Abstract: Provided herein are methods of identifying a protein capable of binding a ligand, the method comprising: (a) contacting the ligand with two or more samples comprising a plurality of proteins in a solution; (b) separating the proteins bound to the ligand (“bound proteins”) from the proteins that are not bound to the ligand (“unbound proteins”) in each sample; (c) denaturing and digesting the bound proteins to form a plurality of peptides in each sample; (d) quantifying a plurality of molecular features contained in the plurality of peptides in each sample, wherein the molecular features are defined as having a mass to charge ratio, retention time, and peak intensity as measured by mass spectrometry; and (e) ranking the molecular features that exhibit a statistically significant difference in quantity between the samples contacted with the ligand and a sample that is not contacted with the ligand (“statistically significant molecular feature”).

Abstract: Methods are disclosed herein for identifying a compound of use in treating a condition treatable by metformin. The methods include determining if the test compound binds a subunit of the mitochondrial electron transport complex IV, and/or alters the function of the mitochondrial electron transport complex IV. Methods for treating a subject with a condition treatable by metformin, are also disclosed. In some embodiments, the condition is type II diabetes.

Abstract: Methods are disclosed herein for identifying a compound of use in treating a condition treatable by metformin. The methods include determining if the test compound binds a subunit of the mitochondrial electron transport complex IV, and/or alters the function of the mitochondrial electron transport complex IV. Methods for treating a subject with a condition treatable by metformin, are also disclosed. In some embodiments, the condition is type II diabetes.

Abstract: Provided herein are methods of identifying a protein capable of binding a ligand, the method comprising: (a) contacting the ligand with two or more samples comprising a plurality of proteins in a solution; (b) separating the proteins bound to the ligand (“bound proteins”) from the proteins that are not bound to the ligand (“unbound proteins”) in each sample; (c) denaturing and digesting the bound proteins to form a plurality of peptides in each sample; (d) quantifying a plurality of molecular features contained in the plurality of peptides in each sample, wherein the molecular features are defined as having a mass to charge ratio, retention time, and peak intensity as measured by mass spectrometry; and (e) ranking the molecular features that exhibit a statistically significant difference in quantity between the samples contacted with the ligand and a sample that is not contacted with the ligand (“statistically significant molecular feature”).

Abstract: The present invention features mass spectrometry data analysis techniques that can be employed to selectively identify analytes differing in abundance between different sample sets. The employed techniques determine the statistical significance of changes to signals associated with mass-to-charge ratios (“m/z-intensity pairs”) between individual samples and sample sets. Based on the statistical significance, changes likely to indicate analyte level differences are identified. Based on intensities of the signals, ratios of analyte abundances can be determined.

Abstract: The present invention features mass spectrometry data analysis techniques that can be employed to selectively identify analytes differing in abundance between different sample sets. The employed techniques determine the statistical significance of changes to signals associated with mass-to-charge ratios (“m/z-intensity pairs”) between individual samples and sample sets. Based on the statistical significance, changes likely to indicate analyte level differences are identified. Based on intensities of the signals, ratios of analyte abundances can be determined.

Abstract: This invention relates generally to a method of operating an ion trap mass spectrometer to determine the resonant excitation frequencies of trapped ions. This can be achieved by: (1) introducing sample ions into the ion trap volume: (2) adjusting the trapping fields so that parent ions having a mass-to-charge ratio of interest which are to undergo collision induced dissociation (CID) are trapped; (3) applying an excitation voltage of predetermined frequency and amplitude across the end caps of the ion trap; (4) scanning the frequency of the excitation voltage in a first direction and monitoring for ejection of the parent ions; (5) repeating steps (1) through (3) and scanning the frequency of the excitation voltage in an opposite direction and monitoring for ejection of the parent ions; (6) averaging the frequencies at which the ions are ejected; and (7) applying that frequency in a subsequent MS/MS scan to promote CID of the parent ions to form daughter ions.