Provided herein is synthesis of a novel acidic acid residue targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker. The novel mass spectrometry-cleavable cross-linking agents can be used in mass spectrometry to facilitate structural analysis of intra-protein interactions in proteins and inter-protein interactions in protein complexes. Also disclosed herein are data based on the novel MS-cleavable homobifunctional cross-linker that are complimentary to amine-reactive sulfoxide-containing MS-cleavable reagents.

The present disclosure provides a method of detecting the presence or amount of a UBE3A protein in a sample, such as a human sample, using mass spectrometry based techniques. The methods described herein are useful for diagnosing Angelman syndrome, as well as monitoring disease progression and treatment effectiveness.

Methods and sets of non-biological reagents (elution reagents, tag isomers, tag reactive groups, crosslinkers) for single or multiplexed capture and gentle elution of biomolecules. Examples are provided using amine- and cysteine-reactive reagents for enrichment of proteins, peptides, and rare peptide modifications.

Described herein are methods such as multi-omic methods for assessing a disease such as cancer. The multi-omic methods may integrate proteomic, transcriptomic, genomic, lipidomic, or metabolomic data. The method screening diseases or disease states. Also described herein are methods for screening for diseases or disease states from biological samples. The methods may include assessing whether a nodule, mass, or cyst is cancerous.

Provided is a high-accuracy analysis method utilizing an enzyme-lined immunoassay. The presence of an analyte 3 can be detected or the abundance of the analyte 3 can be analyzed by: bonding an antibody 5 that is capable of specifically bonding to the analyte 3 immobilized on a solid phase 1 and has an enzyme 7 bonded thereto; then decomposing an enzyme substrate 8, which can generate decomposition products capable of being detected easily with a mass spectrometry, with the enzyme 7 bonded to the antibody 5; and then analyzing the decomposition products 9 and 10 with a mass spectrometry.

A method and corresponding apparatus are disclosed for analysis of a peptide-containing sample. The sample is prepared by adding isotopically-labeled peptides corresponding to endogenous peptides of interest, and the prepared sample is analyzed by liquid chromatography-mass spectrometry (LCMS). Detection in a high-resolution, accurate mass (HRAM) MS1 spectrum of a precursor ion matching an isotopically-labeled peptide triggers acquisition of an MS/MS spectrum (preferably acquired in an ion trap or other fast mass analyzer) to determine if a product ion is present matching a characteristic product ion (e.g., the y.sub.1 ion) of the isotopically-labeled peptide. If the characteristic product ion is present, then a HRAM MS/MS spectrum is acquired for detection and quantitation of the corresponding endogenous peptide.

Provided herein are methods for high throughput quantitation of testosterone utilizing at least two different derivatizing agents of different masses. In another aspect, provided herein are methods for determining the amount of testosterone in each of a plurality of human samples with a single mass spectrometric assay by subjecting each of a plurality of human samples to a different derivatizing agent to generate a differently derivatized testosterone in each of the plurality of samples; combining the plurality of samples to form a multiplex sample; and quantifying the amount of testosterone in each sample by mass spectrometry.

Compositions and methods for identifying free thiols in protein are provided. An exemplary method labeling peptides with a tag to identify free thiols and a tag to identify native disulfide bonds and analyzing the tags using targeted MS.sup.2. In one embodiment, the method provides complete coverage of all 32 cysteine residues in an IgG molecule. In other embodiments the method covers the 16 cysteine residues on the heavy and light chains in an IgG molecule. In another embodiment, the method covers the 5 cysteine residues on each light chain of an IgG molecule. In another embodiment, the method covers the 11 cysteine residues on each heavy chain of an IgG molecule.

MCF7-fibroblast co-cultures are a valuable model of resistance to apoptosis induced by hormonal therapies, such as Tamoxifen and Fulvestrant. These mixed co-cultures demonstrate the induction of mito-sternness and ribo-stemness features. Molecular therapeutic targets were identified through label-free proteomics of MCF7-fibroblast co-cultures, and independently validated using a bioinformatics approach. The resulting Mito-Signature is prognostic of endocrine treatment failure, tumor recurrence, and distant metastasis, and may be used to identify patients at risk of treatment failure. Such patients may be treated with a mitochondrial biogenesis inhibitor to reduce the risk of treatment failure, and/or to increase the effectiveness of the hormone therapy.

The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.