Sets of digital antibodies directed against short epitopes, and methods using same

A method for generating a protein binding profile of a sample comprising a plurality of different proteins, said method comprising:

• (a) contacting said sample with a set of digital antibodies, under conditions that permit binding, wherein the set of digital antibodies comprises at least about 15 digital antibodies, wherein each of the 15 digital antibodies has been characterized to bind specifically to a different epitope consisting of 3 or 4 or 5 consecutive amino acids, and each digital antibody recognizes a plurality of distinct and different proteins that comprise the same epitope to which the digital antibody binds;
• (b) optionally removing an unbound protein;
• and
• (c) detecting binding of protein to said digital antibodies, whereby a protein binding profile of the sample is generated.

A method for generating a library of protein binding profiles for two or more different samples each of which comprises a plurality of proteins, said method comprising:

• (a) contacting a sample with a set of digital antibodies under conditions that permit binding, wherein the set of digital antibodies comprises at least about 15 digital antibodies, wherein each of the 15 digital antibodies has been characterized to bind specifically to a different epitope consisting of 3 or 4 or 5 consecutive amino acids, and each digital antibody recognizes a plurality of distinct and different proteins that comprise the same epitope to which the digital antibody binds;
• (b) optionally removing an unbound protein;
• (c) generating a protein binding profile of the sample being tested by detecting binding of protein to the digital antibodies, whereby a protein binding profile is generated;
• and
• (d) repeating steps (a) through (c) with at least two samples.

A method for characterizing a test sample, comprising:

• (a) contacting the test sample with a set of digital antibodies under conditions that permit binding, wherein the set of digital antibodies comprises at least about 15 digital antibodies, wherein each of the 15 digital antibodies has been characterized to bind specifically to a different epitope consisting of 3 or 4 or 5 consecutive amino acids, and each digital antibody recognizes a plurality of distinct and different proteins that comprise the same epitope to which the digital antibody binds;
• (b) optionally removing an unbound protein;
• (c) generating a protein binding profile of said test sample by detecting binding of protein to the digital antibodies;
• and
• (d) comparing the generated protein binding profile of the test sample with a protein binding profile of a reference sample to characterize the test sample.

A method for determining presence or absence of a bacteria, virus, or cell in a test sample, said method comprising

• (a) contacting the test sample with a set of digital antibodies under conditions that permit binding, wherein the set of digital antibodies comprises at least about 15 digital antibodies, wherein each of the 15 digital antibodies has been characterized to bind specifically to a different epitope consisting of 3 or 4 or 5 consecutive amino acids, and each digital antibody recognizes a plurality of distinct and different proteins that comprise the same epitope to which the digital antibody binds;
• (b) optionally removing an unbound protein;
• (c) generating a protein binding profile of the test sample by detecting binding of protein to the digital antibodies, whereby a protein binding profile is generated;
• and
• (d) comparing the protein binding profile of the test sample with a protein binding profile of a reference sample, whereby presence or absence of the bacteria, virus or cell in the test sample is determined by the comparison.

A method for identifying a test protein in a sample, said method comprising

• (a) contacting a sample comprising or suspected of comprising the test protein with a set of digital antibodies that comprises at least about 15 digital antibodies, wherein each of the 15 digital antibodies has been characterized to bind specifically to a different epitope consisting of 3 or 4 or 5 consecutive amino acids, and each digital antibody recognizes a plurality of distinct and different proteins that comprise the same epitope to which the digital antibody binds;
• and
• (b) determining the identity of the test protein by detecting of binding of the test protein to the set of digital antibodies, wherein at least about six digital antibodies bind the test protein;
• and wherein presence of binding indicates presence of at least about six epitopes in the test protein, wherein the identity of the at least about six epitopes is used to identify the test protein.