Patent Document ID: 9659146
Application ID: 13068026
Patent Flag: 1

Claim One:
1. A method comprising: preparing a biological sample containing proteins; subjecting the sample to analysis by a mass spectrometer; receiving a raw data set from the mass spectrometer, the raw data set representing ion spectra corresponding to peptides or peptide fragments within the sample; identifying peptides, proteins, or gene names from the raw data set by use of a data processor and processing instructions executing thereon, the identifying including transforming the raw data set to a structured data set formatted for pattern recognition using the data processor, the transforming including filtering the raw data set based on chromatographic and elution characteristics of the sample, the identifying further including comparing portions of the structured data set to a protein or gene index thereby identifying the peptides, proteins, or gene names corresponding to the sample; implementing a set of logical rules to selectively filter the peptides, proteins, or gene names identified from the structured data set using filter parameters to isolate filtered peptides, proteins, or gene names; correlating the filtered peptides, proteins, or gene names with corresponding keywords by use of the data processor and the processing instructions executing thereon; calculating peptide abundance from the filtered peptides, proteins, or gene names by use of the data processor and the processing instructions executing thereon; calculating protein abundance from the filtered peptides, proteins, or gene names by use of the data processor and the processing instructions executing thereon; calculating keyword abundance from the filtered peptides, proteins, or gene names, and correlated keywords by use of the data processor and the processing instructions executing thereon; generating, by use of the data processor and the processing instructions executing thereon, a keyword overlap score based on a correlation of the gene names corresponding to the filtered peptides and proteins and the keywords associated with the gene names corresponding to the filtered peptides and proteins; and generating, by use of the data processor and the processing instructions executing thereon, data and graphic pattern representations of peptide functions and interactions based on the calculated peptide abundance, the protein abundance, the keyword abundance, and the keyword overlap score for the filtered peptides, proteins, or gene names, the data and graphic pattern representations being generated for presentation on a display device, wherein the data and the graphic pattern representations identify, quantify, and describe the significant functional relationships for each protein within groups of proteins that are components of the biological sample.