Disclosed are methods of detecting biomarkers in complex biological matrices. The method comprises providing a sample well coated with antibodies specific to target protein biomarker(s), contacting the sample well with a biological sample to capture target biomarkers, digesting target biomarkers, and analyzing the signature peptides resulting from digestion of target biomarkers to determine the amount of one or more protein biomarkers by a mass spectrometry method.

The present invention is directed to a mass spectrometry approach to identifying carcinomas or tissue abnormalities, and distinguishing carcinomas or tissue abnormalities.

Methods for diagnosis or prognosis of a cancer in a subject include isolating one or more nanovesicles from a biological sample obtained from the subject, determining the amount in the biological sample of the one or more nanovesicles, and comparing the amount of the one or more nanovesicles to a control level to thereby diagnose the cancer. The one or more nanovesicles are obtained by depleting the biological sample of exosomes prior to the isolation of the nanovesicles. Methods for identifying a tumor metastasis in a subject are also provided and include fractionating a biological sample from a subject to obtain a fraction including one or more exosomes and one or more nanovesicles having a diameter of about 8-12 nm, and then isolating the one or more nanovesicles to diagnose the tumor metastasis.

The production and use of semiconducting nanopost arrays made by nanofabrication is described herein. These nanopost arrays (NAPA) provide improved laser ionization yields and controllable fragmentation with switching or modulation capabilities for mass spectrometric detection and identification of samples deposited on them.

Methods are provided for detecting the amount of one or more CAH panel analytes (i.e., pregnenolone, 17-OH pregnenolone, progesterone, 17-OH progesterone, dehydroepiandrosterone (DHEA), androstenedione, testosterone, deoxycorticosterone, 11-deoxycortisol, and cortisol) in a sample by mass spectrometry. The methods generally involve ionizing one or more CAH panel analytes in a sample and quantifying the generated ions to determine the amount of one or more CAH panel analytes in the sample. In methods where amounts of multiple CAH panel analytes are detected, the amounts of multiple analytes are detected in the same sample injection.

Method of identifying host-cell proteins in a sample matrix are provided.

Disclosed herein is a chemo-proteomic probe for labelling and monitoring a live microbe interacting with a host cell and for qualitative and quantitative analyses of those proteins involved during a microbe infects the host cell. This probe comprises a functional group for conjugating to a surface protein of a live microbe under a physiological condition; a photo-reactive group for covalent cross-linking to an interacting cell protein of a host; and a tag for isolating the cross-linked complex of the surface protein of said live microbe and the interacting protein of a host cell for qualitative and quantitative proteomics analyses. The probe may further comprise a visualization tag. This technology takes advantage of the high throughput feature of mass spectrometry analysis and combines it with a uniquely designed chemistry to achieve high efficient isolation and analysis of host cell proteins interacting with a pathogen at different stages of an infection.

Provided are compositions and methods for identifying individuals with cancer who will benefit from PD-1 inhibitor therapy. The method comprises determining levels of signaling lymphocyte activation molecule-associated protein (SAP) in an individual and based on the SAP levels, determining if the individual is suitable for PD-1 inhibitor therapy. Also provided is a method of treatment of X-linked lymphoproliferative disease comprising administering to an individual PD-1 inhibitory therapy, with or without SHP2 inhibitors.

Methods for detecting and quantifying one or more microcystin compounds in a sample are described. The methods may include a preconcentration step, and generally utilize an LC-MS or LC-MS/MS analysis with an Orbitrap Fusion mass spectrometer or a QqQ mass spectrometer. The methods provide excellent recoveries and limits of quantification of microcystins.

The present disclosure relates to methods for screening and identifying a fetal trisomy. Certain embodiments of the present disclosure provide a method of screening for a fetal trisomy in a pregnant female subject. The method comprises detecting one or more lipid markers from the subject, wherein the one or more markers is indicative of the risk of a fetal trisomy in the subject, and determining the risk of a fetal trisomy in the pregnant female subject on the basis of the one or more lipid markers detected.