Back to results
US 2003/0119063 A1Published application
High accuracy protein identification
OwnerThang T. Phaminventor
Life of this patent
Estimating the term…
Abstract
The invention provides for the identification of target proteins in a sample based upon multiple sets of peptide fragment mass data obtained from the sample via gas phase ion spectroscopy. The sets of data are the product of analytical conditions that typically differ for each set such that cumulatively the data sets have higher information content than any individual set, thus enhancing the confidence level for accurate target protein identification. Probes, systems, and kits are additionally provided.
Claims59
A method of producing at least one identity candidate for a target protein in a sample, comprising:
- (a) fragmenting proteins in a first sample comprising the target protein to produce a fragmented sample comprising two or mole peptide fragments of the target protein;
- (b) profiling peptide fragment masses in the fragmented sample by gas phase ion spectrometry under at least two different conditions,
- wherein a first condition comprises analyzing a first aliquot of the fragmented sample by the gas phase ion spectrometry to produce a first set of peptide fragment mass data, and
- wherein a second condition comprises fractionating biomolecules in a second aliquot of the fragmented sample by at least one first fractionation technique to produce at least one sub-sample comprising a peptide fragment of the target protein, and analyzing one or more sub-samples by the gas phase ion spectrometry to produce at least a second set of peptide fragment mass data;
- and,
- (c) querying at least one database to produce the at least one identity candidate for the target protein based upon the first and second sets of peptide fragment mass data.
3 more elements
A method of producing at least one identity candidate for a target protein, comprising:
- (a) fragmenting proteins in a first sample comprising the target protein with one or more enzymes to produce a fragmented sample comprising two or more peptide fragments of the target protein;
- (b) profiling peptide fragment masses in the fragmented sample by gas phase ion spectrometry under at least two different conditions,
- wherein a first condition comprises analyzing a first aliquot of the fragmented sample by the gas phase ion spectrometry to produce a first set of peptide fragment mass data, and
- wherein a second condition comprises fractionating biomolecules in a second aliquot of the fragmented sample by at least one first fractionation technique to produce at least one sub-sample comprising a peptide fragment of the target protein, and analyzing one or more sub-samples by the gas phase ion spectrometry to produce al least a second set of peptide fragment mass data;
- and,
- (c) querying at least one database to produce the at least one identity candidate for the target protein based upon the first and second sets of peptide fragment mass data.
3 more elements
A method of producing at least one identity candidate for a target protein, comprising:
- (a) fragmenting proteins in a first sample comprising the target protein with trypsin to produce a fragmented sample comprising two or more peptide fragments of the target protein;
- (b) profiling peptide fragment masses in the fragmented sample by surface enhanced desorption/ionization time-of-flight mass spectrometry under at least two different conditions,
- wherein a first condition comprises analyzing a first aliquot of the fragmented sample by the surface enhanced desorption/ionization time-of-flight mass spectrometry to produce a first set of peptide fragment mass data, and
- wherein a second condition comprises fractionating biomolecules in a second aliquot of the fragmented sample by affinity chromatography to produce at least one sub-sample comprising a peptide fragment of the target protein, and analyzing one or more sub-samples by the surface enhanced desorption/ionization time-of-flight mass spectrometry to produce at least a second set of peptide fragment mass data;
- and,
- (c) querying at least one database to produce the at least one identity candidate for the target protein based upon the first and second sets of peptide fragment mass data.
3 more elements
A system capable of producing at least one identity candidate for a target protein in a sample, comprising:
- (a) one or more adsorbents capable of capturing peptide fragments in the sample under at least two different conditions;
- (b) a gas phase ion spectrometer able to profile masses of peptide fragments captured by the one or more adsorbents tinder the at least two different conditions to provide at least two sets of peptide fragment mass data, each set corresponding to peptide fragments detected under a different condition;
- and,
- (c) a processor, operably connected to the gas phase ion spectrometer, comprising at least one computer program providing logic instructions capable of determining closeness-of-fit between one or more detected peptide fragment masses in the sets of peptide fragment mass data and database entries, which entries correspond to masses of identified proteins or peptide fragments therefrom, thereby producing the at least one identity candidate for the target protein based upon the one or more detected peptide fragment masses.
1 more element
Dependencies are inferred from the claim text.