Library-based approach

Plenary 2. S A Asher et al, e-mail address asher ,vms.cis.pitt.edu/asher+ (RRS, TRRRS). UV RRS is used to probe methodically the secondary structure of proteins and to follow unfolding dynamics. Developing a library based approach to generalize the mediod to any protein. 

Other library-based approaches (such as GMF) would benefit from free availability of databases, containing structural information as well as spectrometric data. The use of widely available free databases would enhance the use of informatics in glycomics to a level comparable to proteomics, where the use of databases is part of daily work in nearly all laboratories. 

This approach is similar to the library-based approach proposed by CCPS (2008), in which the... 

HAZOP leader surveys a standard library of potential deviations to determine which ones are relevant for each node. The node strategy proposed in this paper not only selects the important deviations to be analyzed in a node, but also indicates areference point inside the node for the analysis of each process parameter (flow, level, temperature, pressure), which makes easier the assessment of large nodes. Another difference is that the node strategy can be adjusted by the HAZOP team while the library-based approach considers that the team does not help to create the library (CCPS, 2008), which is exclusively proposed by the leader. 

In contrast to library-based approaches which typically do not involve identification of the biological nature/origin of particular peaks, bioinformatics-enabled approaches identify peaks in MALDl profiles to characterize unknown bacteria (Fig. 6.3b). Bioinformatics-enabled approaches are commonly applied to bacteria with sequenced genomes. Two methods have been used in bioinformatics-enabled approaches bottom-up and top-down methods. Bottom-up methods involve digestion of proteins using enzymes, such as trypsin, prior to MS analysis. The enzymes cleave at well-defined sites (e.g., after every arginine and lysine, in the case of tryptic digestion) of the proteins to create complex peptide mixtures. Peptides in... 

In library-based approaches, bacterial characterization requires comparison of mass spectra of unknowns with those of reference spectra of known bacteria. Though visual inspection can sometimes provide a qualitative assessment of the similarity between mass spectra at the genus and possibly the species levels, software algorithms have been developed to provide more objective and quantitative assessments. Such tools are critically important at the strain level, where spectra of closely related strains are often extraordinarily similar, and reliable discrimination requires sensitive and repeatable measures. Many software solutions, such as custom R packages, Microsoft Excel (Microsoft Corporation, Redmond, WA), MATLAB (MathWoiks, Matick, MA), and BioNumerics (Applied Maths, Sint-Martens-Latem, Belgium), have been applied to enhance analysis (Croxatto et al. 2012 Pavlovic et al. 2013 Sandrin etal. 2013). 

Table 11.1 Overview of studies for profiling human pathogens with MALDI-TOF MS at the strain level Examples of strain categorization (A), strain differentiation (B), and strain identification (C). MRSA methicillin-resistant Staphylococcus aureus, MSSA methicillin-sensitive S. aureus, L library-based approach, P proteomics-based approach, CHCA a-cyano-4-hydroxycinnamic acid, CMBT 5-chloro-2-mercaptobenzothiazole, DHB 2-hydroxy-5-methoxy benzoic acid, FA ferulic acid, HABA 2,4-hydroxyphenylazobenzoic acid, SA 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid), THAP 2,4,6-trihydroxyacetophenon. Adapted and modified from Sandrin et al. (2013)... 

Future applications of MALDI in top-down approaches will need further developments to make fragmentation of large proteins more efBdent (McLuckey 2010). Compared to library-based approaches, proteomics-based approaches are at an advantage with higher level of specificity and independence of producing mass spectral profiles with reproducible relative intensities of mass peaks. 

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