Patent Document ID: 20120283954
Application ID: 13068026
Patent Flag: 0

Claim One:
1. A new method for rapid and accurate determination of the results from measurements utilizing mass spectrometry equipment and methods, comprising the following functional elements for the preferred embodiment: (a) Prompt quantitative measures of significance for sampled protein functions, without the long delay time previously required to interpret the resulting test data in a biological context; (b) Accurate description of the functions of the proteome in terms of protein activity, to determine the relationship between incremental changes in protein abundance and incremental changes in cellular function; (c) Capability to derive meaningful statistical inference from proteomic data to derive previously unmeasured regulation mechanisms and specific biological responses to the stimulus under investigation, based on measured differences in abundance of occurrence within specific classifications, such as protein type or descriptive function keyword; (d) Capability to derive and describe complex network relationships based on quantitative measurement of protein activity between all potential protein pairs, with focus on the underlying signaling mechanisms, including activation, inhibition, feed-forward and feedback signaling loops; (e) Capability to determine the relationships between and among a long list of proteins, with the length limited only by the scope of the investigation, to accurately match the measured data to a compiled network based on biological functions and proteomic identifications, with differentiation between interaction networks that depend primarily on specific stimuli and specific conditions; (f) Capability to derive biological themes and functions based on detailed measurements and analysis of significant changes in abundance of specific proteins and descriptive keyword classifications, as contrasted to mere correct identification of proteins; (g) Provision of robust, accurate, undistorted measurement of peptide characteristics across a wide variety of experimental settings and conditions, to allow examination and analysis of the data in a meaningful context of biological functions; (h) Use of measurements to describe the significant functional relationships and activity for sampled proteins within the cell, to include detailed information on protein signaling networks, to complement the expanding knowledge of genomics;