ass spectrometry (MS) has evolved into one of the most sensitive analytical methods for the structural characterization of molecules.1,2 Ionization is critical for volatilizing sample analytes into a gas-phase. This primer covers a range of options which often require complementary equipment, such as syringe pumps, for efficient ionization.

Electrospray Ionization (ESI)

ESI is the most common form of ionization used for MS.It employs voltage to convert a flow of liquid to generate an electrospray. A combination of heat and acceleration toward the vacuum system forces electrostatically bound particles to dissociate by releasing water and drying the sample. The ions in gaseous phase pass through a voltage gradient before being ejected into the mass analyzer for detection. The use of syringe pumps for aerosolizing the sample can greatly enhance electrospray generation. ESI is mild enough to be used with thermally labile compounds such as proteins and pharmaceuticals...

Atmospheric Pressure Chemical Ionization (APCI) 

A needle generates a voltage discharge at atmospheric pressures which is applied to aerosolized samples in APCI.Precision syringe pumps inject liquid analytes at a controlled flow rate towards a heated gas for volatilization and exposure to ions created by the discharge. The new ions formed by proton transfer are then transported to a vacuum used for electrospray. Other variations of this technique include photoionization as well as well as using a solids probe.

Electron Impact (EI)

EI involves a beam of high-charge electrons bombarding analytes to volatilize them in a vacuum directly. This generates radical ions ejected from the gas phase. These gaseous ions develop further fragmentations which can be detected in great detail by the analyzer. Although cost-effective, this harsh ionization technique is limited to analyzing small and volatile molecules commonly used in gas chromatography such as ammonia or isobutane. Larger biomolecules with tertiary structures such as proteins should be avoided.

Electrospray Derivatives

Desorption electrospray ionization (DESI) is an alternative to direct ionization, where the surface of sample molecules is subjected to ESI, but only the extracted ions from the surface end up being analyzed by MS.DESI is mild enough to be used with labile compounds such as proteins and thermally labile pharmaceuticals. Similarly, nanospray is a highly sensitive form of ESI and can be used for tiny sample volumes.Using delicate syringe pumps, a few microliters of the sample can persist for several minutes by generating a low flow.

Matrix Assisted Laser Desorption Ionization (MALDI)

Analytes are mixed or coated with a solution of an energy-absorbent organic matrix in MALDI.The mixture crystalizes upon drying and the sample entrapped within the matrix is also co-crystallized. A laser bombards the mixture promoting proton transfer in the sample. The combined use of a pulsing laser in a vacuum system results in predominantly singularly charged ions which can be used to measure analytes on time-of-flight (TOF) instruments. MALDI is also the preferred technique for imaging MS.

While most laboratories will have only one or two of these platforms available, it’s important to understand the differences between them so you can plan your experiments wisely. 


1. W. Clark, “Mass spectrometry in the clinical laboratory: determining the need and avoiding pitfalls,” Mass Spec Clin Lab, 1:171-183, 2017.
2. N. Saraswathy and P. Ramalingam, “Mass spectrometry for proteomics,” Concepts & Techniques in Genomics and Proteomics, 12:171-183. 2011.
3. H.D. Dewald, “Electrospray ionization mass spectrometry: fundamentals, instrumentation and applications,” J Chem Educ, 76(1):33-39, 1999.
4. C.N. McEwen, "GC/MS on an LC/MS instrument using atmospheric pressure photoionization," Int J Mass Spec, 259 1:57-64, 2007.
5. Y. Zhang et al., “Coupling of liquid chromatography with mass spectrometry by desorption electrospray ionization (DESI),” Chem Commun, 47(14):4171-73, 2011.
6. R. Juraschek et al., “Nanoelectrospray—more than just a minimized-flow electrospray ionization source,” J Am Soc Mass Spectrom, 10(4):300-308, 1999.
7. W.C. Chang et al., “Matrix-assisted laser desorption/ionization (MALDI) mechanism revisited,” Anal Chim Acta, 582(1):1-9, 2007.

Meet the Sponsor: 

This article is brought to you by Chemyx, Inc. Syringe Pumps by Chemyx are used in top-level biomedical, pharmaceutical, chemical, and petrochemical research, offering highly precise, consistent, and reproducible fluidic delivery. Chemyx pump devices orchestrate the performance of different technologies that make modern research into novel materials, drugs, and energy resources possible. www.chemyx.com

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