The present inventors identified a subpopulation of genes induced by type I and type II IFNs in a human submandibular gland (HSG) epithelial cell line. Unexpectedly, it was found that the majority of genes that are highly up-regulated by IFN- are also highly induced by IFN-. In contrast, there was a substantial group of genes that are highly induced by IFN- only. In target tissues, this identified subpopulation of genes and probes allow different IFN patterns to be discerned, enabling more precise molecular classification of patient subpopulations. The identified gene probes are useful for selecting and monitoring therapy, and for defining efficacy of novel agents in the autoimmune rheumatic diseases.

Composition and methods are provided for the specific manipulation of protein tyrosine phosphatase (PTP) activity, including without limitation manipulation of protein tyrosine phosphatase receptor type gamma (PTPRG). The modulation of PTP activity can be performed in vitro or in vivo, and is useful for therapeutic and research purposes. In some embodiments, an effective dose of a PTP modulator is provided to an individual for preventing or treating disease involving dysregulated tyrosine kinase activity and/or signaling mechanisms involving tyrosine phosphorylation and/or tyrosine kinase activity. In other embodiments, a PTP modulator is utilized in the analysis and screening of phosphatase pathways in a cell.

A two-dimensional liquid chromatography (2D-LC) apparatus and method of its use, the apparatus constructed with (1) a first dimension (first-D) having at least one first chromatography column, (2) at least one multi-port stream selector in fluid communication with the at least one first chromatography column for receiving an effluent therefrom, and (3) a second dimension (second-D) having a plurality of second chromatography columns, each second chromatography column in fluid communication with a corresponding port of the at least one multi-port stream selector for receiving an effluent fraction of the effluent from the at least one first chromatography column, thereby enabling simultaneous chromatographic separation by the plurality of second chromatography columns of a set of multiple effluent fractions outputted from the at least one first chromatography column.

The present application relates to a method of assaying ubiquitination in a sample by combining ubiquitin together with a substrate in a sample containing UBE1, UbcH3, Skp2-isoform 1, Skp1, Cull, Rbx1, Cks1, CDK2 and Cyclin E1 under conditions suitable for ubiquitination to take place, exposing the sample to a labelled binding partner which is specific for the ubiquitin, and measuring the amount of ubiquitin bound to the substrate.

The present invention includes a method for analyzing reactions. The method includes the steps of providing a solution of at least one acceptor chemical and at least one donor chemical. The donor chemical is capable of donating a chemical moiety to the acceptor chemical. The solution further includes at least one controller chemical that affects the reaction between the donor chemical and the acceptor chemical. The solution is then incubated so that a portion of the acceptor chemical reacts with the donor chemical to form an acceptor product. Unreacted donor chemical is separated from the acceptor product. The acceptor product or the donor chemical is then measured using X-ray fluorescence. Another aspect of the present invention includes a method for analyzing protein function. The method includes the steps of providing a solution of at least one acceptor chemical and at least one donor chemical. The donor chemical is capable of donating a chemical moiety to the acceptor chemical. The donor chemical includes a functional group selected from ester, anhydride, imide, acyl halide, and amide. The solution is then incubated so that a portion of the acceptor chemical reacts with the donor chemical to form an acceptor product. Unreacted donor chemical is separated from the acceptor product. The acceptor product or the donor chemical is then measured using X-ray fluorescence. Yet another aspect of the present invention includes a method for analyzing protein function. The method includes the steps of providing a solution of at least one acceptor chemical and at least one donor chemical. The solution is then incubated so that a portion of the acceptor chemical reacts with the donor chemical to form an acceptor product. Unreacted donor chemical is separated from the acceptor product. The acceptor product or the donor chemical is then measured using X-ray fluorescence. An additional analytical method is also used to measure either the acceptor product or the donor chemical.

Methods and compositions are provided for validating immunological detection reagents for use in detecting contaminating host cell components in a biological preparation.

The present invention, in some aspects, relates to systems and methods for determining oxidized proteins, including glutathionylated proteins such as S-glutathionylated proteins. The systems and methods of the invention can be used in vitro (e.g., in cell or tissue culture) or in vivo, for example, to diagnose a person having an oxidative stress condition. For instance, in some cases, the invention can be used to spatially determine the location and/or concentration of oxidized proteins within cells and/or tissues (e.g., through visual detection). In one set of embodiments, a glutathionylated or otherwise oxidized moiety on a protein may be reacted with a detection entity, which may be, for example, fluorescent, radioactive, electron-dense, able to bind to a signaling entity or a binding partner in order to produce a signal, etc. As a specific example, a glutathionylated moiety on a glutathionylated protein may be reacted with an alkylating agent to form an alkylthio moiety; the alkylthio moiety may include a detection entity or otherwise be able to interact with a signaling entity. In some embodiments, other moieties on the protein may be altered or blocked before reaction of the protein with the detection entity. Such moieties on the protein may be, for instance, non-oxidized or non-glutathionylated moieties able to react with the detection entity. As a particular example, in a protein containing a glutathionylated moiety and non-glutathionylated thiol moieties, the thiol moieties may first be altered or blocked prior to reaction of the protein with the detection entity. Also provided in certain aspects of the present invention are kits for determining oxidized proteins, which may include components such as detection entities, alkylating agents, blocking agents, reducing agents, signaling entities, binding partners, antibodies, instructions, and the like.

Some embodiments are directed to a method for the subcellular proteomic analysis of a test biological sample, including metabolic isotopic labelling of proteins of a test biological sample, fixing of the sample, labelling of the test subcellular compartment, laser microdissection of said subcellular compartment, extracting the proteins of said subcellular compartment, reversion of the fixing and proteolysis, analyzing the peptides obtained by mass spectrometry, and identifying the analyzed peptides.

The disclosure provides for mass spectrometry (MS)-cleavable haloacetamide cross-linkers, and uses thereof, including for proteome-wide analysis of protein-protein interactions.

The present disclosure provides a method for accurately measuring post-translational modifications in proteins such as antibodies. In particular, the method pertains to the use of heavy isotopic standards to generate a calibration curve to allow for accurate quantitation of a modified peptide. The method may be used to accurately quantify C-terminal truncation in antibodies using mass spectrometry.