Rapid and quantitative proteome analysis and related methods

Abstract

The invention provides methods for identifying polypeptides. The method can include the steps of simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of the subset of parent polypeptides; comparing the determined masses to an annotated polypeptide index; and identifying one or more polypeptides of the annotated polypeptide index having the determined masses. The method can further include the steps of determining one or more additional characteristics associated with one or more of the parent polypeptides; comparing the determined characteristics to the annotated polypeptide index; and optionally repeating the steps one or more times, wherein a set of characteristics is determined that identifies a parent polypeptide as a single polypeptide in the annotated polypeptide index. The method can additionally include the step of quantitating the amount of the identified polypeptide in a sample containing the polypeptide.

What is claimed is:  
     
         1 . A method for identifying a polypeptide, comprising: 
 (a) simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of said subset of parent polypeptides;    (b) comparing said determined masses to a annotated polypeptide index; and    (c) identifying one or more polypeptides of said annotated polypeptide index having said determined masses.    
     
     
         2 . The method of  claim 1 , further comprising: 
 (d) determining one or more additional characteristics associated with one or more of said parent polypeptides;    (e) comparing said characteristics determined in step (a) and step (d) to said annotated polypeptide index; and    (f) optionally repeating steps (d) and (e) one or more times, wherein a set of characteristics is determined that identifies a parent polypeptide as a single polypeptide in said annotated polypeptide index.    
     
     
         3 . The method of  claim 1 , further comprising quantitating the amount of said identified polypeptide in a sample containing said polypeptide.  
     
     
         4 . The method of  claim 2 , wherein a set of characteristics is determined that identifies two or more parent polypeptides as single polypeptides in said annotated polypeptide index.  
     
     
         5 . The method of  claim 4 , wherein a set of characteristics is determined that identifies each of said parent polypeptides in said subset of parent polypeptides.  
     
     
         6 . The method of  claim 1 , wherein said fragment mass is determined by mass spectrometry in the absence of ion selection for producing fragment ions.  
     
     
         7 . The method of  claim 1 , wherein said fragment mass is determined at an accuracy in ppm of greater than 1 ppm.  
     
     
         8 . The method of  claim 1 , wherein said fragment mass is determined at an accuracy in ppm of 2.5 ppm or greater ppm.  
     
     
         9 . The method of  claim 1 , wherein said fragment mass is determined at an accuracy in ppm of 5 ppm or greater ppm.  
     
     
         10 . The method of  claim 1 , wherein said fragment mass is determined at an accuracy in ppm of 10 ppm or greater ppm.  
     
     
         11 . The method of  claim 1 , wherein said fragment mass is determined at an accuracy in ppm of 100 ppm or greater ppm.  
     
     
         12 . The method of  claim 13 , wherein said characteristics are selected from the group consisting of polypeptide mass, amino acid composition, pI, and order of elution on a chromatographic medium.  
     
     
         13 . A method for identifying a polypeptide, comprising: 
 (a) simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of said subset of parent polypeptides;    (b) comparing said determined masses to an annotated polypeptide index;    (c) identifying one or more polypeptides of said annotated polypeptide index having said determined masses; and    (d) quantitating the amount of said identified polypeptide in a sample containing said polypeptide.    
     
     
         14 . The method of  claim 13 , further comprising: 
 (e) determining one or more additional characteristics associated with one or more of said parent polypeptides;    (f) comparing said characteristics determined in step (a) and step (e) to said annotated polypeptide index; and    (g) optionally repeating steps (e) and (f) one or more times, wherein a set of characteristics is determined that identifies a parent polypeptide as a single polypeptide in said annotated polypeptide index.    
     
     
         15 . The method of  claim 14 , wherein a set of characteristics is determined that identifies two or more parent polypeptides as single polypeptides in said annotated polypeptide index.  
     
     
         16 . The method of  claim 15 , wherein a set of characteristics is determined that identifies each of said parent polypeptides in said subset of parent polypeptides.  
     
     
         17 . The method of  claim 13 , wherein said fragment mass is determined by mass spectrometry in the absence of ion selection for producing fragment ions.  
     
     
         18 . The method of  claim 13 , wherein said fragment mass is determined at an accuracy in ppm of greater than 1 ppm.  
     
     
         19 . The method of  claim 13 , wherein said fragment mass is determined at an accuracy in ppm of 2.5 ppm or greater ppm.  
     
     
         20 . The method of  claim 13 , wherein said fragment mass is determined at an accuracy in ppm of 5 ppm or greater ppm.  
     
