Chemical Sciences: A Manual for CSIR-UGC National Eligibility Test for Lectureship and JRF/Liquid chromatography-mass spectrometry

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Liquid chromatography-mass spectrometry (LC-MS, or alternatively HPLC-MS) is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography (or HPLC) with the mass analysis capabilities of mass spectrometry. LC-MS is a powerful technique used for many applications which has very high sensitivity and specificity. Generally its application is oriented towards the specific detection and potential identification of chemicals in the presence of other chemicals (in a complex mixture).

Liquid chromatography[edit]


A major difference between traditional HPLC and the chromatography used in LC-MS is that in the latter case the scale is usually much smaller, both with respect to the internal diameter of the column and even more so with respect to flow rate since it scales as the square of the diameter. For a long time, 1 mm columns were typical for LC-MS work (as opposed to 4.6 mm for HPLC). More recently 300 µm and even 75 µm capillary columns have become more prevalent. At the low end of these column diameters the flow rates approach 100 nL/min and are generally used with nanospray sources.[1]

Flow splitting[edit]

When standard bore (4.6 mm) columns are used the flow is often split ~10:1. This can be beneficial by allowing the use of other techniques in tandem such as MS and UV. However splitting the flow to UV will decrease the sensitivity of spectrophotometric detectors. The mass spectrometry on the other hand will give improved sensitivity at flow rates of 200 μL/min or less.

Mass spectrometry[edit]

Mass analyzer[edit]

There are a lot of mass analyzers that can be used in LC/MS. Single Quadrupole, Triple Quadrupole, Ion Trap, TOF (time of Flight) and Quadrupole-time of flight (Q-TOF).


Understandably the interface between a liquid phase technique which continuously flows liquid, and a gas phase technique carried out in a vacuum was difficult for a long time. The advent of electrospray ionization changed this. The interface is most often an electrospray ion source or variant such as a nanospray source; however fast atom bombardment, thermospray and atmospheric pressure chemical ionization interfaces are also used.[2] Various deposition and drying techniques have also been used such as using moving belts; however the most common of these is off-line MALDI deposition.[3][4]



LC-MS is very commonly used in pharmacokinetic studies of pharmaceuticals and is thus the most frequently used technique in the field of bioanalysis. These studies give information about how quickly a drug will be cleared from the hepatic blood flow, and organs of the body. MS is used for this due to high sensitivity and exceptional specificity compared to UV (as long as the analyte can be suitably ionised), and short analysis time.

The major advantage MS has is the use of tandem MS-MS. The detector may be programmed to select certain ions to fragment. The process is essentially a selection technique, but is in fact more complex. The measured quantity is the sum of molecule fragments chosen by the operator. As long as there are no interferences or ion suppression, the LC separation can be quite quick. It is common now to have analysis times of 1 minute or less by MS-MS detection, compared to over 10 mins with UV detection.[5][6][7]


LC-MS is also used in the study of proteomics where again components of a complex mixture must be detected and identified in some manner. The bottom-up proteomics LC-MS approach to proteomics generally involves protease digestion and denaturation (usually trypsin as a protease, urea to denature tertiary structure and iodoacetamide to cap cysteine residues) followed by LC-MS with peptide mass fingerprinting or LC-MS/MS (tandem MS) to derive sequence of individual peptides.[8] LC-MS/MS is most commonly used for proteomic analysis of complex samples where peptide masses may overlap even with a high-resolution mass spectrometer. Samples of complex biological fluids like human serum may be run in a modern LC-MS/MS system and result in over 1000 proteins being identified, provided that the sample was first separated on an SDS-PAGE gel or HPLC-SCX.[citation needed]

Drug development[edit]

LC-MS is frequently used in drug development at many different stages including Peptide Mapping, Glycoprotein Mapping, Natural Products Dereplication, Bioaffinity Screening, In Vivo Drug Screening, Metabolic Stability Screening, Metabolite Identification, Impurity Identification, Degradant Identification, Quantitative Bioanalysis, and Quality Control.[9]


  1. Capillary liquid chromatography/mass spectrometry, Kenneth B. Tomer, M. Arthur Moseley, Leesa J. Deterding, Carol E. Parker, Mass Spectrometry Reviews, Vol 13, 1994, pp 431-457
  2. Combined liquid chromatography mass spectrometry. Part III. Applications of thermospray, Patrick Arpino, Mass Spectrometry Reviews, Vol 11, 1992 pp 3-40
  3. Combined liquid chromatography mass spectrometry. Part I. Coupling by means of a moving belt interface, Patrick Arpino, Mass Spectrometry Reviews, Vol 8, 1989 pp 35-55
  4. Coupling matrix-assisted laser desorption/ionization to liquid separations, Kermit K. Murray, Mass Spectrometry Reviews, Vol 16, pp 283-299
  5. Increasing Speed and Throughput When Using HPLC-MS/MS Systems for Drug Metabolism and Pharmacokinetic Screening, Y. Hsieh and W.A. Korfmacher, Current Drug Metabolism Volume 7, Number 5, 2006, Pp. 479-489
  6. Covey TR, Lee ED, Henion JD. 1986. High-speed liquid chromatography/tandem mass spectrometry for the determination of drugs in biological samples. Anal Chem 58:2453-2460.
  7. Thermospray liquid chromatography/mass spectrometry determination of drugs and their metabolites in biological fluids. Covey TR et al. Anal Chem. 1985 Feb;57(2):474-81
  8. Wysocki VH, Resing KA, Zhang Q, Cheng G (March 2005). "Mass spectrometry of peptides and proteins". Methods 35 (3): 211–22. doi:10.1016/j.ymeth.2004.08.013. PMID 15722218. 
  9. LC/MS applications in drug development, Mass Spectrometry Reviews, Mike S. Lee, Edward H. Kerns, Vol 18, 1999, pp 187-279


  • Thurman, E. M.; Ferrer, Imma (2003). Liquid chromatography/mass spectrometry, MS/MS and time of flight MS: analysis of emerging contaminants. Columbus, OH: American Chemical Society. ISBN 0-8412-3825-1. 
  • Ardrey, R. E.; Ardrey, Robert (2003). Liquid chromatography-mass spectrometry: an introduction. London: J. Wiley. ISBN 0-471-49801-7. 
  • McMaster, Marvin C. (2005). LC/MS: a practical user's guide. New York: John Wiley. ISBN 0-471-65531-7. 
  • Wilfried M.A. Niessen, Wilfried M. Niessen (2006). Liquid Chromatography-Mass Spectrometry, Third Edition (Chromatographic Science). Boca Raton: CRC. ISBN 0-8247-4082-3. 
  • Yergey, Alfred L. (1990). Liquid chromatography/mass spectrometry: techniques and applications. New York: Plenum Press. ISBN 0-306-43186-6.