Disclosed are methods for the identification of an individual likely to have steroid resistant nephrotic syndrome (SRNS). The disclosed methods may include detection a plurality of proteins. The plurality of proteins may include, for example, Vitamin D Binding Protein (VDBP), Alpha-1 Acid Glycoprotein 2 (AGP-2), Fetuin A, prealbumin, and NGAL in a urine sample obtained from said individual. The methods may further include detection of Alpha-1 Acid Glycoprotein 1 (AGP-1), Alpha-1 B Glycoprotein (A1BG), Thyroxine binding globulin, hemopexin, and alpha-2 macroglobulin.

The present invention relates to a method of measuring pS396 Tau in a sample comprising the steps of i-iv, i) Treating a CSF sample from a subject suffering or suspected to be suffering from a Tau pathology with trypsin, ii) Subjecting the sample in step i) to a desphosphorylation agent and subsequently take part of the sample aside for step iv) before proceeding to step iii) with the remaining sample, iii) Subjecting the dephosphorylated sample from step ii) to a second trypsin treatment, iv) Measuring the amount of the Tau peptides (SPVVSGDTSPR) corresponding to Tau residues 396-406 in the samples from step ii) and step iii) using LC-MS.

The field of this invention relates to immunohistochemistry (IHC) and in situ hybridization (ISH) for the targeted detection and mapping of biomolecules (e.g., proteins and miRNAs) in tissues or cells for example, for research use and for clinical use such by pathologists (e.g., biomarker analyses of a resected tumor or tumor biopsy). In particular, the use of mass spectrometric imaging (MSI) as a mode to detect and map the biomolecules in tissues or cells for example. More specifically, the field of this invention relates to photocleavable mass-tag reagents which are attached to probes such as antibodies and nucleic acids and used to achieve multiplex immunohistochemistry and in situ hybridization, with MSI as the mode of detection/readout. Probe types other than antibodies and nucleic acids are also covered in the field of invention, including but not limited to carbohydrate-binding proteins (e.g., lectins), receptors and ligands. Finally, the field of the invention also encompasses multi-omic MSI procedures, where MSI of photocleavable mass-tag probes is combined with other modes of MSI, such as direct label-free MSI of endogenous biomolecules from the biospecimen (e.g., tissue), whereby said biomolecules can be intact or digested (e.g., chemically digested or by enzyme).

The embodiments of the present disclosure provide a method for analyzing a body fluid proteome. The method comprises: obtaining a sample to be tested I enriched with low-abundance proteins by removing high-abundance proteins in an initial sample A using an affinity technique; obtaining a sample to be tested II enriched with low-abundance proteins by removing high-abundance proteins in an initial sample B using chemical precipitation, wherein the initial sample A and the initial sample B are obtained from a same body fluid sample of a same subject; obtaining a proteome data set I by performing proteomic analysis on the sample to be tested I; obtaining a proteome data set II by performing proteomic analysis on the sample to be tested II; and determining a final quantified proteome data set of the body fluid sample based on the proteome data set I and the proteome data set II.

Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

Compositions and methods for detecting, characterizing and identifying proteoforms including, for example, determining presence or absence of a particular post-translational modification or a post-translational modification of a particular amino acid in a proteoform, and determining the location(s) of one or more post-translational modifications in the amino acid sequence of a proteoform.

Engineered promiscuous biotin ligases and methods of using them in proximity labeling are described. In particular, the invention provides novel biotin ligase variants having increased promiscuous biotinylation activity capable of proximity labeling of proteins in live cells in as little as 10 minutes.

The present invention generally pertains to methods of characterizing crosslinking sites of a protein of interest. In particular, the present invention pertains to the use of size exclusion chromatography, peptide mapping and subunit analysis to identify and quantify crosslinking sites of a protein of interest and determine a contribution of crosslinking to the formation of high molecular weight species.