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Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. [ 1 ] [ 2 ] Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm.
Andromeda is a peptide search engine based on probabilistic scoring, developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry. It can handle data with arbitrarily high fragment mass accuracy and is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides. It can ...
The possible peptide that has the most similar spectrum will have the highest chance to be the right sequence. However, the number of possible peptides may be large. For example, a precursor peptide with a molecular weight of 774 has 21,909,046 possible peptides. Even though it is done in the computer, it takes a long time. [17] [18]
A peptide spectral library is a curated, annotated and non-redundant collection/database of LC-MS/MS peptide spectra. One essential utility of a peptide spectral library is to serve as consensus templates supporting the identification of peptides and proteins based on the correlation between the templates with experimental spectra. [citation ...
Peptide fragmentation notation using the scheme of Roepstorff and Fohlman (1984). [5] A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum. [5] Peptide fragment ions are indicated by a, b, or c if the charge is retained on the N-terminus and by x, y or z if the charge is maintained on the C ...
One type of spline implementation passes through each Cα guide point, producing an exact but choppy curve. Both hand-drawn and most computer ribbons (such as those shown here) are smoothed over about four successive guide points (usually the peptide midpoint) to produce a more visually pleasing and understandable representation.
A curve with a triple point at the origin: x(t) = sin(2t) + cos(t), y(t) = sin(t) + cos(2t) In general, if all the terms of degree less than k are 0, and at least one term of degree k is not 0 in f, then curve is said to have a multiple point of order k or a k-ple point.
The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. [3] The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and ...