Method and devices are provided for assessing tissue samples from a plurality of tissue sites in a subject using molecular analysis. In certain aspects, devices of the embodiments allow for the collection of liquid tissue samples and delivery of the samples for mass spectrometry analysis.

In shotgun proteomics, generally only a fraction of peptides from a parent protein are actually detected. Because a large portion of the protein sequence is not detected, it is often impossible to determine whether the expressed protein is present in a modified, spliced, or truncated form. Provided herein are methods and systems for analyzing polypeptides which allow for the increase of the mean sequence coverage of a protein concomitant with bioinformatics analysis in order to distinguish putative proteoforms with improved amino acid resolution. Aspects of the invention include (1) a deep sequencing strategy to provide more protein sequence coverage than is typically achieved, and (2) a computational approach to view protein expression across its full length and identify regions of the protein that are potentially subject to such regulation. This technology has global utility in proteomics and will be of particular use for the analysis of biosimilar protein drug therapeutics.

A method for determination of identity of at least one entity from a mass spectrum of at least one entity and from additional data from chemical, physical, biochemical or biological analysis of at least one entity for each entity having the steps of a) collecting analytical data from mass spectrum of the entity, b) obtaining a plurality and prevalences of candidate identities, c) calculation of its score, and d) determining the identity of an entity as the candidate identity with the score closest to the score that would correspond to the true identity of the entity. The entity may be any chemical or biological entity, in particular a peptide, a protein, a lipid, a nucleic acid, a metabolite or a small molecule.

Methods and systems for separating and/or quantifying compounds, using differential mobility spectrometry (DMS) are provided herein. In accordance with various aspects of the applicants' teachings, the methods and systems can provide for the quantification of one or more compounds, for example, using isomeric labels that can be less costly to produce relative to conventional tags that incorporate stable-isotope labels. The present teachings can quantify the relative amount of a compound based on the effect of using an easily charged functional group as well as a functional group positioned at a resonant or non-resonant position through a DMS. In some aspects, methods and systems in accordance with various aspects of the present teachings provide for the detection and/or quantification of the analytes labeled with isomeric tags that can be differentiated via a DMS upstream of a first stage mass analyzer and/or prior to fragmentation of the labeled analyte, for example.

The invention belongs to the field of chemical analysis and detection, and specifically relates to a pretreatment method for LC-MS detecting metabolomics of Aspergillus flavus. The method includes: culturing a strain of Aspergillus flavus; quenching the Aspergillus flavus; disrupting the cell membrane of Aspergillus flavus, and extracting a metabolome. The invention adopts a cold glycerol buffer solution combined with a rapid filtration method for quenching, and a MeOH/DCM/ACN/EA/HCOOH mixture is used as an metabolome extract, thereby achieving the object of efficiently extracting different polar compounds, and metabolome compound coverage is high; pretreatment of the cell metabolomics of Aspergillus flavus by the method of the invention can ensure the repeatability and stability of the metabolomics analysis method and reduce the false positive of the test results.

A microorganism identification method includes steps of: obtaining a mass spectrum through mass spectrometry of a sample including microorganisms; reading, from the mass spectrum, a mass-to-charge ratio m/z of a peak associated with a marker protein; and identifying which bacterial species of the genus Campylobacter are included in the microorganisms in the sample based on the mass-to-charge ratio m/z. The microorganism identification method is further characterized in that at least one of the following 18 marker proteins is used as the marker protein, S10, L23, S19, L22, L16, L29, S17, L14, L24, S14, L18, L15, L36, S13, S11 (Me), L32, and L7/L12.

Described herein is a kit of materials prepared for assays that involve determining relative abundance and/or absolute abundance of various targeted peptides. The kit may comprise trigger versions of target peptides with masses offset from the respective target peptides by predetermined and known amounts. The trigger peptides may be present in amounts that may be readily detected via a mass spectrometry analysis. When mixed with samples that are analyzed, detection of the trigger peptides indicates where in the mass-spectrometer output the target peptide may be found. The kit may include a predetermined amount of synthetic versions of one or more of the target peptides. A measured relative abundance of this synthetic peptide relative to that of the target peptides yields an absolute quantitative value of the target peptide. Also disclosed is a method of preparing a plurality of samples to be submitted for mass spectrometer analysis in parallel.

The disclosed methods are directed to preparing polypeptides for multi-attribute analysis. The polypeptides are optionally denatured, reduced, and/or alkylated before being subjected to a first digestion. Following the first digestion the large and small fragments resulting from the digestion are separated from each other. A second digestion is then performed on the larger of the fragments. All of the fragments from the two digestions are then analyzed chromatographically, electrophoretically, or spectrometrically, or a combination of these methods. The methods are especially useful for the preparation of therapeutic polypeptides for analysis, especially those that are not easily cleaved.

Disclosed are methods and systems using liquid chromatography/tandem mass spectrometry (LC-MS/MS and 2D-LC-MS/MS) for the analysis of ascorbic acid in biological samples.

The invention generally relates to methods for determining whether a peptide includes aspartate or isoaspartate. In certain aspects, methods of the invention involve binding an aspartate/isoaspartate residue in a peptide with a label to produce a labeled peptide. The labeled peptide is then ionized. The ionizing process causes the label to undergo rearrangement in a gas phase at a higher rate if the label is bound to the aspartate residue as compared to if the label is bound to the isoaspartate residue. The methods of the invention then involve performing a mass spectrometry analysis to detect the rearrangement of the label, thereby determining whether the peptide includes aspartate or isoaspartate.