Compare and Contrast the Way in Which Proteomics Studies are Performed in Current Literature

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Proteomics techniques have continued to develop in recent times and in the process giving researchers a perfect opportunity to conduct new studies in different ways compared to the way it used to be done ten years ago (Van Eyk 24). The introduction of the human genome project in 2003 was seen as an improved way of conducting proteomic studies through the use of a genomic database in proteomic analysis. The process of protein identification has been made much easier through the rapid growth of computer technology which has enabled researchers to build database searching engines (Van Eyk 43). This paper will discuss some of the major factors that have contributed to the development of proteomic studies over the last decade and how developed techniques have affected proteomics studies.

Techniques used to conduct proteomic have been changing over the years due to rapid growth in technology. The type of technique used in proteomic studies is entirely dependent on the purpose of the study (Walker 123). There are three major types of proteomics namely structural, expression and structural proteomics. Each type of proteomic is unique and requires specific techniques and approaches to determine its specific characteristics (Walker 123). Proteome analysis is conducted entirely for protein identification and characterization. Each technique has its strengths and limitation and therefore there is no ideal technique for all kinds of studies (Walker 150).

Mass spectrometry is considered as a primary tool for all proteomic studies. There has been a great improvement in terms of techniques and approaches of conducting proteomic studies in the last ten years (Walker 150). There are several factors that play a very vital in determining the appropriate technique to be used in proteomic analysis. The two major factors include the simplicity and complexity of the protein sample and the purpose of the study (Kline 67). Both clinical and pharmaceutical studies have increased in the last ten years and in the process affecting how proteomic studies are done (Kline 69). Fundamental research in clinical and pharmaceutical studies has largely impacted proteomic analysis and in the process leading to the improvement of available techniques. Clinical and pharmaceutical studies have been critical in disease detection and drug discovery and in the process motivating researchers to continue developing new proteomic techniques (Kline 72).

The shotgun proteomic techniques have been developed in recent years and have proved to be reliable tools for studying protein expression (Dunphy 123). Despite the significant improvements made in the ways of conducting proteomic analysis, some challenges are still being faced in conducting specific proteomics studies. Challenges such as poor post-transitional modification technology, low resolution with high mass and the time consumed in conducting the experiments have contributed in limiting specific proteomic studies (Dunphy 124). The Human Genome Project (HUGO) that was completed in early 2003 has made a huge impact in proteomic studies through the use of the genomic database linked with an MS software in proteomic analysis. The Human Genome Project has improved expression proteomic studies in a great way due to the fact that genomic and proteomic studies complement each other (Dunphy 134).

The use of computer technology in proteomic analysis has become very popular in recent years because computer technology has helped a great deal in making proteomic studies much simpler (Yee 89). Computer abilities such as processing and storage have helped researchers a great deal in building huge databases for proteins and peptides identification. Proteins identification was very difficult ten years ago due to the limited storage capacity of computers (Yee 89). This technology has continued to improve because the storage capacity of transistors has been doubling after every two years. Currently, several databases are being used in proteins identification by the use of search engines such as sequest and mascot. There are three major types of proteomics on which proteomic studies are normally done. These major proteomics include structural, functional and expression proteomics (Yee 103). Current techniques that are used to conduct proteomic studies on these three types of proteomics are completely different from the way the studies used to be conducted ten years ago (Walker 64).

Expression proteomics are normally classified into qualitative and quantitative proteomics (Kline 18). The studies conducted on this type of proteomics involve comparing the total protein expression under two different conditions with an aim of determining whether there is any change in the expression of proteins. There are several techniques used to perform expression proteomic studies in proteins and peptides (Kline 18). The first technique is the differential display technique that is used to compare two samples to find out whether there are any differences between them. When comparing a normal cell and an abnormal cell ten years ago, the one dimensional gel electrophoresis method and the two dimensional gel electrophoresis with staining dyes were the commonly used methods in the differential display technique (Whitfield 52).

The differences gel electrophoresis method was introduced in 1997 and allows the separation of multiple protein extracts on the same gel in order to avoid gel-to-gel variation (Whitfield 129). The different protein extracts are normally labeled with florescent dyes. All differential display techniques have been in use since 2004 with the two dimensional differences gel electrophoresis being regarded as the most powerful technique in recent times. The second technique used to study expression proteomics is the shotgun proteomic technique. This technique is both non-visual and non-gel and is used to identify many proteins in a given sample (Whitefield 129). The technique identifies as many proteins as possible and uses the bottom-up technique where the protein sample under study is digested first before being separated. In 2001, Multi-dimensional Liquid Chromatography (MDLC) runs were used to identify approximately 1500 proteins in a yeast whole-cell (Vinci 34). Ten years ago, large scale shotgun proteomic technique employed the use of column configurations such as Mudpit with strong cation exchange and reverse chromatography for protein fractionating (Vinci 34).

Cation exchange method has since been replaced to improve some specific aspects in proteins (Vinci 35). The methods that are currently used include anion exchange chromatography, affinity chromatography, isoelectric focusing and capillary electrophoresis. Gel electrophoresis is another new method that has been introduced in which proteins are separated by size, digested and then analyzed (Vinci 35). More recently, the use of two dimensional chromatography separations was developed in which the first and the second columns have a PH of 10 and 6 respectively. The third commonly used technique in conducting expression proteomic studies is the labeling proteomic technique that is used to determine the protein level in a living organism (Vinci 45).

