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It correlates collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences. [21] SIMS Open source: SIMS was designed to perform unrestricted PTM searches over tandem mass spectra. [22] SimTandem Freeware: SimTandem is a database search engine for identification of peptide sequences from LC ...
The peptide's intact mass is known from the mass spectrum, and Sequest uses this information to determine the set of candidate peptides sequences that could meaningfully be compared to the spectrum by including only those near the mass of the observed peptide ion.
Protein sequence interpretation: a scheme new protein to be engineered in a yeast. It is often desirable to know the unordered amino acid composition of a protein prior to attempting to find the ordered sequence, as this knowledge can be used to facilitate the discovery of errors in the sequencing process or to distinguish between ambiguous results.
Mascot identifies proteins by interpreting mass spectrometry data. The prevailing experimental method for protein identification is a bottom-up approach, where a protein sample is typically digested with trypsin to form smaller peptides.
The number of points accessible is multiplied by the portion of surface area each point represents to calculate the ASA. The choice of the 'probe radius' does have an effect on the observed surface area, as using a smaller probe radius detects more surface details and therefore reports a larger surface.
For a peptide spectral library, to reach a maximal coverage is a long-term goal, even with the support of scientific community and ever-growing proteomic technologies. [ citation needed ] However, the optimization for a particular module of the peptide spectra library is a more manageable goal, e.g. the proteins in a particular organelle or ...
Repeatedly blowing up the singular points of a curve will eventually resolve the singularities. The main task with this method is to find a way to measure the complexity of a singularity and to show that blowing up improves this measure. There are many ways to do this. For example, one can use the arithmetic genus of the curve.
Point a is an ordinary point when functions p 1 (x) and p 0 (x) are analytic at x = a. Point a is a regular singular point if p 1 (x) has a pole up to order 1 at x = a and p 0 has a pole of order up to 2 at x = a. Otherwise point a is an irregular singular point.