Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments
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Proteomic studies require analytical methods capable of separating, identifying and quantifying thousands of proteins. Consequently, developing separation methodologies with high resolving power necessary to separate complex protein samples prior to protei ...
Peptides are an attractive class of molecules for the development of therapeutics because they combine unique properties such as high binding affinity, excellent target specificity, low toxicity and a relatively small mass. However, the short in vivo half- ...
We present a method to grid-enable tandem mass spectrometry protein identification. The implemented parallelization strategy embeds the open-source x!tandem tool in a grid-enabled workflow. This allows rapid analysis of largescale mass spectrometry experim ...
The development of innovative bioanalytical technologies that enable the discovery of new therapeutics or the creation of systems for rapid, accurate and parallel analyses has gained an extraordinary interest in the biomedical sector in the last 10-15 year ...
A novel nanopore based digestion strategy has been developed by directly adding a macroporous material as catalyst to the conventional in-solution reaction system. Without increasing the enzyme or protein concentrations, this simple digestion approach exhi ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. ...
Tandem affinity purification (TAP) is a generic two-step affinity purification protocol that enables the isolation of protein complexes under close-to-physiological conditions for subsequent analysis by mass spectrometry. Although TAP was instrumental in e ...
In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...
The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported, cont ...
In proteomic analysis of complex samples at the peptide level (termed shotgun proteomics), an effective prefractionation is crucial to decrease the complexity of the peptide mixture for further analysis. In this perspective, the high-resolving power of the ...