Some aspects of this invention provide reagents and methods for the sensitive, quantitative and simultaneous detection of target analytes in complex biological samples by liquid chromatography tandem mass spectrometry (LC MS/MS). Some aspects of this invention provide affinity reagents encoded with mass reporters for the sensitive and quantitative translation of an analyte of interest into a mass tag. The reagents and methods provided herein have general utility in analyte detection and encoding, for example, in biomolecular profiling, molecular diagnostics, and biochemical encoding.

Disclosed is a method of desorbing an adsorbed material by subjecting to energy a diazirine adsorbed on a solid surface or a layer on the solid surface, which causes the diazirine to form a carbene and nitrogen gas; and using the energy of the resultant nitrogen gas to desorb the adsorbed material from the solid surface or a layer on the same. Also disclosed is a method of reacting the resultant carbene with (a) a material in the gas phase proximal to the first solid surface; (b) a material adsorbed on a second solid surface proximal to the first solid surface; or (c) a second solid surface proximal to the first solid surface.

Systems and methods to characterize dimerization interfaces at the subdomain level of a protein are provided. An exemplary method includes digesting a protein dimer sample into subdomains, labeling the digested protein sample, isolating labeled dimeric and monomeric subdomain fragments, and peptide mapping the labeled sample to determine where the dimer fragments are labeled and where the dimer fragments are not labeled. Regions that show decreased labeling extents in the dimer fraction than that in the monomer fraction are likely involved or in close proximity to the dimerization interface.

Provided herein are methods for developing selected reaction monitoring mass spectrometry (LC-SRM-MS) assays.

Set forth herein are methods useful for identifying disease biomarkers, particularly for diseases such as clear cell renal cell carcinoma (ccRCC). In some examples, the methods set forth herein are useful for monitoring the prognosis of patients having a disease such as ccRCC.

Provided are methods for determining the amount of lacosamide in a sample using mass spectrometry. The methods generally involve ionizing lacosamide in a sample and detecting and quantifying the amount of the ion to determine the amount of lacosamide in the sample.

Provided herein are methods for identifying new biomarkers for various diseases using proteomics, peptidomics, metabolics, proteoglycomics, glycomics, mass spectrometry and machine learning. The present disclosure also provides glycopeptides as biomarkers for various diseases such as cancer and autoimmune diseases.

Disclosed herein are methods of diagnosing or prognosing aggressive prostate cancer in a subject and methods of treating a subject with aggressive prostate cancer. For example, the methods can include measuring increased expression of aggressive prostate cancer-related molecules (such as FOLH1, SPARC, TGFB1, CAMKK2, NCOA2, EGFR, or PSA) and optionally administering a therapeutically effective amount of aggressive prostate cancer therapy.

The present invention relates to a composition for screening various signal peptides to select specific ones that allow efficient secretion of a target protein to out of host cells. The present invention also relates to a method for selecting specific signal peptides that express a target protein in host cells and efficiently secrete the target protein to out of the host cells. The use of the composition and/or method according to the present invention enables ultrafast selection of optimal signal peptides for a target protein through barcoding sequences corresponding to the signal peptides, leading to the maximization of the production yield of the recombinant protein.

Synthesis of a sulfoxide-containing homobifunctional cysteine-reactive mass spectrometry-cleavable cross-linker for mapping intra-protein interactions in a protein and inter-protein interactions in a protein complex is provided. Methods for mapping intra-protein interactions in a protein and inter-protein interactions in a protein complex and cross-linking mass spectrometry for identifying one or more cross-linked peptides using the cross-linker are provided.