The application of proteomic techniques to fungal protein identification and quantification

James G. Rohrbough, John N Galgiani, Vicki H. Wysocki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations


The number of sequenced genomes has increased rapidly in the last fewyears, supporting a revolution in bioinformatics that has been leveraged by scientists seeking to analyze the proteomes of numerous biological systems. The primary technique employed for the identification of peptides and proteins from biological sources is mass spectrometry (MS). This analytical process is usually in the form of whole-protein analysis (termed "top-down" proteomics) or analysis of enzymatically produced peptides (known as the "bottom-up" approach). This article will focus primarily on the more common bottom-up proteomics to include topics such as sample preparation, separation strategies, MS instrumentation, data analysis, and techniques for protein quantification. Strategies for preparation of samples for proteomic analysis, as well as tools for protein and peptide separation will be discussed. A general description of common MS instruments along with tandem mass spectrometry (MS/MS) will be given. Different methodologies of sample ionization including matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) will be discussed. Data analysis methods including database search algorithms and tools for protein sequence analysis will be introduced. We will also discuss experimental strategies for MS protein quantification using stable isotope labeling techniques and fluorescent labeling. We will introduce several fungal proteomic studies to illustrate the use of these methods. This article will allow investigators to gain a working knowledge of proteomics along with some strengths and weaknesses associated with the techniques presented.

Original languageEnglish (US)
Title of host publicationAnnals of the New York Academy of Sciences
Number of pages14
Publication statusPublished - Sep 2007

Publication series

NameAnnals of the New York Academy of Sciences
ISSN (Print)00778923
ISSN (Electronic)17496632


ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Rohrbough, J. G., Galgiani, J. N., & Wysocki, V. H. (2007). The application of proteomic techniques to fungal protein identification and quantification. In Annals of the New York Academy of Sciences (Vol. 1111, pp. 133-146). (Annals of the New York Academy of Sciences; Vol. 1111).