The labeling proteomic approach is used to study the disease process and cellular response to stress by the use of stable isotope tags to label proteins or peptides (Yee 78). This type of technique can also be incorporated in into the shotgun studies. In the year 1999, the isotope coded affinity tag was introduced as the first approach of stable isotope label with other techniques for protein and peptides being introduced afterwards (Yee 79). There are four tagging methods that have been in use over the last ten years namely chemical labeling, enzymatic labeling, metabolic labeling and isotopic labeling. Chemical and metabolic labeling methods are used to label proteins whereas enzymatic and isotopic labeling methods are used to label peptides (Yee 79).

Recently, the stable isotope labeling with amino aids in cell culture technique has been developed as an alternative to the isotope coded affinity tag technique (Vinci 122). This change of technique was done because the isotope-coded affinity tag technique only interacts with proteins that have cysteine thus limiting the process of identifying multiple proteins. The isobaric tag for relative and absolute quantization was developed in the year 2004 specifically for peptides labeling (Vinci 122). Both the stable isotope labeling with amino acids in cell culture method together with the isobaric tag for relative and absolute quantization methods can be used to compare multiple samples together. The label free proteomic technique in another technique used in proteomic studies especially in clinical research. This technique is preferred in clinical research mainly because of its reproducibility nature (Whitfield 51). There are many approaches that have been developed such as the relative quantification by peak intensity method and the relative quantification by spectral counting method (Whitfield 51).

The relative quantification by peak intensity method and the relative quantification by spectral counting method are integrated with statistical evolution with an aim of finding out the differences in protein expression (Walker 34). There is another approach which can be used to determine the protein abundance index and afterwards be exponentially modified to determine the absolute protein quantification. In the year 2007, the absolute protein expression profiling method was described as the modified form of the spectral counting approach which was later developed into absolute protein expression with is normally utilized as a quantitative proteomic tool (Walker 99). The protein profiling technique is used to screen samples directly with limited or without the use of chromatography for purification (Walker 99).

The surface enhanced laser desorption/ionization method was commercialized in 1997 specifically for protein profiling through targeting the protein chip array composed of various chromatographic, immunologic or enzymatic surfaces (Kline 81). The surface enhanced lasers desorption/ionization approach is also used for high-throughput for drug discovery and biomarkers. Another approach used in the protein profiling technique is the imaging mass spectrometry approach which uses matrix assisted laser desorption/ionization to visualize the tissue sample (Kline 81). Structural proteomic studies are normally performed to find out the structural shape of the protein such as the three dimensional shapes and at the same time determine the complexity of the protein structure (Walker 74). The analysis of the protein structure is very important in determining the site of phosphorylation and glycosylation. There are two popular methods that are normally used to determine the site of phosphorylation. Both of these methods have been used in the past and are still being used in current proteomic studies (Walker 74). The immobilized metal affinity chromatography is considered as a simple approach for phosphorylated protein enrichment. The major limitation of this approach is the low recovery of phosphorylated peptides (Walker 76).

The other commonly used technique in phosphoproteome analysis is the chemical derivatization approach which has selectivity to phosphate functional groups. This approach ah been developed to perform relative quantization studies of protein phosphorylation and in the process remove the phosphate functional group before use. More than half of the proteins in mammals are glycosylated which facilitates protein functions. Determining the site of glycosylation is regarded as the key to modern research (Walker 89). Ten years ago, it was very difficult to determine the site of glycosylation by the use of enzymatic and chemical methods which were used to release N- and O-likened oligosaccharide and finally in analyzing glycan by the use of different methods such as nucleomagnetic resonance and electro spray ionization (Walker 89). Recently, the electron capture dissociation and electron transfer dissociation methods have been introduced which has made it quite possible to determine the site of glycosylation with the help of collision induced dissociation.

The collision induced dissociation and electron capture dissociation methods are performed individually in separate samples (Yee 94). The collision induced dissociation is known to have extensive fragmentation of the glycan with little peptide backbone cleavages whereas the electron transfer dissociation is characterized by extensive fragmentation of the peptide backbone with little fragmentation of the of the glycan moiety that gives the possibility of identifying the site of glycosylation (Yee 94). Functional proteomics focus on macromolecular networks such as the metabolic network to understand and analyze the role of a specific protein in a specific network through the analysis of protein interactions (Yee 94). There are several approaches used to protein interactions and have been in use for the last ten years until now. The first technique is biochemical analysis that is used to analyze multi-protein complex through the use of methods such as the bimolecular interaction analysis mass spectrometry. The other methods to study functional proteomic include molecular biology and computational prediction (Dunphy 125).

In conclusion, there are many factors that have contributed to the development of proteomic studies in the last ten years. The recent change of proteomic studies has been enhanced by increase clinical and pharmaceutical studies experienced in the last ten years. The introduction of the human genome project and the development of computer technology have led to the development of new techniques in proteomic studies that have made current research different techniques to be different from those that were in existence ten years ago. In case this trend continues, more improved techniques of proteomic studies will be developed in the future.

Works Cited

Dunphy, Cherie. Molecular Pathology of Hematolymphoid diseases. New York: Springer, 2010. Print.

Kline, Kelli. Quantitative Proteomic Method Development for the Analysis of the intact Human Heart. Denver: ProQuest, 2009. Print.

Van Eyk, Jennifer. Clinical Proteomics: From Diagnosis to Therapy. New York: Willey-VCH, 2008. Print.

Vinci, Victor. Handbook of Industrial Cell Culture: Mammalian, Microbial and Plant Cells. New York: Hamana Press, 2003. Print.

Walker, John. The Proteomics Protocols Handbook. New York: Hamana Press, 2005. Print.

Whitfield, Phillip. Methods in Animal Proteomics. New York: John Wiley and Sons, Springer, 2010. Print.

Yee, Joon. Genomic and Proteomic profiling of Mammalian Cells under High Productivity. New York: ProQuest, 2008. Print.

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Compare and Contrast the Way in Which Proteomics Studies are Performed in Current Literature

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