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Mass Spectrometry Methods for Studying Glycosylation in Cancer
Protein glycosylation is a highly complex and regulated posttranslational modification. In this process several glycosyltransferase families are involved. In cancer this delicate equilibrium is disrupted leading to glycosylation changes on glycoconjugates, namely, glycoproteins. One of the major consequences is the increase of sialylated oligosaccharide chains in glycoproteins. Here we describe an experimental methodology focused in the enrichment and characterization of sialic acid containing glycopeptides by MALDI mass spectrometry and the subsequent data analysis. (Source: Springer protocols feed by Protein Science)
Source: Springer protocols feed by Protein Science - May 16, 2013 Category: Biochemistry Source Type: news

Permethylated N-Glycan Analysis with Mass Spectrometry
Protein glycosylation plays an important role in multiple cell functions, and aberrations of protein glycosylation are associated with various malignancies including cancer. In this chapter, we provide a detailed protocol for MALDI MS analysis of permethylated N-glycans extracted from human serum proteins. The protocol includes procedures for N-glycan purification and in-solution permethylation, structural elucidation of permethylated N-glycans by MALDI-QIT-TOF MS, and construction of indices to quantify levels of certain types of glycosylation, such as fucosylation, which may serve as a potential disease biomarker. (Sourc...
Source: Springer protocols feed by Protein Science - May 16, 2013 Category: Biochemistry Source Type: news

Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data
We describe the fundamental parameters to be considered at each step along the way and how data processing, either by an individual or by software, must approach the analysis. (Source: Springer protocols feed by Protein Science)
Source: Springer protocols feed by Protein Science - May 16, 2013 Category: Biochemistry Source Type: news

Feature Selection and Machine Learning with Mass Spectrometry Data
Mass spectrometry has been used in biochemical research for a long time. However, its potential of discovering proteomic biomarkers using protein mass spectra aroused tremendous interest in last few years. In spite of its potential of biomarker discovery, it is recognized that identification of meaningful proteomic features from mass spectra needs careful evaluation. Hence, extracting meaningful feature(s) and discriminating the samples based on these features is still an open area of research. Several research groups are actively involved in making the process as perfect as possible. In this chapter, we provide a review o...
Source: Springer protocols feed by Protein Science - May 16, 2013 Category: Biochemistry Source Type: news

Employment of Complementary Dissociation Techniques for Body Fluid Characterization and Biomarker Discovery
Proteomic analysis of biological fluids has become the de facto method for biomarker discovery over the past half decade. Mass spectrometry, in particular, has emerged as the premier technology to perform such analysis. This shift in the prevailing choice of analytical method is primarily due to the rapid evolution of mass spectrometry technology, with advances in acquisition speed, increased resolving power and mass accuracy, and the development of novel fragmentation methods. The benefits of using one of these new fragmentation methods, electron-transfer dissociation, as a complement to the traditional dissociation techn...
Source: Springer protocols feed by Protein Science - May 1, 2013 Category: Biochemistry Source Type: news