Peptide mapping of proteins in human body fluids using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

 I. Introduction 3A. Human Body Fluids as Sources for Clinical Markers 3B. Plasma 3C. Cerebrospinal Fluid 5D. Saliva 5E. Urine 5  II. Review of Typical Materials and Methods 5A. General 5B. Human Plasma Samples 5C. Human CSF Samples 5D. Human Saliva Samples 6E. Human Urine Samples 6F. Tryptic Digestion of Proteins 6G. Desalting 6H. Direct Infusion and Capillary Interface 6I. Mass Spectrometry 6J. Data Analysis 7 III. Results and Discussion 7 IV. Conclusions 12 Acknowledgments 13 References 13Human body fluids have been rediscovered in the post‐genomic era as great sources of biological markers and perhaps particularly as sources of potential protein biomarkers of disease. Analytical tools that allow rapid screening, low sample consumption, and accurate protein identification are of great importance in studies of complex biological samples and clinical diagnosis. Mass spectrometry is today one of the most important analytical tools with applications in a wide variety of fields. One of the fastest growing applications is in proteomics, or the study of protein expression in an organism. Mass spectrometry has been used to find post‐translational modifications and to identify key functions of proteins in the human body. In this study, we review the use of human body fluids as sources for clinical markers and present new data that show the ability of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) to identify and characterize proteins in four human body fluids: plasma, cerebrospinal fluid (CSF), saliva, and urine. The body fluids were tryptically digested without any prior separation, purification, or selection, and the digest was introduced into a 9.4 T FTICR mass spectrometer by direct‐infusion electrospray ionization (ESI). Even though these samples represent complex biological mixtures, the described method provides information that is comparable with traditional 2D‐PAGE data. The sample consumption is extremely low, a few microliters, and the analysis time is only a few minutes. It is, however, evident that the separation of proteins and/or peptides must be included in the methodology, in order to detect low‐abundance proteins and other proteins of biological relevance. © 2002 Wiley Periodicals, Inc. Mass Spec Rev 21:2–15, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/mas.10016