Protein screening and detection method

A mass spectrometry fragmentation based method for selecting a polypeptide from a library of polypeptides, comprising:

• a. deep sequencing a tagged nucleic acid library comprising a plurality of polypeptide-encoding sequences each bound to one or more unique detection tags,
• wherein the one or more unique detection tags comprise nucleotide sequences encoding corresponding unique polypeptide sequences, wherein one or more unique polypeptide detection tags are generated when the one or more unique detection tags are expressed;
• b. creating a database comprising a plurality of predicted polypeptide mass spectrometry fragmentation patterns for each detection tag of the one or more detection tags bound to of the plurality of polypeptide-encoding sequences, the plurality of predicted mass spectrometry fragmentation patterns being based on the one or more unique detection tags in isolation and on the polypeptide detection tags;
• c. expressing the tagged polypeptide library from the tagged nucleic acid library, thereby generating a plurality of polypeptides each bound to one or more unique polypeptide detection tags;
• d. selecting a tagged polypeptide from the tagged polypeptide library in a selection step, yielding a selected tagged polypeptide;
• e. separating the one or more unique polypeptide detection tags from the selected tagged polypeptide, yielding one or more unique isolated detection tags;
• f. identifying the one or more unique isolated polypeptide detection tags by generating a fragmentation pattern of the one or more unique isolated polypeptide detection tags by mass spectrometry;
• g. matching the fragmentation pattern of the one or more unique isolated polypeptide detection tags with a corresponding predicted polypeptide mass spectrometry fragmentation pattern from the predicted polypeptide mass spectrometry fragmentation patterns created in step b., thereby identifying the one or more unique isolated polypeptide detection tags;
• and
• h. selecting, from the tagged nucleic acid library one or more sequences encoding the one or more unique isolated polypeptide detection tags bound to the corresponding polypeptide-encoding nucleic acid sequence, thereby selecting a polypeptide library of polypeptides.

A mass spectrometry fragmentation based method for selecting a polypeptide from a library of polypeptides, comprising:

• a. generating a tagged nucleic acid library encoding a tagged polypeptide library comprising a plurality of library members that each comprises a polypeptide and a detection tag, which are separated by a first severable element;
• b. deep sequencing the tagged nucleic acid library encoding the tagged polypeptide library comprising the plurality of library members, thereby obtaining a plurality of nucleic acid sequences from the tagged nucleic acid library;
• c. creating a database comprising a plurality of predicted mass spectrometry fragmentation patterns by predicting a predicted fragmentation pattern by mass spectrometry for each of a plurality of detection tags encoded by a tag-encoding sequence from the plurality of nucleic acid sequences, the plurality of predicted mass spectrometry fragmentation patterns based on the one or more unique detection tags in isolation;
• d. expressing the tagged polypeptide library from the tagged nucleic acid library;
• e. selecting a selected polypeptide from the tagged polypeptide library;
• f. severing the first severable element, thereby yielding an isolated detection tag;
• g. identifying the isolated detection tag by generating a fragmentation pattern of the isolated detection tag by mass spectrometry and matching the fragmentation pattern with the plurality of predicted mass spectrometry fragmentation patterns;
• and
• h. choosing from the plurality of nucleic acid sequences a nucleic acid sequence comprising an isolated tag-encoding sequence encoding the isolated detection tag, thereby selecting a tagged polypeptide member of the tagged polypeptide library associated with the isolated detection tag.