PubMed Health⌕ Search

PubMed · 12117762

Advances in proteomic technologies.

Abstract

Proteomics is a rapidly emerging set of key technologies that are being used to identify proteins and map their interactions in a cellular context. With the sequencing of the human genome, the scope of proteomics has shifted from protein identification and characterization to include protein structure, function and protein-protein interactions. Technologies used in proteomic research include two-dimensional gel electrophoresis, mass spectrometry, yeast two-hybrids screens, and computational prediction programs. While some of these technologies have been in use for a long time, they are currently being applied to study physiology and cellular processes in high-throughput formats. It is the high-throughput approach that defines and characterizes modern proteomics. In this review, we discuss the current status of these experimental and computational technologies relevant to the three major aspects of proteomics-characterization of proteomes, identification of proteins, and determination of protein function. We also briefly discuss the development of new proteomic technologies that are based on recent advances in analytical and biochemical techniques, engineering, microfabrication, and computational prowess. The integration of these advances with established technologies is invaluable for the drive toward a comprehensive understanding of protein structure and function in the cellular milieu.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Martin L Yarmush, Arul Jayaraman. 2002-03-22. Advances in proteomic technologies.. https://doi.org/10.1146/annurev.bioeng.4.020702.153443

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

Proteomic response to intracellular proteins of Monascus pilosus grown under phosphate-limited complex medium with different growth rates and pigment production.

Monascus pigments are important colorings in food applications. Rice containing potassium phosphate and sodium nitrate was reported as a good pigment-producing medium for Monascus in previous studies. We found that the lack of potassium phosphate in this medium depressed red pigment production in cultivated Monascus pilosus. However, the influence of phosphate limitation on the biochemical metabolisms concerning culture growth and pigment production in Monascus remains unknown. Here, we used proteomic analysis by two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS), tandem mass spectrometry (MS/MS), and database interrogation to separate and identify the proteins of M. pilosus grown between the lack of potassium phosphate and the control media. Phosphate limitation to this complex medium induced an up-regulation of aldehyde dehydrogenase and several glycolytic enzymes in Monascus relative to the control. In contrast, the metabolic enzymes such as glucosamine:fructose-6-phosphate aminotransferase and ADP-ribosylation factor 1 were up-regulated in the control.

Electrophoresis, Gel, Two-Dimensional↗

Toward an integrated microchip sized 2-D polyacrylamide slab gel electrophoresis device for proteomic analysis.

We describe a miniaturized instrument capable of performing 2-DE. Our miniaturized device is able to perform IEF and polyacrylamide slab gel electrophoresis (PASGE) in the same unit. It consists of a compartment for a first-dimensional IEF gel, which is connected to a second-dimensional PASGE gel. The focused samples are automatically transferred from the IEF gel to the PASGE gel by electromigration. Our preliminary experiments show that the device is able to focus and separate a mixture of proteins in approximately 1 h, excluding the time required for the staining procedure. On average, the gel-to-gel retardation factor (Rf) variation was 6.2% (+/-0.9%) and pI variation was 2.5% (+/-0.6%). Separated protein spots were excised from stained gels, digested with trypsin, and further identified by MS, thus enabling direct proteomic analysis of the separated proteins.

Electrophoresis, Gel, Two-Dimensional↗

Proteomic analysis of human very low-density lipoprotein by two-dimensional gel electrophoresis and MALDI-TOF/TOF.

Biochemical studies of lipoproteins have shed light on their composition, highly contributing to the comprehension of their function. Due to the complexity of their structure, however, an in-depth structural analysis, in terms of components and PTMs, may still unravel important players in physiological and pathological processes of lipid metabolism. In this study, we performed a protein map of very low-density lipoprotein (VLDL) using a 2-DE MALDI-TOF/TOF proteomic approach. Several VLDL-associated apolipoproteins were identified, including five isoforms of apoE, three isoforms of apoC-IV, and one isoform each of apoC-III, apoM, apoA-I, and apoA-IV. Notably, we also identified seven isoforms of apoL-I and two isoforms of prenylcysteine lyase as new VLDL-associated proteins. Furthermore, we were able to identify PTM of apoE, which was found to be differently O-glycosylated at Thr212 residue, and PTM of apoL-I which we described, for the first time, to be phosphorylated at Ser296. While the physiological relevance of our finding remains to be assessed, we believe that our results will be useful as reference for future studies of VLDL structure in specific physiopathological conditions.

Electrophoresis, Gel, Two-Dimensional↗