Jimmy K. Eng

TL;DR: This work describes an alternate method of calculating the cross correlation score that does not require FFTs and can be computed efficiently in a fraction of the time and allows all candidate peptides to be scored by the cross correlated function, potentially mitigating the need for the preliminary score.

TL;DR: The implementation of the pluggable scoring algorithm is introduced and implementations of two TANDEM compatible scoring functions are provided, one previously described scoring function compatible with PeptideProphet and one very simple scoring function that quantitative researchers may use to begin their development.

TL;DR: It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results, which reduces computer requirements and researcher efforts for analysis of the results.

TL;DR: The open-source Computational Proteomics Analysis System (CPAS) contains an entire data analysis and management pipeline for Liquid Chromatography Tandem Mass Spectrometry proteomics, including experiment annotation, protein database searching and sequence management, and mining LC-MS/MS peptide and protein identifications.

TL;DR: In this paper, a method for correlating a peptide fragment mass spectrum with amino acid sequences derived from a database is provided, where the peptide is analyzed by a tandem mass spectrometer to yield a peptides fragment spectrum, and a plurality of fragments of the sequence are identified and the masses and m/z ratios of the fragments are predicted and used to form a predicted mass spectrum.