Proteomics technologies and challenges

Abstract

Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.

Fig. 1

The workflow of proteomics technologies. 2-D PAGE: two-dimensional polyacrylamide gel electrophoresis; ESI: electrospray ionization; ICAT: isotope-coded affinity tag; iTRAQ: isobaric tags for relative and absolute quantification; LTQ: linear ion trap quadrupole; MALDI: matrix-assisted laser desorption/ionization; MudPIT: multidimensional protein identification technology; PTM: post-translational modification; SELDI: surface-enhanced laser desorption/ionization; TOF MS: time-of-flight mass spectrometry.