Real-time search (RTS) for mass spectrometry is described. In one aspect, a mass spectrometer can identify a candidate peptide for a product ion spectrum by searching a mass spectral database. While executing the search of the mass spectral database, a candidate peptide score representing a confidence of a match between the product ion spectrum and a theoretical mass spectrum stored in the mass spectral database is generated. A failing score can be promoted to a passing result based on attributes of the candidate peptide.

The present disclosure relates to a group of peptide compounds and their use in identifying molecules that stimulate proteasome or immunoproteasome are disclosed herein. Composition matters and methods of uses are within the scope of this disclosure.

The combined use of natural-abundance stable-isotopic analysis of bulk materials and DNA genotyping of biological materials is a highly-specific (˜1:1×10.sup.17) fingerprinting method for identifying such products in supply chains.

A method for testing for the presence and quantification of A1-type beta-casein variants or A2-type beta-caseins, in milk and milk derived dairy products, using chymotrypsin digestion followed by LC-MS analysis to determining the concentrations of beta-casein digestion peptides and using the concentrations to calculate the amounts of A1-type beta-casein variants or A2-type beta-casein variants present.

The present disclosure provides a method for accurately measuring post-translational modifications in proteins such as antibodies. In particular, the method pertains to the use of heavy isotopic standards to generate a calibration curve to allow for accurate quantitation of a modified peptide. The method may be used to accurately quantify C-terminal truncation in antibodies using mass spectrometry.

The present disclosure relates generally to the analysis of immune checkpoint proteins involved in cancer. In particular, the present disclosure provides material and methods for determining abundance ratios of various immune checkpoint proteins (e.g., PD-1, PD-L1, and PD-L2) present in a biospecimen sample based on quantification of peak area using mass spectrometry analysis. The methods disclosed herein provide an alternative platform for diagnosing and treating cancer, especially in cases limited by ineffective antibody recognition.

The present disclosure provides “all-in-one” cartridges which contain necessary reagents and materials to isolate/preconcentrate targeted proteins from blood plasma and ionize them for mass spectrometry detection. In another configuration, the cartridges include proteolytic enzymes to digest the proteins into smaller peptides in addition to preconcentration and ionization for mass spectrometry detection.

Bead-based analytical assays suitable for detecting changes in the abundance of target analytes in biological samples are disclosed. In an embodiment, an assay involves incubating a sample with one or several beads that are capable of binding several distinct analytes in an amount sufficient for detection by mass spectrometry from a single bead.

The present invention is directed to a mass spectrometry approach to identifying non-Spitzoid melanoma, and distinguishing non-Spitzoid nevi from non-Spitzoid malignant melanoma.

A method for characterizing a target peptide through a detection approach such as mass spectrometry is provided, including: introducing at least one guard molecule to mix with the target peptide; and applying the detection approach for the characterization of the target peptide. Each guard molecule is configured to have similar characteristics as the target peptide, yet is still distinguishable therefrom by the detection approach, such as having a mass spectrometry-distinguishable different M/z value compared with the target peptide. The method can be used to characterize a neoantigen peptide through mass spectrometry, upstream of which the method can further include steps for tissue sample preparation, HLA molecules enrichment, elution, clean-up, and purification. Some or all of these steps can be configured to be executed in a substantially automatic manner with little or no manual intervention. A system for implementing the neoantigen analysis method is further provided.