Mass spectrometric based assay for presence of a protein without the use of a standard

1. A mass spectrometric based assay for presence of a protein in a sample without the use of a standard for the protein, comprising the steps of:

predicting one or more of the proteolytic fragments of a protein based on one or more of an amino acid sequence for the protein and a translation of a gene sequence for the protein;

predicting one or more of the fragments produced from one or more of the proteolytic fragments of the protein when the proteolytic fragment is subjected to collision induced dissociation;

providing a sample containing proteolytic fragments of a protein;

loading at least a portion of the sample on a chromatographic column;

subjecting at least a portion of the eluent from the chromatographic column to multiple reaction monitoring, the transmitted parent ion m/z range of each multiple reaction monitoring scan including a m/z value of one or more of the predicted proteolytic fragments of the protein and the transmitted daughter ion m/z range of each multiple reaction monitoring scan including a m/z value of one or more of the predicted collision induced dissociation fragments of the predicted proteolytic fragments;

measuring the ion signal of the m/z value range encompassing one or more of the predicted collision induced dissociation fragments m/z value using said multiple reaction monitoring;

performing a substantially full product ion scan on a m/z value range encompassing a predicted proteolytic fragment m/z value when the measured ion signal corresponding to one or more collision induced dissociation fragments of the predicted proteolytic fragment is above a specified signal threshold;

measuring the ion signals associated with the parent-daughter ion transitions of said substantially full product ion scan;

selecting as the parent-daughter ion transition for an assay of the presence of the protein in a sample a parent-daughter ion transition of said substantially full product ion scan, wherein the selected parent-daughter ion transition for the assay corresponds to a transition where the transmitted parent ion is a proteolytic fragment of said protein, and wherein the selected parent-daughter ion transition has, relative to the measured ion signals associated with the other parent-daughter ion transitions for said protein, one or more of the approximately highest ion signal and the approximately highest signal-to-noise ratio; and

refining the selection of the predicted collision induced dissociation fragments of the predicted proteolytic fragments based on at least one or more of the measured full product ion scans;

subjecting at least a portion of the eluent from the chromatographic column to multiple reaction monitoring, the transmitted parent ion m/z range of each multiple reaction monitoring scan including a m/z value of one or more of the refined daughter ion m/z range of each multiple reaction monitoring scan including a m/z value of one or more of the refined predicted collision induced dissociation fragments of the predicted proteolytic fragments; and

measuring the ion signal of the m/z value range encompassing one or more of the refined predicted collision induced dissociation fragments m/z value using said multiple reaction monitoring.

2. The method of claim 1 , wherein the sample containing proteolytic fragments of a protein is derived from at least one of a physiological fluid, a cell lysate, a tissue lysate, and combinations thereof.

3. The method of claim 2 , wherein the physiological fluid comprises one or more of blood, serum, plasma, sweat, tears, urine, cerebrospinal fluid, peritoneal fluid, lymph, vaginal secretion, semen, spinal fluid, ascetic fluid, saliva, sputum, breast exudates, and combinations thereof.

4. The method of claim 2 , wherein the physiological fluid comprises blood.

5. The method of claim 4 , wherein the blood sample is depleted of at least six most abundant proteins before proteolytic fragmentation of the protein.

6. The method of claim 4 , wherein the blood sample is plasma or serum.

7. The method of claim 4 , wherein the blood sample contains the protein in a concentration of less than 100,000 attomoles/microliter.

8. The method of claim 4 , wherein the blood sample contains the protein in a concentration of less than 10,000 attomoles/microliter.

9. The method of claim 4 , wherein the blood sample contains the protein in a concentration of less than 1,000 attomoles/microliter.

10. The method of claim 4 , wherein the blood sample contains the protein in a concentration of less than 100 attomoles/microliter.

11. The method of claim 4 , wherein the blood sample contains the protein in a concentration of less than 10 attomoles/microliter.

12. The method of claim 4 , wherein the blood sample contains the protein in a concentration of less than about 1 attomoles/microliter.

13. The method of claim 1 , wherein the proteolytic fragments of a protein comprise tryptic peptides.

14. The method of claim 1 , wherein the sample containing proteolytic fragments of a protein further comprises a concentration standard for one or more of the predicted proteolytic fragments of the protein, said concentration standard selected based on the parent-daughter ion transition selected as an assay of the presence of the protein in the biological sample.

15. The method of claim 1 , wherein said step of subjecting at least a portion of the eluent from the chromatographic column to multiple reaction monitoring comprises using a triple quadrupole ion trap mass spectrometer.

16. The method of claim 15 , wherein the ion trap comprises a linear trap.

17. The method of claim 1 , wherein said step of measuring the ion signal of the m/z value range encompassing one or more of the predicted collision induced dissociation fragments m/z value using said multiple reaction monitoring comprises: sequencing the transmitted parent ion when the measured ion signal corresponding to one or more collision induced dissociation fragments of the predicted proteolytic fragment is above the specified signal threshold; and performing said substantially full product ion scan on a m/z value range encompassing said sequenced transmitted parent ion when the sequence of the sequenced transmitted parent ion corresponds to a proteolytic fragment of the protein.

18. The method of 17 , further comprising the step of: measuring the charge state of the transmitted parent ion when the measured ion signal corresponding to one or more collision induced dissociation fragments of the predicted proteolytic fragment is above a specified signal threshold.