The invention generally relates to mass tag analysis for rare cells and cell free molecules. In certain embodiments, the invention provides an apparatus including an essentially non-absorbent membrane having at least one pore, a microwell operably associated with the essentially non-absorbent membrane, and an electric field generator. The apparatus may be configured such that an electric field produced by the electric field generator operably interacts with a sample in the microwell and expels a droplet of the sample through the at least one pore in the essentially non-absorbent membrane. In certain embodiments, apparatuses of the invention are used for detection, and optionally quantification, of a target analyte from a heterogeneous sample, such as a rare target analyte (e.g., rare cell) from a biological sample.

Methods of analyzing a drug polypeptide conjugate using tandem mass spectrometry involving dual tandem mass tags (TMTs) are described. Provided herein is an integrated method using TMTs to obtain three analytical measurements, termed “triple play”, which enables identification of the drug occupancy, normalization between multiple samples and triggering of additional MS/MS to identify and localize conjugation site(s) of the payload. Also described is a method of multiplexing conjugation reactions in a single run with TMT labeling for enhanced throughput capability, while maintaining the same sensitivity with current mass spectrometry instrumentation.

The present disclosure is directed at an antibody conjugate having an antibody and a tag, wherein one or more element(s) present in the antibody exhibit an isotope ratio which differs from the naturally occurring isotope ratio of the one or more element(s), wherein the amount of the isotope which is less-common in nature, is increased to at least 4% of the atoms of the respective element in the antibody, as well as uses thereof.

The present invention provides a set of novel isobaric chemical tags, also referred herein as SUGAR (Isobaric Multiplex Reagents for Carbonyl Containing Compound). These labeling tags are compact and easy to synthesize at high yield and purity in just a few steps using commercially available starting materials. The tagging reagents of the present invention comprise: a) a reporter group, having at least one atom that is optionally isotopically labeled; b) a balancing group, also having at least one atom that is optionally isotopically labeled, and c) an aldehyde, ketone, or carboxylic acid reactive group. The multiplex SUGAR tags are able to react with an aldehyde, ketone, or carboxylic acid group of the molecule to be tagged, which offers the capability for labeling and quantitation of glycans, proteins/peptides, and fatty acids.

A method for determining a quantity of an analyte in a liquid sample, comprises: adding a known quantity of an internal standard comprising an isotopically labeled version of the analyte to the sample; (b) providing a continuous stream of the sample having the internal standard to an inlet of a Liquid Chromatography Mass Spectrometry (LCMS) system; and repeatedly performing the steps of: performing a data-independent analysis of the precursor ion species using a mass analyzer, whereby mass spectra of a plurality of fragment-ion species are acquired; calculating one or more degree-of-matching scores that relate to either a number of ions of the internal standard that overlap between results of the data-independent analysis and tabulated mass spectral data of the internal standard; and performing quantitative tandem mass spectrometric analyses of the internal standard and the analyte if each of the degree-of-matching scores meets a respective degree-of-matching condition.

The present provides a Positional Isotopomer NMR Tracer Analysis (PINTA) method that can be used to noninvasively assess rates of hepatic mitochondrial oxidation (V.sub.CS) and/or pyruvate carboxylase (V.sub.PC) flux in a subject. In certain embodiments, the methods utilize a combined NMR/gas chromatography-mass spectrometry analysis of plasma following infusion of [3-.sup.13C]lactate and glucose tracer. The method of the invention provides investigators with a tool to non-invasively examine the role of altered hepatic mitochondrial metabolism and study the effects of therapeutic interventions for the treatment of non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and type 2 diabetes (T2D).

Described herein are methods for screening for a disease state. The method may include obtaining multiple data sets, and identifying the disease state based on a combination of the data sets. The data sets may include biomolecule measurements obtained by multiple methods, such as through the use of particles and reference biomolecules.

Liquid chromatography-free methods for quantitating a target protein in a sample are provided. One embodiment provides a liquid chromatography-free method for quantifying target antibodies in a sample including the steps of spiking the sample with a labeled internal standard antibody, digesting the antibodies in the sample to produce peptides, fractionating the peptides; and quantifying the target antibodies using a direct infusion MS.sup.2 system containing one or more ion traps and two or more quadrupole mass filters and an electrospray ionizer, wherein the method is liquid chromatography-free.

The present disclosure provides for a universal lipid quantitative standard (ULQS) comprising a plurality of isotopically labeled lipid standards that can be used with any analytical mass spectrometry techniques known in the art. The ULQS includes at least one isotopically labeled lipid species from one or more of the following lipid classes: i) phospholipids; ii) lysophospholipids; iii) cholesterol esters; iv) triacylglycerols; v) diacylglycerols; vi) ceramides; and vii) sphingomyelins.

In some embodiments, a mass spectrometry tag may comprise a linker region, a mass balance region, and a reporter region. The mass spectrometry tag may be configured to fragment in a mass spectrometer via an energy dependent process to produce multiple reporter molecules. For example, the reporter region of the tag may be configured to produce at least two reporter molecules via fragmentation. In some embodiments, one or more regions of the tag may comprise at least one heavy isotope. In some such embodiments, the ability to fragment into multiple reporter molecules as well as the placement and/or number of heavy isotope(s) allows the mass spectrometry tag to be distinguished from other similar mass spectrometry tags. In some such embodiments, the ability to distinguish between tags having the same or substantially similar total mass to charge ratio and reporter region mass may allow the system to have a greater multiplexing capacity than conventional systems.