Journal of The American Society for Mass Spectrometry

, Volume 30, Issue 9, pp 1779–1789 | Cite as

Quantitation of Super Basic Peptides in Biological Matrices by a Generic Perfluoropentanoic Acid-Based Liquid Chromatography–Mass Spectrometry Method

  • Jianzhong WenEmail author
  • Weixun Wang
  • Keun-Joong Lee
  • Bernard K. Choi
  • Paul Harradine
  • Gino M. Salituro
  • Lucinda Hittle
Research Article


Peptides represent a promising modality for the design of novel therapeutics that can potentially modulate traditionally non-druggable targets. Cell-penetrating peptides (CPPs) and antimicrobial peptides (AMPs) are two large families that are being explored extensively as drug delivery vehicles, imaging reagents, or therapeutic treatments for various diseases. Many CPPs and AMPs are cationic among which a significant portion is extremely basic and hydrophilic (e.g., nona-arginine). Despite their attractive therapeutic potential, it remains challenging to directly analyze and quantify these super cationic peptides from biological matrices due to their poor chromatographic behavior and MS response. Herein, we describe a generic method that combines solid phase extraction and LC-MS/MS for analysis of these peptides. As demonstrated, using a dozen strongly basic peptides, low μM concentration of perfluoropentanoic acid (PFPeA) in the mobile phase enabled excellent compound chromatographic retention, thus avoiding co-elution with solvent front ion suppressants. PFPeA also had a charge reduction effect that allowed the selection of parent/ion fragment pairs in the higher m/z region to further reduce potential low molecular weight interferences. When the method was coupled to the optimized sample extraction process, we routinely achieved low digit ng/ml sensitivity for peptides in plasma/tissue. The method allowed an efficient evaluation of plasma stability of CPPs/AMPs without fluorescence derivatization or other tagging methods. Importantly, using the widely studied HIV-TAT CPP as an example, the method enabled us to directly assess its pharmacokinetics and tissue distribution in preclinical animal models.


Cell-penetrating peptides Antimicrobial peptides Perfluoropentanoic acid Peptide quantitation LC-MS 



The authors gratefully acknowledge Scott E. Fauty and the Biochemical Toxicology & Toxicokinetics group in Merck & Co., Inc. (West Point, PA, USA) for conducting the in vivo PK experiment. We thank Drs. Christine Fandozzi, Kevin Bateman, Vincenzo Pucci, Rena Zhang, Raymond Evers and Jerome Hochman for insightful discussions.

Compliance with Ethical Standards

Conflict of Interest

The authors were employed by Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA, during the work described in this article. The authors declare no competing financial interest.

Supplementary material

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ESM 1 (DOCX 856 kb)


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Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Pharmacokinetics, Pharmacodynamics and Drug MetabolismMerck & Co., Inc.RahwayUSA

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