Abstract: The present application provides biligand and triligand protein-catalyzed capture (PCC) agents that specifically bind VEGF, as well as the use of these capture agents as detection, diagnosis, and treatment agents.

Abstract: Methods are provided for identifying biomarker proteins that exhibit differential expression in subjects with a first lung condition versus healthy subjects or subjects with a second lung condition. Also provided are compositions comprising these biomarker proteins and methods of using these biomarker proteins or panels thereof to diagnose, classify, and monitor various lung conditions. The methods and compositions provided herein may be used to diagnose or classify a subject as having lung cancer or a non-cancerous condition, and to distinguish between different types of cancer (e.g.

Abstract: The present application provides novel compositions, methods, and assays for use in identification of appropriate diagnostic markers in blood. These compositions, methods, and assays are capable of distinguishing normal levels of detectable markers from changes in marker levels that are indicative of changes in health status.

Abstract: The present application provides biligand and triligand protein-catalyzed capture (PCC) agents that specifically bind VEGF, as well as the use of these capture agents as detection, diagnosis, and treatment agents.

Abstract: The invention described herein is a tool developed for the analysis of proteomic mass spectrometry (MS) data to identify and characterize glycoproteins. The tool is designed to perform four main tasks, separately, or as needed: optimize the selection of glycopeptides for MS/MS, identify glycopeptide spectra from MS/MS data, characterize the sugar moieties of identified glycopeptide spectra, and match the glycosylated precursor to its parent protein. The design and implementation for each of these components is described in more depth in this patent application.

Abstract: The present invention features computer methods and systems for comparing biomolecules across biological samples. In these methods, mass spectrometry measurements are obtained on biomolecules in two or more samples. These measurements are then processed and analyzed by the methods described herein to render them more comparable. We refer to this technology as “Constellation Mapping” (CM). The resulting data, constellation maps, can be used to compare the abundance of biomolecules across samples, and, when done in real time, can be used to select differentially abundant biomolecules for subsequent LC/MS-MS.

Abstract: The present invention is directed to computer automated methods and systems for identifying and characterizing biomolecules in a biological sample. Mass spectrometry measurements are obtained on biomolecules in a sample. These measurements are analyzed to determine the abundance of the biomolecules in the sample, and the abundance measurements are coupled with one or more distinguishing characteristics of biomolecules they are associated with, thereby permitting computer-mediated comparison of abundances of biomolecules from multiple biological samples.