Abstract: In various aspects, provided are methods and devices for the depletion of two or more proteins from a sample, such as, for example, blood serum, blood plasma, cerebrospinal fluid and/or urine samples. In various embodiments, the methods deplete three or more proteins from a sample by contacting the sample with at least one chromatographic medium, the at least one chromatographic medium being capable of removing albumin, IgG, and a third abundant protein from the sample. In various embodiments, the devices comprise a first chromatography column functionalized to substantially remove a first abundant protein from the sample; a second chromatography column in serial fluidic communication with the first chromatography column and functionalized to substantially remove a second abundant protein from the sample; and a first chromatography disk in serial fluidic communication with the second chromatography column and functionalized to substantially remove a third protein from the sample.

Abstract: The methods of the invention exploit the mass-to-charge ratio dependent motion of ions in an electrodynamic ion traps in synergy with a charge quenching process. In an electrodynamic ion trap, each mass-to-charge ratio is characterized by a unique set of frequencies of motion. Accordingly, by tailoring the time-varying electrical potential of the ion trap the invention controls which ions are allowed or retained in the ion trap and which ions are subjected to charge quenching reactions. Control of ion retention and charge quenching is used to improve sample throughput, dynamic mass range and signal discrimination in the mass spectrometry of multiply charged ions.