Back to the future: The human protein index (HPI) and the agenda for post-proteomic biology

Anderson, Norman G.; Matheson, A. C.; Anderson, N. Leigh

doi:10.1002/1615-9861(200101)1:1<3::aid-prot3>3.3.co;2-k

Cited by 23 publications

(29 citation statements)

References 11 publications

(5 reference statements)

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“…The proteome analysis of Helicobacter pylori and other bacterial pathogens is reviewed [18,19], as well as proteomics and human diseases [20]. In [21], the human proteome index as precursor of proteomics is summarized.…”

Section: Investigating Gene Expression: Proteome Analysismentioning

confidence: 99%

Possibilities to improve automation, speed and precision of proteome analysis: A comparison of two-dimensional electrophoresis and alternatives

2001

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Proteome analysis requires fast methods with high separation efficiencies in order to screen the various cell and tissue types for their proteome expression and monitor the effect of environmental conditions and time on this expression. The established two-dimensional gel electrophoresis (2-DE) is by far too slow for a consequential screening. Moreover, it is not precise enough to observe changes in protein concentrations. There are various approaches that promise faster, automated proteome analysis. This article concentrates on capillary (CT isoelectric focusing coupled to mass spectrometry (CIEF-MSn) and preparative IEF followed by size-exclusion chromatography, hyphenated with MS (PIEF-SEC-MS). These two approaches provide a similar separation pattern as the established 2-DE technique and therefore allow for the continued use of data based on this traditional approach. Their performances have been discussed and compared to 2-DE, evaluating 169 recent articles. Data on analysis time, automation, the detection limit, quantitation, peak capacity, mass and pI accuracy, as well as on the required sample amount are compared in a table.

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Section: Investigating Gene Expression: Proteome Analysismentioning

confidence: 99%

Possibilities to improve automation, speed and precision of proteome analysis: A comparison of two-dimensional electrophoresis and alternatives

2001

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“…With the availability of many completed genomes, we now have the opportunity to study protein expression levels, structures, modifications and interactions in complex systems, which will lead to a comprehensive understanding of their biological function [1][2][3][4]. It is estimated that there may be as many as 400 000 protein products of the human genome, and about 20 000 proteins are expressed in a particular type of cell [5].…”

Section: Introductionmentioning

confidence: 99%

Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli

Yan¹,

Devenish²,

Wait

et al. 2002

Proteomics

202

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Separation and relative quantitation of complex protein mixtures remain two of the most challenging aspects of proteomics. Here an advanced technique called fluorescence difference 2-D gel electrophoresis technology (2D-DIGE) has been applied to a model system study of the Escherichia coli proteome after benzoic acid treatment. The molecular weight and charge matched cyanine dyes enable pre-electrophoretic labelling of control and treated samples which are then mixed and run in the same gel. Pooled control and treated samples labelled with Cy trade mark 3 were used as an internal standard for both Cy5 labelled control and treated E. coli samples. Together with DeCyder trade mark imaging analysis software, more accurate quantitative analysis than conventional two-dimensional polyacrylamide gel electrophoresis was achieved. Using matrix-assisted laser desorption/ionization-time of flight and quadrupole-time of flight mass spectrometry a total of 179 differentially expressed protein spots were identified. These included enzymes, stress related and substrate (e.g. amino acids, maltose, ribose and TRP repressor) binding proteins. Of the spots analysed, 77% contained only one protein species per spot, hence the change in protein expression measured was solely attributed to the identified protein. Many membrane proteins and protein isoforms were identified indicating both adequate solubilization of E. coli samples and potential post-translational modification. The results indicate that the regulatory mechanisms following benzoic acid treatment of E. coli are far more complicated than hitherto expected.

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“…During the past decade, large amounts of protein sequence data have been deposited in a number of data bases as a result of different genome projects [1,2,3]. Few of these protein sequences are known from expressed and characterised proteins -most have been deduced from the corresponding nucleic acid sequences.…”

Section: Introductionmentioning

confidence: 99%

"Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping

et al. 2003

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We describe here a new approach for the identification of affinity-bound proteins by proteolytic generation and mass spectrometric analysis of their antibody bound epitope peptides (epitope excision). The cardiac muscle protein troponin T was chosen as a protein antigen because of its diagnostic importance in myocardial infarct, and its previously characterised epitope structure. Two monoclonal antibodies (IgG1-1B10 and IgG1-11.7) raised against intact human troponin T were found to be completely cross reactive with bovine heart troponin T. A combination of immuno-affinity isolation, partial proteolytic degradation (epitope excision), mass spectrometric peptide mapping, and database analysis was used for the direct identification of Tn T from bovine heart cell lysate. Selective binding of the protein was achieved by addition of bovine heart cell lysate to the Sepharose-immobilised monoclonal antibodies, followed by removal of supernatant material containing unbound protein. While still bound to the affinity matrix the protein was partially degraded thereby generating a set of affinity-bound, overlapping peptide fragments comprising the epitope. Following dissociation from the antibody the epitope peptides were analysed by matrix assisted laser desorption-ionisation (MALDI) and electrospray-ionisation (ESI) mass spectrometry. The peptide masses identified by mass spectrometry were used to perform an automated database search, combined with a search for a common "epitope motif". This procedure resulted in the unequivocal identification of the protein from biological material with only a minimum number of peptide masses, and requiring only limited mass-determination accuracy. The dramatic increase of selectivity for identification of the protein by combining the antigen-antibody specificity with the redundancy of peptide sequences renders this "affinity-proteomics" approach a powerful tool for mass spectrometric identification of proteins from biological material.

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Back to the future: The human protein index (HPI) and the agenda for post-proteomic biology

Cited by 23 publications

References 11 publications

Possibilities to improve automation, speed and precision of proteome analysis: A comparison of two-dimensional electrophoresis and alternatives

Possibilities to improve automation, speed and precision of proteome analysis: A comparison of two-dimensional electrophoresis and alternatives

Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli

"Affinity-proteomics": direct protein identification from biological material using mass spectrometric epitope mapping

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