Service Providers

Local labs where proteomics services are available.

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Council for Scientific and Industrial Research

The Systems Biology group at CSIR apply techniques that allow global analysis of the state of proteins in biological systems.

Location

Western Cape

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University of Cape Town IDM Proteomics Core

The IDM proteomics core provides mass spectrometry services for researchers and collaborators from the University of Cape Town as well as other facilities. Our quantitative analyses are based mainly on label-free workflows including discovery and targeted analysis.

Location

Western Cape

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North-West University Analytical Platform

A resource offering analytical and instructional expertise in mass spectrometric analysis.

Location

North West

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Center for Proteomic and Genomic Research

Combine cutting-edge, information-rich genomic and proteomic technologies with bio-computational applications to convert biological samples into digital information and scientific knowledge.

Location

Western Cape

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North-West University Analytical Platform

A resource offering analytical and instructional expertise in mass spectrometric analysis.

Location

North West

 
 

Proteomics

Data Generation

There are thousands of proteins expressed in cells, tissues and present in biological fluids. Traditionally they were analysed individually. Antibodies binding to a single protein enables individual protein detection. Using immunohistochemistry a particular protein's localisation and abundance can be visualised within cells and tissues. Western Blot and ELISA allow fairly accurate relative quantitation of individual proteins.

In proteomics determining the relative abundance of many proteins simultaneously provides information on the interactions and functions of those proteins within the biological system.

Two-dimensional difference gel electrophoresis (2D DIGE), separates multiple proteins by charge and size. The size of the spots on the gel indicated the quantity of protein present. The spots of interest are then excised and identified by mass spectrometry. While offering protein-centric quantitation, relatively few proteins are visualised and identified.
 
The most common technique in proteomics is liquid chromatography coupled tandem mass spectrometry (LC-MSMS). It is possible to detect whole proteins by mass spectrometry (Top-down proteomics). It is, however, more common to digest the proteins into peptides and then use mass spectrometry to detect the peptides, later inferring the identity and abundance of the proteins from the detected peptides, referred to as bottom-up proteomics.

In targetted proteomics, peptides fragments from selected proteins are isolated and detected by LC-MSMS, providing accurate and specific quantification of a few known proteins. In discovery proteomics, the most abundant proteins are indiscriminately detected and quantitated by LC-MSMS. The quantitation is not as robust as the above techniques, but the large number of proteins identified makes it most valuable.

2D DIGE

Two-Dimensional Difference Gel Electrophoresis, separates proteins that have been tagged with fluorescent dyes by two dimensional gel electrophoresis. This allows direct relative protein abundance comparisons to be made.

Targeted Proteomics

Using mass spectrometry it is possible to select specific peptides from known proteins. These targeted proteins can then be specifically and accurately quantified.

Discovery Proteomics

Using mass spectrometry peptide masses and intensity are measured. The peptides are then fragmented and the fragmentation spectrum used the identify the proteins from which they originate.

 

Proteomics datasets uploaded to public repositories can be downloaded and mined for additional data. The databases entries need to contain a minimum amount of information for submission. This information describes the experiment, methods of data generation, and data processing. Uploaded data comprises raw data files and results.

Panorama Public

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Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow.

Peptide Atlas

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PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.

iProX

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"iProX is an integrated proteome resources center in China, which is built to accelerate the worldwide data sharing in proteomics. iProX is composed of a data submission system and a proteome database. The submission system is established under the guidance of the data-sharing policy made by ProteomeXchange consortium."

ProteomeXchange

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The ProteomeXchange Consortium was established to provide globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories, and to encourage open data policies in the field

JPOST

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A proteomic database named jPOST (Japan ProteOme STandard Repository/Database) to integrate proteome datasets generated from multiple projects and institutions.

MassIVE

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MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements.

 

Data Analysis Toolkits

Mass Spectrometry data requires multiple data analysis steps. First, the spectra need to be matched to theoretical peptides. False discovery rates for peptide spectral matches need to be calculated. The protein identifications need to be interpolated. Protein quantitation then needs to be determined. These tools have been compiled into pipelines,  but can also be run separately.

Seattle Proteome Center Proteomics Tools

"The Seattle Proteome Center (SPC) is committed to providing free, open-source, software projects in support of cutting-edge proteomics research."

MaxQuant

"MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data."

ProteoWizard

"ProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis"

CRUX

"The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data"

 

Bioinformaticians

Bioinformaticians are available to assist you with your project.

 

The earlier you contact them the more assistance they will be able to offer. In particular, the experimental design is critical in ensuring the success of any project. Contacting a statistician and ensuring your experiment has enough statistical power will go a long way to ensuring its success. Selecting the best technology for your project will ensure you get the best results for the your project. Omics research is costly, choosing the most appropriate technology for you experiment and budget is therefor critical.

 

Runing a pilot study and having an expert check the quality of the results before continuing with the bulk of the analysis is also important. The pilot project will also allow you to familiaries youself with the sample analysis process and the data generated and the means of analysis, before embarking on the whole project.

 

Once you have produced the data, you will realise omics technologies produce mountains on data. It often requires some expertise in handelling big data, to deal with the amounts of data produced. Fortunatly we have tools and resources to store and process your data making it easy for you to understand. Contact our team of expert bioninformaticians for assistance on all levels of your project.

Dr Shaun Garnett

Post-Doctoral Fellow at University of Cape Town

Fields

  • Transcriptomics

  • Proteomics

  • Differential Abundance Statistics

Expertise

  • Liquid Chromatorgaphy

  • Mass Spectrometry

  • Discovery Proteomics

  • Statistics

  • Expression Data Functional Annotation

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Tools

Literature

Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World

Journal of Biomolecular Techniques (2018)

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Bell, L., Calder, B., Hiller, R., Klein, A., Soares, N. C., Stoychev, S. H., Vorster, Barend C., Tabb, D. L.

 

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