Abstract: A method for identifying peptides using tandem mass spectrometry takes the spectrum for a peptide to be analyzed and uses a scoring function to score a match between the spectrum and each candidate peptide in a peptide database. The scoring function has a value corresponding to a number of fragment peaks in the spectrum that match fragment peaks in a spectrum of the candidate peptide. Using the match scores, a generating function of the spectrum is computed to determine the number of peptide reconstructions at each value of the scoring function. The generating function is then used to determine the number of candidate peptides for each match score and the probability of a peptide having a given match score to the spectrum. A spectral probability can be determined by calculating the total probability of all peptides with scores equal to or larger than the given match score.

Abstract: Protein samples are processed to create a mixture of modified and unmodified or overlapping peptides which are analyzed using mass spectrometry. Correlations between the MS/MS spectra of peptide pairs allow the noise in individual MS/MS spectra to be greatly reduced. A small number of peptide reconstructions can be generated that are likely to contain the correct one. This allows for the de novo reconstruction of protein sequences and peptide and modification identification through a database search using extremely fast pattern matching, rather than time-consuming matching of spectra against databases.

Abstract: Protein samples are processed to create a mixture of modified and unmodified or overlapping peptides which are analyzed using mass spectrometry. Correlations between the MS/MS spectra of peptide pairs allow the noise in individual MS/MS spectra to be greatly reduced. A small number of peptide reconstructions can be generated that are likely to contain the correct one. This allows for the de novo reconstruction of protein sequences and peptide and modification identification through a database search using extremely fast pattern matching, rather than time-consuming matching of spectra against databases.

Abstract: A method for identifying peptides using tandem mass spectrometry takes the spectrum for a peptide to be analyzed and uses a scoring function to score a match between the spectrum and each candidate peptide in a peptide database. The scoring function has a value corresponding to a number of fragment peaks in the spectrum that match fragment peaks in a spectrum of the candidate peptide. Using the match scores, a generating function of the spectrum is computed to determine the number of peptide reconstructions at each value of the scoring function. The generating function is then used to determine the number of candidate peptides for each match score and the probability of a peptide having a given match score to the spectrum. A spectral probability can be determined by calculating the total probability of all peptides with scores equal to or larger than the given match score.

Abstract: A system and method for detecting structural damage in a layered structure, the method compromising: providing an array of optical fibers attached to the layered structure; providing a laser source for emitting light into the optical fibers; providing a thermal imaging device; transferring laser light beam through each of the optical fibers of the array; acquiring at least one thermal image of an external surface of the layered structure; and detecting existence of one or more hot spots on the external surface indicative of a location of damage in the layered structure.

Abstract: A system and method for detecting structural damage in a layered structure, the method compromising: providing an array of optical fibers attached to the layered structure; providing a laser source for emitting light into the optical fibers; providing a thermal imaging device; transferring laser light beam through each of the optical fibers of the array; acquiring at least one thermal image of an external surface of the layered structure; and detecting existence of one or more hot spots on the external surface indicative of a location of damage in the layered structure.

Abstract: A new Eulerian Superpath approach to fragment assembly in DNA sequencing that resolves the problem of repeats in fragment assembly is disclosed. The invention provides for the reduction of the fragment assembly to a variation of the classical Eulerian path problem. This reduction opens new possibilities for repeat resolution and allows one to generate provably optimal error-free solutions of the large-scale fragment assembly problems.

Abstract: There is disclosed herein an invention which relates to the fields of genetic engineering, microbiology, and computer science, that allows a user, whether they be a molecular biologist or a clinical diagnostician, to calculate and design extremely specific oligonucleotide probes for DNA and mRNA hybridization procedures. The probes designed with this invention may be used for medical diagnostic kits, DNA identification, and potentially continuous monitoring of metabolic processes in human beings. The key features design oligonucleotide probes based on the GenBank database of DNA and mRNA sequences and examine candidate probes for specificity or commonality with respect to a user-selected experimental preparation. Two models are available: a Mismatch Model, that employs hashing and continuous seed filtration, and an H-Site Model, that analyzes candidate probes for their binding specificity relative to some known set of mRNA or DNA sequences.