Bead arrays suitable for analysis by mass spectrometry are disclosed. In an embodiment, a bead array includes multiple reactive sites, each of the reactive sites being capable of binding multiple distinct target analytes.

Provided is a method for analyzing a sample containing a sialic-acid-containing glycan including a sialic-acid-linkage specific modification, based on mass spectrum data of the sample, including steps of: detecting, from the mass spectrum data, a representative peak for each isotope peak cluster; detecting, from the representative peaks, an isomer peak cluster including multiple ion peaks estimated to be identical in the number of sialic acids and the glycan composition exclusive of the sialic acids; estimating a glycan composition for each representative peak according to predetermined glycan search conditions; creating a mass spectrum with an annotation added for each isomer peak cluster to indicate a correspondence between each peak in one cluster and a peak in a mass spectrum, and displaying the annotated mass spectrum on a display section; and creating a table relating each estimated glycan-composition candidate to an isomer peak cluster, and displaying the table on the display section.

Provided herein are methods, techniques and processes for selecting one or more peptides for virus detection (e.g., influenza, SARS-CoV-2) in clinical samples using mass spectrometry. Methods for selecting a combination of peptides to identify one or more disease states in a patient can include: (i) selecting the one or more disease states; (ii) collecting information on proteins associated with the one or more disease states being present within the subject; (ii) in silico digesting individual proteins associated with the one or more disease state to obtain possible workflow peptides; (iv) collecting filtering data associated with the possible workflow peptides; (iv) analyzing the possible workflow peptides for coverage of the one or more disease states and for mass spectrometry detection and resolution; and (iv) selecting the combination of peptides from the possible workflow peptides based on the analyzing step.

The present application is directed to methods and systems for identifying small molecule compounds in mixtures using a library comprising calculated structures and corresponding calculated mass spectral fragmentation patterns of known and/or hypothetical small molecule compounds that may be in the mixture and screening of a mass spectrum of the mixture using the library to identify matching fragmentation patterns. If a mass spectral fragmentation pattern present in the mass spectrum of the mixture matches a calculated fragmentation pattern of one of the known or hypothetical compounds this confirms the identity of a compound in the mixture as the known or hypothetical compound. The method represents a platform method that can be used for a multitude of purposes related to the screening and identification of compounds in mixtures. Therefore the methods and systems of the present application represent an approach that is uniquely capable of navigating chemical space and providing a understanding of desired families and pharmacophores.

The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the ALK, Ros, Ron, Ret, TS, and/or FGFR1 proteins that are particularly advantageous for quantifying the ALK, Ros, Ron, Ret, TS, and/or FGFR1 proteins directly in biological samples that have been fixed in formalin by the methods of Selected Reaction Monitoring (SRM) mass spectrometry, or as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein the 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 the biological sample using the Liquid Tissue™ reagents and protocol and the ALK, Ros, Ron, Ret, TS, and/or FGFR1 proteins are 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 ALK, Ros, Ron, Ret, TS, and/or FGFR1 fragment peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.

The present invention provides a compound of formula (I), formula (II), formula (III), (IV) or a salt thereof, compositions and methods of making the compound, methods and reagents for measuring the compound, and kits using the same. The use of a compound of formula (I), formula (II), formula (III), or formula (IV) for assessing or monitoring kidney function in a subject, determining predisposition to developing reduced kidney function, classifying a subject according to level of kidney function, and diagnosing or monitoring chronic kidney disease is also described.

Detecting glycosaminoglycans (GAGs) and/or determining the level of one or more glycosaminoglycans can be useful, e.g., in identifying or monitoring various medical conditions, the status of patients having various medical conditions, and/or the response to treatment of individuals having various medical conditions. The present invention provides methods for detecting glycosaminoglycans and/or determining the level of glycosaminoglycans through the use of, e.g., mass spectrometry.

Disclosed are specifically a marker polypeptide of a Bothrops atrox-like thrombin and a method thereof for detecting species source and content of a snake venom-like thrombin and an application, relating to the technical field of snake venom detection. An amino acid sequence of the marker polypeptide is EAYNGLPAK (SEQ ID NO:1), and the marker polypeptide may be used to detect the species source and content of the snake venom-like thrombin in a sample. The marker polypeptide of the present disclosure may play an important role in characterizing the species source and content of the snake venom-like thrombin in the sample, and fill in the blank of a quality standard of snake venom of the Bothrops atrox.

Methods are described for determining the amount of insulin in a sample. Provided herein are mass spectrometric methods for detecting and quantifying insulin and C-peptide in a biological sample utilizing enrichment and/or purification methods coupled with tandem mass spectrometric or high resolution/high accuracy mass spectrometric techniques. Also provided herein are mass spectrometric methods for detecting and quantifying insulin and b-chain in a biological sample utilizing enrichment and/or purification methods coupled with tandem mass spectrometric or high resolution/high accuracy mass spectrometric techniques.

The present invention provides a method of preparing a sample for an analytic procedure, said sample comprising at least one protein, polypeptide or peptide molecule, and said method comprising fragmenting said molecule using at least one moving magnetic body.