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Figure 5 | Biology Direct

Figure 5

From: Proteomic and bioinformatic analysis of epithelial tight junction reveals an unexpected cluster of synaptic molecules

Figure 5

Data collection and criteria for scoring of hits. (A) Filemaker prototype for data entry. (B) Equations and scoring criteria for generation of the tight junction proteomics database. #Peptides matched to hit is defined as the number of peptides found using fingerprint analysis that has been matched to a particular protein in the SwissProt UniProt database. %Coverage is defined as the percent of amino acid sequence of the particular protein that has been represented by the peptides found. #MS file is defined as the number of file(s) used in fingerprint analysis, which is the same as the number of times a particular band is analyzed by mass spectroscopy (see Supplementary Figure S2A). MW of hit in Daltons is defined as the molecular mass of the matched protein. The cutoff is calculated from an average peptide mass of 1000 Daltons and a 10% coverage of a cellular protein with modal molecular mass 50 kD, i.e. 5 peptides and 5000 Daltons per protein. The "revised MW" is based on the molecular mass of the particular protein, corrected for the number of transmembrane, signal peptide, lipid modification, and sugar modification groups. A correction of 3500 Daltons is used for transmembrane and signal peptide regions based on the average number of amino acids in those sequences. A correction of 2000 Daltons is used for lipid and sugar modifications to cover two average peptide lengths when the modifications are at the ends of the peptides. Lipid and sugar modification sites are obtained from SwissProt UniProt database. The "adjusted cutoff" is calculated from the cutoff and the ratio of the "revised MW" to MW, adjusted once for the MW and a second time for the coverage.

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