The present invention is directed to methods for fertility prediction in animals, and in particular dairy cows. The methods allow detection of the likelihood of conception upon insemination of a cow based on the analysis of properties of milk of the cow, and in particular the mid-infrared (MIR) spectrum of the milk. Such methods also enable selection of cows for insemination and fertility classification of cows. Software and systems for carrying out the methods of the invention are also provided. The present invention also provides methods for deriving reference MIR spectra representative cows with good or poor likelihoods of conception upon insemination. These reference MIR spectra can be used for fertility prediction in cows to be tested.

A mass spectrometry method comprises: providing a multiplexed sample comprising a mixture of biomolecule-containing samples respectively tagged with mass tags; acquiring MS2 spectra by data-dependent acquisition (DDA) of the multiplexed sample or another mass tagged mixture of the samples during chromatographic elution; acquiring MS2 spectra by data-independent acquisition (DIA) during the elution; forming a spectral library from the DDA MS2 spectra comprising a plurality of the MS2 spectra and the biomolecule retention times; matching fragment-ion peaks in the DIA MS2 spectra to fragment-ion peaks in the MS2 library spectra to find matched biomolecules; determining a total abundance for each matched biomolecule from the DIA MS2 spectra at each of a plurality of retention times; determining abundances of respective reporter ions from the DIA MS2 spectra at the plurality of retention times; and deconvoluting relative abundances of the biomolecules in each respectively tagged biomolecule-containing sample based on the determined abundances.

Described are methods and uses employing metabolomic data to diagnose an asthma disease state or a Chronic Obstructive Pulmonary Disease (COPD) state. Further described are methods of uses of employing metabolomic data to distinguish between asthma and COPD. In particular, urinary metabolomic profiles are employed to enable differential diagnosis of asthma and COPD.

Provided herein are methods of obtaining and applying measurements of metabolites to diagnosing ASD in a subject, particularly children, with high specificity and sensitivity. The metabolites can be measured in urine, serum, and whole blood samples.

A method for determining in a sample, by liquid chromatography/mass spectrometry, the presence, absence, or amount of one or more or a plurality of analytes is described. The method comprises subjecting the sample to an ionization source under conditions suitable to produce one or more ions detectable by mass spectrometry from each of the one or more of the analytes; measuring, by liquid chromatography/mass spectrometry, the amount of the one or more ions from each of the one or more analytes; and using the measured amount of the one or more ions to determine the presence, absence, or amount of each of the one or more or plurality of analytes in the sample.

The present disclosure provides a system comprising a communication interface and computer for assigning a label to the biomolecule fingerprint, wherein the label corresponds to a biological state. The present disclosure also provides a sensor arrays for detecting biomolecules and methods of use. In some embodiments, the sensor arrays are capable of determining a disease state in a subject.

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides with unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Disclosed are compositions and methods for performing a proteomic analysis. Particularly disclosed are compositions and methods for preparing a sample for quantitative single-cell proteomics.