Systems and methods for targeted therapy based on single-cell stimulus perturbation response. In one embodiment, a method for optimizing stimulus combinations for therapy includes receiving a cell sample, treating the cell sample with a plurality of stimuli by treating a different portion of the cell sample with one of the plurality of stimuli for each of the plurality of stimuli, labeling the cell sample with a plurality of metal-conjugated probes, analyzing the cell sample using a mass spectrometer, obtaining mass spectrometry data from the mass spectrometer, identifying subpopulations within the cell sample using the mass spectrometry data, computing stimulus effects, generating a nested-effects model using the mass spectrometry data, and scoring stimuli combinations using the computing device, wherein the stimulus combinations are combinations made from the plurality of stimuli.

A method for quantifying at least one microorganism group via at least one mass spectrometry analysis. The method includes at least one separation and fragmentation step. The method moreover includes a step that involves measuring the amount of at least one representative peptide or at least one protein representing the microorganism group. The at least one representative peptide or the at least one protein is obtained after the at least one separation and fragmentation step and serves as a quantification marker(s). The amount of the quantification marker(s) is directly correlatable to the amount of the at least one microorganism group.

The present invention relates to the field of nephrology. More specifically, the present invention provides methods and compositions useful for more precisely estimating glomerular filtration rate (GFR). In a specific embodiment, a method for calculating the estimated glomerular filtration rate (eGFR) in a patient comprises the steps of (a) measuring the level of one or more metabolites using mass spectrometry from a blood sample obtained from the patient; and (b) calculating the eGFR using an algorithm that utilizes the measured levels of the one or more metabolites.

The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the Epidermal Growth Factor Receptor (EGFR) protein that are particularly advantageous for quantifying the EGFR protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from said biological sample using the Liquid Tissue™ reagents and protocol and the EGFR protein is quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of an EGFR peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.

Provided herein is a method for authenticating animal hide gelatins using peptide markers found animal hide gelatin hydrolysates. The method can be used to authenticate animal hide gelatins derived from donkey hide, horse hide, pig hide, and cattle hide.

The present invention relates to a process for the prediction of cell culture performance data of sample cells, a process for the isolation of said cells and a device for the prediction of cell culture performance data of sample cells.

The present invention relates a method for the diagnosis, prediction or risk stratification for mortality and/or disease outcome of a subject that has or is suspected to have sepsis, comprising determining the presence and/or level of antitrypsin (ATT) or fragments thereof in a sample taken from said subject and/or determining the presence and/or level of transthyretin (TTR) or fragments thereof, wherein the presence and/or level of ATT and/or TTR or fragments thereof is correlated with an increased risk of mortality and, wherein said increased risk of mortality and/or poor disease outcome is given if the level of ATT is below a certain cut-off value and/or the level of fragments thereof is above a certain cut-off value and/or said increased risk of mortality and/or poor disease outcome is given if the level of TTR is below a certain cut-off value and/or the level of fragments thereof is below a certain cut-off value. The invention relates in general to the use of ATT and/or TTR or its fragments for the diagnosis of sepsis, and to nucleotides of SEQ ID NO. 2 to 14.

A method for modification of solid substrates with proteins for efficient surface preconcentration of an analyte from multi-component samples before the detection based on desorption-ionization mass spectrometry and immunochemical assays. The claimed subject is a method of modification of surfaces used as substrates for desorption-ionization mass spectrometry and immuno-chemical assays. The method is based on electronebulization (electrospraying) of protein solution, depending on the intended application either enzymes, lectins, or antibodies. The formed charged electrospray is dried in real time by its passing through an evaporation compartment and the resulting beam of desolvated ions impacts onto the surface and binds to it firmly. Such modified surface can be then used for a selective interaction with an affinity partner of the deposited protein, its preconcentration or enzymatic modification followed by an analysis by means of desorption-ionization mass spectrometry or immunochemical assays.

Provided are methods for determining the amount of lacosamide in a sample using mass spectrometry. The methods generally involve ionizing lacosamide in a sample and detecting and quantifying the amount of the ion to determine the amount of lacosamide in the sample.

The invention relates to a method for determining the presence of at least one distinct polypeptide in a biological sample comprising contacting the biological sample with a hydrolyzing agent, wherein the hydrolyzing agent is capable of hydrolyzing the distinct polypeptide in a sequence-specific manner such that at least one distinct peptide having a predetermined peptide measured accurate mass would result if the at least one distinct polypeptide were present in the biological sample, to obtain a hydrolyzed sample; bringing the hydrolyzed sample in contact with a substrate comprising at least one immobilized binding partner, wherein the at least one immobilized binding partner is capable of specifically binding the distinct peptide; removing the hydrolyzed sample from the substrate in a manner such that the distinct peptide would remain bound to the immobilized binding partner; contacting the substrate with an elution solution, wherein the distinct peptide would dissociate from the immobilized binding partner into the elution solution; subjecting a portion of the elution solution to liquid chromatography to segregate a plurality of molecules in the portion of the elution solution to obtain sorted molecules; determining the measured accurate mass of at least one sorted molecule present in the elution solution; and determining the presence of the at least one distinct polypeptide in the biological sample when a measured accurate mass of at least one molecule is substantially equal to the predetermined peptide measured accurate mass.