Mass spectrometry–based functional proteomics: from molecular machines to protein networks
Nature MethodsPublished 27 September 2007
Thomas Köcher, Giulio Superti‐Furga
Citations237
SJR quartileQ1
SJR score17.25
SNIP8.40
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TL;DR
Different options regarding protein-complex purification strategies, mass spectrometry analysis and bioinformatic methods according to the specific question that is being addressed are reviewed.
Abstract
The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A variety of mass spectrometry-based approaches allow characterization of cellular protein assemblies under near-physiological conditions and subsequent assignment of individual proteins to specific molecular machines, pathways and networks, according to an increasing level of organizational complexity. An appropriate analytical strategy can be individually tailored--from an in-depth analysis of single complexes to a large-scale characterization of entire molecular pathways or even an analysis of the molecular organization of entire expressed proteomes. Here we review different options regarding protein-complex purification strategies, mass spectrometry analysis and bioinformatic methods according to the specific question that is being addressed.
Keywords
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111 Citations2005Darren Hamelinck, Heping Zhou +6 more
This study establishes reliable normalization for antibody microarray data, criteria for assessing normalization performance, and the capability of antibody microarrays for serum-protein profiling and multiparametric sample classification.
Proceedings of the National Academy of SciencesMass spectrometry of ribosomes and ribosomal subunits
108 Citations1998Dennis R. Benjamin, Carol V. Robinson +3 more
Nanoflow electrospray ionization has been used to introduce intact Escherichia coli ribosomes into the ion source of a mass spectrometer and the pattern of dissociation correlates strongly with predicted features of ribosomal protein-protein and protein-RNA interactions.
Analytical ChemistryAbsolute Quantification of Proteins in Solutions and in Polyacrylamide Gels by Mass Spectrometry
107 Citations2004Jan Havliš, Andrej Shevchenko
It is observed that in-gel digestion compromised the quantification accuracy by affecting the recovery of individual peptides and, therefore, the provided estimates might be strongly influenced by the selection of reference peptides.
Molecular and Biochemical ParasitologyPurification and characterization of proteasomes from Trypanosoma brucei
76 Citations1996Shao-bing Hua, Wah-Yuen To +3 more
Some quantitative differences in the substrate specificities between the proteasomes from bloodstream and procyclic forms were indicated, which may play a role in determining the differential protein turnovers at two different stages of development of T. brucei.
Journal of Biological ChemistryFunctional Assignment of the 20 S Proteasome from Trypanosoma brucei Using Mass Spectrometry and New Bioinformatics Approaches
73 Citations2001Lan Huang, Richard J. Jacob +5 more
To evaluate the capabilities of bioinformatics methods employed for identifying homologs of a protein of interest, the results suggest that neither the traditional query engines, BLAST and FASTA, nor specialized software developed for analysis of sequence information obtained by mass spectrometry are able to identify even closely related sequences at statistically significant scores.
PROTEOMICSA modified tandem affinity purification tag technique for the purification of protein complexes in mammalian cells
65 Citations2004Robert Drakas, Marco di Prisco +1 more
A modified TAP tag technique is presented that allows sufficient recovery of proteins from mouse fibroblasts growing in monolayer cultures and allows protein identification by mass spectrometry.
Journal of Biological ChemistryProtein Stoichiometry of a Multiprotein Complex, the Human Spliceosomal U1 Small Nuclear Ribonucleoprotein
54 Citations2004Elisabeth O. Hochleitner, Berthold Kastner +5 more
Quantitative mass spectrometry has great potential for the determination of the stoichiometry of multiprotein complexes, and the use of the isotope-coded, amine-specific reagent nicotinoyl-N-oxysuccinimide was found to be advantageous because of its greatermass spectrometric sensitivity.
Immunological ReviewsCharting protein complexes, signaling pathways, and networks in the immune system
50 Citations2006Angela Bauch, Giulio Superti‐Furga
How recent advances in high‐throughput proteomic technologies, involving biochemical purification methods and mass spectrometry analysis, can be applied systematically to the characterization of protein complexes and the computation of molecular networks is described.
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