z 269, and now the m/z 285 is the most intense (the base), with the m/z 303 
ion still present.  The m/z 355 ion is still present and about 80% intensity.  
At CE=25V, the m/z 355 parent has all but disappeared although is detected, and 
the product ions are only present, with no change in relative intensity.  At 
CE=30V, the spectrum is not distinct from CE=25V.  Anyone have an idea what 
this ion may be?

I suppose that the significant presence of background ions is something 
"inevitable" and that everyone gets around it by just refusing to include 
spectral acquisitions whose lower mass range limit would include the presence 
of background ions.  My background intensities taper off at m/z 400, and quite 
a few published reports seem to use this as a set low m/z range limit 

I am curious if other people have different experiences and whether they have 
triumphed in eliminating or all but eliminating the presence of these ions by, 
say, setting up and operating instruments in something like semiconductor 
fabrication "clean room" environments.


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