The present invention concerns a method for identifying and using a biomarker, or creating a proteome profile, indicative of a reduced response to a drug in a patient involving a thermal shift assay on a sample. The method comprises the steps of a) heating a sample from a patient b) separating soluble from insoluble protein, c) analysing either or both the soluble and insoluble protein fractions of step b) to determine the melting temperature.

The present invention relates to methods for identifying high molecular mass lipids in samples. Such high molecular mass lipids may be useful as biomarkers for the identification of disease.

The invention relates to a method for the preparation of living, microbial samples and microorganisms for subsequent mass spectrometric measurement and evaluation. Findings which can be derived from such a measurement can particularly serve the faster identification of microorganisms in the microbial sample according to species/subspecies and/or the fast determination of resistance/sensitivity of the microorganisms to antimicrobial substances and/or the further characterization of microorganisms, for example in respect of pathogenicity, virulence and metabolism. According to a preferred embodiment of the invention, the preparation particularly takes place directly on a mass spectrometric sample support.

A computer implemented method for calibrating a customer mass spectrometry instrument (118) for quantifier-qualifier-ratio check is proposed. The method comprises the following steps: a) at least one manufacturer-site standardization, wherein a set of samples of a subject and a set of calibrator samples are measured in multiple replicates on a plurality of mass spectrometry instruments (114), wherein each measurement comprises multiple reaction monitoring with quantifier and qualifier transition for analyte and internal standard, wherein at least three adjustment factors are determined from the measurements of the set of samples of a subject and the set of calibrator samples, wherein a first adjustment factor α depends on a difference between analyte and internal standard, wherein a second adjustment factor β depends on a difference between samples of a subject and calibrator samples for analyte quantifier-qualifier-ratio, wherein a third adjustment factor γ depends on a difference between samples of a subject and calibrator samples for the internal standard quantifier-qualifier-ratio; b) at least one transfer step, wherein the adjustment factors are electronically transferred to a customer mass spectrometry instrument (118); c) at least one customer-site calibration, wherein the customer-site calibration comprises at least one calibration measurement, wherein a set of calibrator samples is measured on the customer mass spectrometry instrument (118) and quantifier-qualifier-ratios are determined therefrom, wherein target values for quantifier-qualifier-ratios for analyte and for internal standard are set by applying the adjustment factors on the determined quantifier-qualifier-ratios.

The state of protein phosphorylation and glycosylation can be key determinants of cellular physiology such as early stage cancer, but the development of phosphoproteins and/or glycoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate, for the first time, a strategy to isolate and identify phosphoproteins/glycoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs by isolating from small volume of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer than in healthy controls. Several novel biomarkers were validated in individual patients using Paralleled Reaction Monitoring for targeted quantitation. Similarly a group of glycoproteins in plasma EVs are identified. The study demonstrated that the development of phosphoproteins and/or glycoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.

The present invention generally pertains to methods of detecting host cell proteins. In particular, the present invention pertains to the use of a novel activity-based protein profiling probe to identify host cell proteins with lipase activity in a pharmaceutical formulation.

The present invention relates to the field of protein characterization, and in particular to methods for characterizing high molecular weight species of a therapeutic protein by implementing a workflow including using a post-column denaturation-assisted SEC-MS method that allows highly specific, sensitive, and comprehensive characterization of high molecular weight species.

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.

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.

The present disclosure provides methods of identifying or certifying an animal that consumed a traceable diet comprising a C.sub.1 metabolizing microorganism.