1. A method for measuring the level of the Hepatocyte Growth Factor Receptor (cMET) protein in a biological sample, comprising detecting andor quantifying the amount of one or more modified or unmodified cMET fragment peptides in a protein digest prepared from said biological sample using mass spectrometry; and calculating the level of modified or unmodified cMET protein in said sample; and
wherein said level is a relative level or an absolute level.
2. The method of claim 1, further comprising the step of fractionating said protein digest prior to detecting andor quantifying the amount of one or more modified or unmodified cMET fragment peptides.
3. The method of claim 2, wherein said fractionating step is selected from the group consisting of gel electrophoresis, liquid chromatography, capillary electrophoresis, nano-reversed phase liquid chromatography, high performance liquid chromatography, or reverse phase high performance liquid chromatography.
4. The method of claim 1, wherein said protein digest of said biological sample is prepared by the Liquid Tissue\u2122 protocol.
5. The method of claim 1, wherein said protein digest comprises a protease digest.
6. The method of claim 5, wherein said protein digest comprises a trypsin digest.
7. The method of claim 1, wherein said mass spectrometry comprises tandem mass spectrometry, ion trap mass spectrometry, triple quadrupole mass spectrometry, MALDI-TOF mass spectrometry, MALDI mass spectrometry, andor time of flight mass spectrometry.
8. The method of claim 7, wherein the mode of mass spectrometry used is Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), andor multiple Selected Reaction Monitoring (mSRM).
9. The method of claim 1, wherein the cMET fragment peptide comprises an amino acid sequence as set forth as SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12.
10. The method of claim 1, wherein the biological sample is a blood sample, a urine sample, a serum sample, an ascites sample, a sputum sample, lymphatic fluid, a saliva sample, a cell, or a solid tissue.
11. The method of claim 10, wherein the tissue is formalin fixed tissue.
12. The method of claim 10, wherein the tissue is paraffin embedded tissue.
13. The method of claim 10, wherein the tissue is obtained from a tumor.
14. The method of claim 13, wherein the tumor is a primary tumor.
15. The method of claim 13, wherein the tumor is a secondary tumor.
16. The method of claim 1, further comprising quantifying a modified or unmodified cMET fragment peptide.
17. The method of claim 16, wherein quantifying the cMET fragment peptide comprises comparing an amount of one or more cMET fragment peptides comprising an amino acid sequence of about 8 to about 45 amino acid residues of cMET as shown in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, or SEQ ID NO:12 in one biological sample to the amount of the same cMET fragment peptide in a different and separate biological sample.
18. The method of claim 17, wherein quantifying one or more cMET fragment peptides comprises determining the amount of the each of the cMET fragment peptides in a biological sample by comparison to an added internal standard peptide of known amount, wherein each of the cMET fragment peptides in the biological sample is compared to an internal standard peptide having the same amino acid sequence.
19. The method of claim 18, wherein the internal standard peptide is an isotopically labeled peptide.
20. The method of claim 19, wherein the isotopically labeled internal standard peptide comprises one or more heavy stable isotopes selected from 18O, 17O, 34S, 15N, 13C, 2H or combinations thereof.
21. The method of claim 1, wherein detecting andor quantifying the amount of one or more modified or unmodified cMET fragment peptides in the protein digest indicates the presence of modified or unmodified cMET protein and an association with cancer in the subject.
22. The method of claim 21, further comprising correlating the results of said detecting andor quantifying the amount of one or more modified or unmodified cMET fragment peptides, or the level of said cMET protein to the diagnostic stagegradestatus of the cancer.
23. The method of claim 22, wherein correlating the results of said detecting andor quantifying the amount of one or more modified or unmodified cMET fragment peptides, or the level of said cMET protein to the diagnostic stagegradestatus of the cancer is combined with detecting andor quantifying the amount of other proteins or peptides from other proteins in a multiplex format to provide additional information about the diagnostic stagegradestatus of the cancer.
24. The method of claim 1, further comprising selecting for the subject from which said biological sample was obtained a treatment based on the presence, absence, or amount of one or more cMET fragment peptides or the level of cMET protein.
25. The method of claim 1, further comprising administering to the patient from which said biological sample was obtained a therapeutically effective amount of a therapeutic agent, wherein the therapeutic agent andor amount of the therapeutic agent administered is based upon amount of one or more modified or unmodified cMET fragment peptides or the level of cMET protein.
26. The method of claim 24, wherein therapeutic agents bind the cMET protein andor inhibit its biological activity.
27. The method of claim 1, wherein the biological sample is formalin fixed tumor tissue that has been processed for quantifying the amount of one or more modified or unmodified cMET fragment peptides employing the Liquid Tissue\u2122 protocol and reagents.
28. The method of claim 1, wherein said one or more modified or unmodified cMET fragment peptides is two or more, three or more, four or more, five or more, six or more, eight or more, or ten or more of the peptides in Table 1.
29. The method of claim 1, comprising quantifying the amount of the peptides in Table 2.
30. A composition comprising one or more, two or more, three or more, four or more, five or more, six or more, eight or more, or ten or more of the peptides in Table 1 or antibodies thereto.
31. The composition of claim 30 comprising one or two of the peptides of Table 2 or antibodies thereto.
32. The composition of claim 30, wherein said composition is substantially pure or free of other cellular components selected from any combination of other proteins, membranes lipids andor nucleic acids.
