The present invention provides methods for the fractionation of low molecular weight proteins from mixed protein populations, and proteins obtained by said methods. The methods described herein may find application in, but are not limited to, the detection and/or quantitation of low abundance and/or low molecular weight proteins in biological samples.

Provided is an accurate, minimally invasive method for diagnosing dementia or mild cognitive impairment. The method for examining the likelihood of mild cognitive impairment or dementia, or the risk of dementia includes the steps of: measuring the amount of stereoisomers of proline in the biological sample collected from a subject; and comparing the level of D-proline with a reference value.

MCF7-fibroblast co-cultures are a valuable model of resistance to apoptosis induced by hormonal therapies, such as Tamoxifen and Fulvestrant. These mixed co-cultures demonstrate the induction of mito-sternness and ribo-stemness features. Molecular therapeutic targets were identified through label-free proteomics of MCF7-fibroblast co-cultures, and independently validated using a bioinformatics approach. The resulting Mito-Signature is prognostic of endocrine treatment failure, tumor recurrence, and distant metastasis, and may be used to identify patients at risk of treatment failure. Such patients may be treated with a mitochondrial biogenesis inhibitor to reduce the risk of treatment failure, and/or to increase the effectiveness of the hormone therapy.

The disclosure relates to quantitative analysis of proteins in different species, including plant species. Disclosed are methods that utilize conserved peptides across species to be used as isotope labeled internal standards, which are then used for absolute quantification of proteins. For example, a method for quantitative protein analysis of two or more species is disclosed, the method including determining a set of common peptides that are common for the two or more species, creating a set of isotope-labeled peptides out of the set of common peptides, adding a predefined amount of the labeled peptides to a sample from one of the two or more species, performing mass spectrometry to create first intensity values for a group of peptides from the sample and second intensity values for the labeled peptides, and calculating a quantitative amount of the group of peptides based on the first intensity values and the second intensity values.

A method of purifying Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV-CATCHER), designed for high-throughput analysis of low-abundance small-RNA cargos by next-generation sequencing, and use of this method for preparing purified populations of biological particles or cells from a biological sample for in vitro evaluation of a patient's risk of developing and for treating a severe viral infection; for enhancing therapeutic effectiveness of convalescent plasma therapy in a patient at risk for a severe coronavirus infection, and for treating a patient with a severe coronavirus infection, are described.

The present disclosure relates to sulfoxide-based reagents suitable in the mass spectrometric determination of analyte molecules such as peptides as well as adducts of such reagents and analyte molecules and applications of the reagents and adducts. Further, the present disclosure relates to methods for the mass spectrometric determination of analyte molecules.

A plurality of measured product ion spectra are produced using a DIA tandem mass spectrometry method. One or more product ions are retrieved from a spectral library of known compounds or one or more theoretical product ions are calculated for the known compounds of a database. The one or more product ions or one or more theoretical product ions for each known compound are compared to the measured product ion spectra to identify one or more known compounds in the sample. A database of related known compounds is searched using one or more known compounds, producing one or more matching related compounds and one or more product ions for each related compound. The one or more product ions for each related compound are compared to the measured product ion spectra to identify one or more related compounds in the sample.

Provided herein are isotopically labeled reagents, including isotopically labeled small molecules and peptides, that can be used to detect and/or quantify β-N-methylamino-L-alanine (BMAA) in a sample. The reagents can be used as stable isotope labeled standards in analytical methods, including in conjunction with mass spectrometry, to detect and/or quantify BMAA in a sample, such as a protein sample from a subject.

Disclosed are methods for improving compound detection and characterization. Methods for characterizing a sample are disclosed. The methods can include providing a sample to a liquid chromatography system capable of sample separation to generate sample components; analyzing sample components by multiplexed targeted selected ion monitoring (SIM) to generate an inclusion list; and performing iterative mass spectral data-dependent acquisition (DDA) from the inclusion list, to identify individual sample components thereby characterizing the sample. In one example, multiplexed targeted SIMs and iterative MS2 DDA acquisition is used to increase robust compound identification for cell culture medium analysis.

The present invention relates to a method for identifying and/or authenticating a sample, comprising adding at least one chemical compound to the sample, determining a level of the at least one compound after addition to the sample; comparing the level of the at least one compound to a reference level and identifying the sample based on the comparison with the reference sample and the effect of the sample on the level of the at least one compound. The invention further relates to the use of the at least one compound in the method for identifying and/or authenticating a sample. Further, the invention relates to the use of a kit comprising the at least one compound in the inventive method. In addition, the invention relates to a composition comprising the at least one compound. Further, the invention relates to a kit comprising the compositions provided herein, e.g. for calibrating the methods provided herein and/or the instruments employed in the methods provided herein.