Bioinformatics

Bioinformatics is the application of information technology to the field of molecular biology. The primary goal of bioinformatics is to increase our understanding of biological processes. What sets it apart from other approaches, however, is its focus on developing and applying computationally intensive techniques (e.g., data mining, and machine learning algorithms) to achieve this goal.

Proteomics

Proteomics refers to the study of proteins, which are vital parts of any living organism. Proteins are the main components of the physiological metabolic pathways of cells. Proteomics is therefore of high importance to medical research and clinical diagnostics.

Proteomics is one of the key technologies for the development of individual medicine, which is the future of medicine in general. Arguable proteomics is more important than genomics because the genome is fixed for life while the proteome is changing from day to day. Proteomics will therefore continue to have a large impact on both medical research and clinical diagnostics.

Protein Mass Spectrometry

Protein Mass Spectrometry refers to the application of mass spectrometry (MS) to the study of proteins. Mass spectrometry is an important emerging method for the characterization of proteins. The two primary methods for ionization of whole proteins are ElectroSpray Ionization (ESI) and Matrix-Assisted Laser Desorption/Ionization (MALDI). In keeping with the performance and mass range of available mass spectrometers, two approaches are used for characterizing proteins. In the first, intact proteins are ionized by either of the two techniques described above, and then introduced to a mass analyser. This approach is referred to as "top-down" strategy of protein analysis. In the second, proteins are enzymatically digested into smaller peptides using a protease such as trypsin. Subsequently these peptides are introduced into the mass spectrometer and identified by peptide mass fingerprinting or tandem mass spectrometry. Hence, this latter approach (also called "bottom-up" proteomics) uses identification at the peptide level to infer the existence of proteins.

Whole protein mass analysis is primarily conducted using either Time-of-Flight (TOF) MS, or Fourier Transform Ion Cyclotron Resonance (FT-ICR). These two types of instrument are preferable here because of their wide mass range, and in the case of FT-ICR, its high mass accuracy. Mass analysis of proteolytic peptides is a much more popular method of protein characterization, as cheaper instrument designs can be used for characterization. Additionally, sample preparation is easier once whole proteins have been digested into smaller peptide fragments. The most widely used instrument for peptide mass analysis are the MALDI time-of-flight instruments as they permit the acquisition of PMFs at high pace (1 PMF can be analysed in approx. 10 sec). Multiple stage quadrupole-time-of-flight and the quadrupole ion trap also find use in this application.

Mass Spectrometry (MS) is a prerequisite for Proteomics-related research. It is the tool that provides the data which is needed for research in order to make a breakthrough in both medical research and clinical diagnostics. Without MS there would be no Proteomics that would be worth mentioning.

MS is a critical tool for Proteomics! For many researchers around the world Proteomics is pretty much defined by MS. MS is the key technology in Proteomics and will continue to be used extensively in Proteomics during the next 10 years.

Bioinformatics

Bioinformatics is the application of information technology to the field of molecular biology, but in simple terms it means the development of software tools for analyzing biological and medical data.

Software tools in Bioinformatics are alpha and omega of MS-based Proteomics, and its role will only increase in the future. The most important areas will be protein quantification, protein sequencing, analysis of posttranslational modifications, correlation analysis, and pathway analysis.

Access to some type of data processing software is critical for continued use of MS. Without software development in Bioinformatics there won't be much MS results from research that are worth discussing. It is of course possible to work on a MS-related project without using a professional software tool, but such work is always hard and extremely time consuming. Today, the majority time during such a project is put on data analysis, which would be drastically reduced if professional software tools were used instead.

Today, the bottleneck in both Proteomics and MS lies in the lack of professional software tools.

The future of medicine lies in short- and middle-term personalized diagnostics using MS, in which patient's personal data are used to stratify the disease, select an optimal therapy and monitor its progress. This requires developing state-of-the-art software tools in Bioinformatics.

Proteomics is critical for the future of medical research and clinical diagnostics. MS is critical for Proteomics research. Bioinformatics is critical for MS. Therefore, state-of-the-art software tools in Bioinformatics are of highest importance for Proteomics, as well as the future of medical research and clinical diagnostics!