Disclosed are methods for identifying one or more amino acid molecules and nucleic acid molecules encoding such amino acid molecules of at least two proteomes that are conserved, unique or express at higher or lower levels in at least one of the proteomes. Expression libraries are used that produce the proteome, and in one embodiment, may produce the proteome from at least one cDNA expression library in one to five reactions. Anti-proteome antibodies are prepared that selectively bind to one of the proteomes and binding with at least one second proteome compared.

Combining presynaptic proteins, neuronal pentraxin 2 (NPTX2) and neurexin 2 (NRXN2), with respective postsynaptic functional partners GluA4-containing glutamate receptor (AMPA4) and neuroligin 1 (NLGN1), and enhancing excitatory synaptic activities in areas of the hippocampus and cerebral cortex. As early damage of such excitatory circuits in Alzheimer's disease (AD) correlates with cognitive losses, plasma neuron-derived exosome (NDE) levels of these two pairs of synaptic proteins are quantified and serve as biomarkers. NDE contents of all four proteins decrease significantly in AD dementia and diminished levels of AMPA4 and NLGN1 correlate with the extent of cognitive losses. Prior to the onset of dementia, NDE levels of all but NPTX2 are significantly lower than those of matched control subjects and levels of all decline significantly with the development of dementia. Reductions in NDE levels of these excitatory synaptic proteins are indicators of cognitive losses and reflect progression of severity of AD.

The invention provides a method of identifying a peptide interaction site on a target protein wherein the target protein modulates the phenotype of a mammalian cell, using mammalian encoded peptides (SEPs) such as short open reading frame (sORF) encoded peptides. The invention further provides a method for the identification of new therapeutic targets and protein interaction sites for use in drug discovery.

Disclosed herein are methods, compositions, probes, assays and kits for identifying a lipid binding protein as a drug binding target. Also disclosed herein are methods, compositions, and probes for mapping a ligand binding site on a lipid binding protein, identification of lipid binding proteins, generating drug-lipid binding protein profiles, high throughput drug screening, and identification of drugs as potential lipid binding protein ligands.

Disclosed herein are methods and compounds for profiling a lysine reactive protein. Also described herein are methods, compounds, and compositions for identifying a small molecule fragment ligand that interacts with a reactive lysine residue.

This disclosure comprises devices and methods for determining the identity of individual protein molecules in a complex mixture.

The present invention provides compositions comprising chimeric polypeptides that bind to free ubiquitin proteins or free ubiquitin-like proteins with high affinity, as well as chimeric polypeptides that bind to both free and conjugated ubiquitin proteins or free and conjugated ubiquitin-like proteins, and methods of using the chimeric polypeptides to determine the amount of free or toal ubiquitin or free or total ubiquitin-like proteins in various types of samples.

The present disclosure describes an activity-dependent regulated polynucleotide capable of detecting dendritic structural plasticity. The present disclosure also describes methods of using in high throughput screens and kits containing the same.

The present disclosure provides a system comprising a communication interface and computer for assigning a label to the biomolecule fingerprint, wherein the label corresponds to a biological state. The present disclosure also provides a sensor arrays for detecting biomolecules and methods of use. In some embodiments, the sensor arrays are capable of determining a disease state in a subject.

The present invention relates to a method for the absolute quantification of naturally processed HLA-restricted cancer peptides, i.e. the determination of the copy number of peptide(s) as presented per cell. The present invention can not only be used for the development of antibody therapies or peptide vaccines, but is also highly valuable for a molecularly defined immuno-monitoring, and useful in the processes of identifying of new peptide antigens for immunotherapeutic strategies, such as respective vaccines, antibody-based therapies or adoptive T-cell transfer approaches in cancer, infectious and/or autoimmune diseases.