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The mechanism by which silver staining of proteins in polyacrylamide gels interferes with mass spectrometry of peptides produced by proteolysis has been investigated. It was demonstrated that this interference increases with time between silver staining and gel processing, although the silver image is constant. This suggested an important role of the formaldehyde used in silver staining development in this interference process. Consequently, a formaldehyde-free staining protocol has been devised, using carbohydrazide as the developing agent. This protocol showed much increased peptide coverage and retained the sensitivity of silver staining. These results were however obtained at the expense of an increased background in the stained gels and of a reduced staining homogeneity.
Sequence coverage in MS analysis of protein digestion-derived peptides is a key issue for detailed characterization of proteins or identification at low quantities. In gel-based proteomics studies, the sequence coverage greatly depends on the protein
Summary: In anticipation of the individualized proteomics era and the need to integrate knowledge from disease studies, we have augmented our peptide identification software RAId DbS to take into account annotated single amino acid polymorphisms, pos
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon phylogene
Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of meta data
The influence of thiol blocking on the resolution of basic proteins by two-dimensional electrophoresis was investigated. Cysteine blocking greatly increased resolution and decreased streaking, especially in the basic region of the gels. Two strategie