The invention provides methods for predicting whether compounds are cardiotoxic by analyzing their effects on the ratios of concentrations of metabolites in cultured heart muscle cells.

A separation device separates an unknown intact mAb or reduced mAb subunits of a known mAb class from a sample. M An ion source device ionizes the mAb. A mass spectrometer fragments the ionized mAb using an ECD device and mass analyzes resulting product ions using a mass analyzer, producing one or more product ion spectra. Theoretical product ion peaks are calculated for one or more constant portions of the mAb class. The theoretical product ion peaks are removed from the one or more product ion spectra, producing one or more difference product ion spectra. De novo sequencing is applied to the one or more difference product ion spectra, producing one or more candidate sequences for one or more variable portions of the mAb. A genome database is searched for matches to the one or more candidate sequences, producing one or more matched sequences for the one or more variable portions.

The present invention relates to a method for the characterization of peptide:MHC binding polypeptides, e.g. by mass spectrometry and an analysis of the recognized peptide space, i.e. in order to identify peptides that can be bound in the context of their presentation by MHC, and those who cannot be bound.

The disclosure features systems and methods that include: exposing a biological sample to an ion beam that is incident on the sample at a first angle to a plane of the sample by translating a position of the ion beam on the sample in a first direction relative to a projection of a direction of incidence of the ion beam on the sample; after each translation of the ion beam in the first direction, adjusting a focal length of an ion source that generates the ion beam; and measuring and analyzing secondary ions generated from the sample by the ion beam after adjustment of the focal length to determine mass spectral information for the sample, where the sample is labeled with one or more mass tags and the mass spectral information includes populations of the mass tags at locations of the sample.

The invention relates to selection of precursors from a measured mobility-mass map for tandem mass spectrometry and is based on processing a peak list from measured signals and clustering these peaks in the mobility-mass space.

Certain embodiments are directed to methods for preparing or processing FFPE samples for subsequent analysis of antibodies or other proteins contained within the FFPE sample. In certain aspects, preparing or processing a FFPE sample can include, but is not limited to (i) deparaffinizing a portion of the FFPE specimen, (ii) decrosslinking the deparaffinized sample portion, (iii) homogenizing the decrosslinked portion, and (iv) fractionating the homogenized portion, wherein isolated antibodies or proteins having a higher order structure that can be bound by capture agents, e.g., immunoglobulin capture agents.

The present disclosure relates to methods of improved identification of peptides, for example, antigenic peptides. In particular, the present disclosure relates to methods of more accurately identifying human leukocyte antigen (HLA) peptides by utilizing classification systems. The disclosure also provides for utilizing the described methods for the field of personalized cancer therapies, such as adoptive cellular therapy (ACT).

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.

Provided herein are surfactant compounds that can be used to aid in preparation of protein samples for analysis, for example by mass spectrometry.

The present invention provides methods and systems for isotyping and quantification of antibodies based on immunocapture and/or Liquid Chromatography-Mass Spectrometry (LC-MS) analysis. These antibodies are induced by the administration of pharmaceutical products. The immunocapture method comprises contacting samples with a solid support, wherein the pharmaceutical product has been cross-linked directly to the solid support. The MS analysis includes conducting peptide mapping, selecting unique peptides and fragment ions to generate MRM (multiple reaction monitoring) transitions, optimizing collision energy, and determining a LLOQ (lower limit of quantification).