Current Proteomics - Volume 9, Issue 2, 2012

To fully integrate molecular analysis with histology, it is essential to further develop and evaluate in situ tissue section-based technologies that are sensitive, quantitative, and high-throughput. In the proteomics field, immunohistochemistry (IHC) is the method of choice for in situ measurement of protein levels in histological sections. However, matrix- assisted laser desorption ionization-imaging mass spectrometry (MALDI-IMS) and related methods are emerging as additional multiplex in situ protein analysis tools. In this review, we discuss the application of these techniques in biomedical research and describe three newly developed technologies: multiplex tissue immunoblotting, indirect layered peptide array, and layered electrophoretic transfer (LET). In particular, we emphasize the LET technology as a novel in situ separation tool that allows for a more comprehensive proteomic analysis of a tissue sample while maintaining the important two-dimensional histological architecture.

High performance liquid chromatography (HPLC) in tandem with mass spectrometry (MS) is widely used in chemical and biochemical analysis of the content of measured samples, especially in so-called omics science. Currently, there are methods for processing and analyzing the measured data sets from proteomics as well as metabolomics. However, only some of the problems of processing and analyzing tasks have been compensated for, and even in these cases, they have only been considered independently. Therefore, the current state of data handling is studied. This review describes the currently available methods and techniques commonly used in HPLC-MS for processing and analysis. All the main types of processing and most popular methods are mentioned. However, any overview will fail to be exhaustive. Therefore, some additional literature that goes into further detail is recommended. The review itself reveals some of the important shortcomings of the current state of the art. A list of relevant subtopics relating to different research focuses is provided in the conclusion.

Bone and soft tissue sarcomas are a diverse group of malignancies derived from mesenchymal tissue. Numerous different sub-types of sarcoma can be identified histologically and this reflects the capacity of mesenchymal precursor cells to differentiate along recognisable somatic lineages, although some sarcomas do not display any clear line of differentiation and form tumours with no obvious normal cellular counterpart. The morphological heterogeneity of sarcomas is paralleled by differences in biological behaviour that contribute to difficulties in understanding tumour progression and patterns of response to treatment. Although five-year survival rates of up to 80% can be achieved for localised sarcomas, some specific high-grade histological subtypes continue to portent poor prognosis, and metastasis at presentation remains a common problem. Identifying in advance the chemosensitivity of primary sarcomas, those sarcomas destined to metastasise, and successfully treating metastatic disease continues to pose a significant challenge. Proteomic analysis combined with mass spectroscopy and bioinformatics is a powerful approach to analysing molecular abnormalities responsible for the biological behaviour of sarcomas. Investigating abnormalities downstream of the genome using protein expression analysis has several important advantages over DNA sequencing or mRNA expression studies in cancer research. Sophisticated proteomic technologies have only recently been applied to the study of sarcomas with the principle aim of discovering new disease-specific biomarkers that will facilitate more accurate classification of sarcomas into clinically relevant sub-types as well as identifying novel therapeutic targets. This article will review recent developments and summarise the emerging role of proteomic analysis in the strategy of applying molecular classification to both the diagnosis and targeted treatment of sarcomas.

Our earlier publications have indicated the importance of protein secretion in the interaction between roots and microbes [1]. In this review, we highlight the more recent discoveries on proteins in the rhizosphere and how they are used during plant-microbe communication. In addition, we include a survey of novel approaches to the study of the rhizosphere, the dynamics and trends of proteomics in this decade and new opportunities to focus proteomic studies. Therefore, the purpose of this review is to summarize the current literature looking at the interactions between roots and soil microbes, with an emphasis on the exchange of proteins between organisms.

During recent years, various bio-analytical tools are being utilized in the study of peptides and proteins in the field of proteomics. Particularly, the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is an extensively used tool for investigating the different aspects. Although the results and achievements made through this tool are remarkable, however, the technique is quite complex, hard to interpret and routine analyses of bulk samples are quite expensive and not always commercially viable. IR spectroscopy is an established analytical tool evolved as a replacement/ assistance for certain investigations in proteomics. It is used in various mass ranges of peptides and proteins. This role of IR and NIR is elaborated in this review. The modified materials in their different derivatized forms are used in binding the peptides and proteins out of complex biofluids and analyzed with IR and NIR spectrophotometers. However, a strategy of desalting, pre-concentration can be applied before IR investigations to minimize the stray absorptions. Silica is modified in different ways to bind the serum entities and is employed in the proteome identifications.

Vibrational spectroscopic imaging has become an essential tool for tissue analyses in life science and represents a modern analytical technique enabling the detection and characterization of molecular components of biological samples. It is based on the absorption of IR radiation by vibrational transitions in covalent bonds and enables global analysis of samples, with resolution close to the cellular level. Advantage of vibrational spectroscopic imaging is the acquisition of local molecular expression profiles, while maintaining the topographic integrity of the tissue by avoiding time-consuming extraction, purification and/or separation steps, respectively. With this nondestructive analytical method it is possible to get both qualitative and quantitative information of heterogeneous samples and unique chemimorphological information about the tissue status, which represents an important benefit for future analytical interpretation of pathological changes of a tissue.