The present invention includes a novel method and system for identification of microorganisms in samples that proteins and other biological material from non-microorganism sources (e.g., proteins of mammalian origin) that can interfere with identification of the microorganisms. The methods and systems described herein include use of a single-use chromatography medium to purify intact proteins prior to mass spectrometry analysis. The chromatography medium and the methods described herein can rapidly and efficiently remove of a substantial portion of interfering biological material (e.g., mammalian proteins) from a crude cell lysate while preserving high signal strength and removing enough of the interfering protein(s) to allow for identification of the microorganism(s) by mass spectrometry analysis.

The present invention relates to method of diagnosis of diseases associated with synaptic degeneration, in particular of Creutzfeldt-Jakob-Disease or Alzheimer's Disease, and to the use of β-synuclein as a biomarker for diagnosing or assessing the status of diseases associated with synaptic degeneration, in particular of Creutzfeldt-Jakob-Disease or Alzheimer's Disease.

Chemoproteomic methods for detecting and profiling electrophilic post-translational modifications (PTMs) and oxidative PTMs in proteins are described. The methods including contacting a proteomic mixture with a probe having hydrazine and an affinity handle to form a covalent linkage between the hydrazine moiety of the probe and the endogenous electrophilic PTM or the endogenous oxidative PTM. The resulting derivatized proteins are labelled with an tag via a click chemistry reaction. The labelled proteins can then be detected or profiled using techniques such as, for example, fluorescence imaging or mass spectrometry. Also described are protein conjugates having a covalent linkage formed by reaction of a hydrazine or oxyamine moiety of a probe with an electrophilic or oxidative PTM of a protein.

The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

A sample group forming section 24 classifies samples derived from microorganisms into groups according to empirical information showing the species or strain of each sample. A differential analysis section 27 performs a differential analysis using a peak matrix created based on the result of the grouping. An operator enters group rearrangement conditions concerning the drug resistance of microorganisms. Under the entered conditions, a sample group rearranging/rearrangement-cancelling section 25 rearranges the already formed groups by selecting or merging groups using another kind of previously registered empirical information which shows the drug resistance of each group. The differential analysis section 27 performs a differential analysis using a peak matrix newly created based on the result of the rearrangement of the groups. Thus, differential analysis results concerning the resistance to different drugs can be sequentially acquired as the group rearrangement condition is successively changed.

Methods of determining the stoichiometry of a viral capsid and/or determining the heterogeneity of protein components in a viral capsid are disclosed.

The invention relates to peptide mass fingerprinting technique for the proteins such as Human insulin and insulin analogs. The insulin analogues can vary at least by one amino acid, which is elusive to distinguish by currently available analytical methods. The invention further allows sequence confirmation of the peptide wherein the run time of the method is forty minutes. This method could be applied for molecules up to 50 kDa.

The present invention is directed to methods for using particles (e.g, microparticulate, nanoparticulate; magnetic, non-magnetic) comprising surfaces comprising capture moieties as described herein, to remove an interference as described herein, or enrich biomarkers, prior to a diagnostic test.

Methods for achieving complete sequence coverage of monoclonal antibodies by trypsin digestion and dual-column LC-MS system are provided. The disclosed method improves upon current techniques for standard peptide mapping.

The invention provides a sample preparation method (100) comprising: providing a sample (10) comprising an organic molecule (20), wherein the organic molecule (20) comprises a target group (21), wherein the target group (21) is a nucleophilic group and/or an acidic group; a derivatization stage (110) comprising: derivatizing the target group (21) of the organic molecule (20) with a moiety (31) comprising one or more of (i) a hydrocarbon comprising group and (ii) a 3rd period atom comprising group, wherein the 3rd period atom is selected from the group consisting of Si, P, and S, thereby providing a derivatized organic molecule (30); a separation stage (120) comprising: subjecting the sample (10) to a separation process to provide a fraction (35) comprising the derivatized organic molecule (30); and a preparation stage (130) comprising: introducing the derivatized organic molecule (30) into a porous single crystal (40), to provide a derivatized organic molecule doped porous single crystal (50).