     
         21 . The method of  claim 13 , wherein said fragment mass is determined at an accuracy in ppm of 10 ppm or greater ppm.  
     
     
         22 . The method of  claim 13 , wherein said fragment mass is determined at an accuracy in ppm of 100 ppm or greater ppm.  
     
     
         23 . The method of  claim 13 , wherein said characteristics are selected from the group consisting of polypeptide mass, amino acid composition, pI, and order of elution on a chromatographic medium.  
     
     
         24 . A method for identifying a polypeptide, comprising (a) determining two or more characteristics associated with said polypeptide, or a fragment thereof, one of said characteristics being mass of a fragment of said polypeptide, said fragment mass being determined by mass spectrometry in the absence of ion selection for producing fragment ions; 
 (b) comparing said characteristics associated with said polypeptide to a polypeptide identification index; and    (c) identifying one or more polypeptides in said polypeptide identification index having said characteristics.    
     
     
         25 . The method of  claim 24 , further comprising 
 (d) determining one or more additional characteristics associated with said polypeptide; and    (e) comparing said characteristics determined in step (a) and step (d) to said polypeptide identification index.    
     
     
         26 . The method of  claim 24 , further comprising quantitating the amount of said identified polypeptide in a sample containing said polypeptide.  
     
     
         27 . The method of  claim 24 , wherein said polypeptide identification index is an annotated peptide index.  
     
     
         28 . The method of  claim 24 , wherein said fragment mass is determined at an accuracy in ppm of 1 ppm or greater ppm.  
     
     
         29 . The method of  claim 24 , wherein said fragment mass is determined at an accuracy in ppm of 2.5 ppm or greater ppm.  
     
     
         30 . The method of  claim 24 , wherein said fragment mass is determined at an accuracy in ppm of 5 ppm or greater ppm.  
     
     
         31 . The method of  claim 24 , wherein said fragment mass is determined at an accuracy in ppm of 10 ppm or greater ppm.  
     
     
         32 . The method of  claim 24 , wherein said fragment mass is determined at an accuracy in ppm of 100 ppm or greater ppm.  
     
     
         33 . The method of  claim 24 , wherein three or more characteristics of said polypeptide are determined.  
     
     
         34 . The method of  claim 24 , wherein four or more characteristics of said polypeptide are determined.  
     
     
         35 . The method of  claim 24 , wherein five or more characteristics of said polypeptide are determined.  
     
     
         36 . The method of  claim 24 , wherein said characteristics are selected from the group consisting of polypeptide mass, amino acid composition, pI, and order of elution on a chromatographic medium.  
     
     
         37 . A method for identifying a polypeptide, comprising 
 (a) determining two or more characteristics associated with said polypeptide, or a fragment thereof, one of said characteristics being mass of a fragment of said polypeptide, said fragment mass being determined by mass spectrometry at an accuracy in ppm of greater than 2.5 ppm;    (b) comparing said characteristics associated with said polypeptide to a polypeptide identification index; and    (c) identifying one or more polypeptides in said polypeptide identification index having said characteristics.    
     
     
         38 . The method of  claim 37 , further comprising 
 (d) determining one or more additional characteristics associated with said polypeptide; and    (e) comparing said characteristics determined in step (a) and step (d) to said polypeptide identification index.    
     
     
         39 . The method of  claim 37 , further comprising quantitating the amount of said identified polypeptide in a sample containing said polypeptide.  
     
     
         40 . The method of  claim 37 , wherein said polypeptide identification index is an annotated peptide index.  
     
     
         41 . The method of  claim 37 , wherein said fragment mass is determined at an accuracy in ppm of 5 ppm or greater ppm.  
     
     
         42 . The method of  claim 37 , wherein said fragment mass is determined at an accuracy in ppm of 10 ppm or greater ppm.  
     
     
         43 . The method of  claim 37 , wherein said fragment mass is determined at an accuracy in ppm of 100 ppm or greater ppm.  
     
     
         44 . The method of  claim 37 , wherein three or more characteristics of said polypeptide are determined.  
     
     
         45 . The method of  claim 37 , wherein four or more characteristics of said polypeptide are determined.  
     
     
         46 . The method of  claim 37 , wherein five or more characteristics of said polypeptide are determined.  
     
     
         47 . The method of  claim 37 , wherein said characteristics are selected from the group consisting of polypeptide mass, amino acid composition, pI, and order of elution on a chromatographic medium.