33. The composition of claim 30, wherein said peptides are isotopically labeled internal standard peptides that comprises one or more, two or more, or three or more, heavy stable isotopes selected from 18O, 17O, 34S, 15N, 13C, 2H or combinations thereof.
34. The composition of claim 32, wherein said peptides are isotopically labeled internal standard peptides that comprises one or more, two or more, or three or more, heavy stable isotopes selected from 18O, 17O, 34S, 15N, 13C, 2H or combinations thereof.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A method for providing a visual resource of a participant to a video conference, comprising:
determining that the participant is joining or departing the video conference;
accessing a visual resource that identifies the participant; and
presenting the visual resource to at least one other participant to the video conference.
2. The method of claim 1, wherein the visual resource is an image.
3. The method of claim 1, wherein the visual resource is a video clip.
4. The method of claim 1, wherein the visual resource is an avatar.
5. The method of claim 1, further comprising modifying the visual resource.
6. A method for providing a visual resource of a participant to a video conference, comprising:
determining whether video of the participant is degraded or not present;
accessing a visual resource that corresponds to the participant when the video is degraded or not present; and
presenting the visual resource to at least one other participant to the video conference.
7. The method of claim 6, wherein the visual resource is an image.
8. The method of claim 6, wherein the visual resource is a video clip.
9. The method of claim 6, wherein the visual resource is an avatar.
10. The method of claim 6, further comprising modifying the visual resource.
11. A method for providing visual resources of participants to a video conference, comprising:
waiting for a roll call to be initiated;
creating a video roll call of the participants to the video conference that includes a visual resource for each of the participants; and
displaying the video roll call.
12. The method of claim 11, wherein the video roll call is a composite roll call.
13. The method of claim 11, wherein the video roll call is a sequential display of the visual resources.
14. The method of claim 11, wherein at least one of the visual resources is an image.
15. The method of claim 11, wherein at least one of the visual resources is a video clip.
16. The method of claim 11, wherein at least one of the visual resources is an avatar.
17. The method of claim 11, further comprising modifying the visual resource.
18. A computer-readable medium containing computer-executable instructions that, when executed by a processor, cause the processor to perform a method for providing a visual resource of a participant to a video conference, the method comprising:
determining that the participant is joining or departing the video conference;
accessing a visual resource that identifies the participant; and
presenting the visual resource to at least one other participant to the video conference.
19. The medium of claim 18, wherein the visual resource is an image.
20. The medium of claim 18, wherein the visual resource is a video clip.
21. The medium of claim 18, wherein the visual resource is an avatar.
22. The medium of claim 18, wherein the method further comprises modifying the visual resource.
23. A computer-readable medium containing computer-executable instructions that, when executed by a processor, cause the processor to perform a method for providing a visual resource of a participant to a video conference, the method comprising:
determining whether video of the participant is degraded or not present;
accessing a visual resource that corresponds to the participant when the video is degraded or not present; and
presenting the visual resource to at least one other participant to the video conference.
24. The medium of claim 23, wherein the visual resource is an image.
25. The medium of claim 23, wherein the visual resource is a video clip.
26. The medium of claim 23, wherein the visual resource is an avatar.
27. The medium of claim 23, wherein the method further comprises modifying the visual resource.
28. A computer-readable medium containing computer-executable instructions that, when executed by a processor, cause the processor to perform a method for providing visual resources of participants to a video conference, the method comprising:
waiting for a roll call to be initiated;
creating a video roll call of the participants to the video conference that includes a visual resource for each of the participants; and
displaying the video roll call.
29. The medium of claim 28, wherein the video roll call is a composite roll call.
30. The medium of claim 28, wherein the video roll call is a sequential display of the visual resources.
31. The medium of claim 28, wherein at least one of the visual resources is an image.
32. The medium of claim 28, wherein at least one of the visual resources is a video clip.
33. The medium of claim 28, wherein at least one of the visual resources is an avatar.
34. The medium of claim 28, wherein the method further comprises modifying the visual resource.
35. A device for providing a visual resource of a participant to a video conference, comprising:
a processor that determines that the participant is joining or departing the video conference, accesses a visual resource that identifies the participant, and presents the visual resource to at least one other participant to the video conference.
36. The device of claim 35, wherein the visual resource is an image.
37. The device of claim 35, wherein the visual resource is a video clip.
38. The device of claim 35, wherein the visual resource is an avatar.
39. The device of claim 35, wherein the processor also modifies the visual resource.
40. A device for providing a visual resource of a participant to a video conference, comprising:
a processor that determines whether video of the participant is degraded or not present, accesses a visual resource that corresponds to the participant when the video is degraded or not present, and presents the visual resource to at least one other participant to the video conference.
41. The device of claim 40, wherein the visual resource is an image.
42. The device of claim 40, wherein the visual resource is a video clip.
43. The device of claim 40, wherein the visual resource is an avatar.
44. The device of claim 40, wherein the processor also modifies the visual resource.
45. A device for providing visual resources of participants to a video conference, comprising:
a processor that waits for a roll call to be initiated, creates a video roll call of the participants to the video conference that includes a visual resource for each of the participants, and causes the video roll call to be displayed.
46. The device of claim 45, wherein the video roll call is a composite roll call.
47. The device of claim 45, wherein the video roll call is a sequential display of the visual resources.
48. The device of claim 45, wherein at least one of the visual resources is an image.
49. The device of claim 45, wherein at least one of the visual resources is a video clip.
50. The device of claim 45, wherein at least one of the visual resources is an avatar.
51. The device of claim 45, wherein the processor also modifies the visual resource.