The present invention provides methods for improved label-free absolute quantification of relatively low abundant polypeptides by liquid chromatography/mass spectrometry analysis of peptide products obtained from simple or complex polypeptide mixtures. The methods for absolute quantification include MS signals from a set of qualified ions of peptide products of a relatively high abundant polypeptide to improve quantification of a relatively low abundant polypeptide.

The invention relates to an activated form of procaine, and the use of the activated procaine, or salts or solvates thereof, to label amine-containing compounds, such as N-glycans, amine-containing amino acids, amine-containing peptides, amine-containing proteins, or other amine-containing compounds in a sample. Use of activated procaine as a label allows for sensitive detection of compounds labeled with it both by fluorescence and by mass spectrometry.

Methods for identification and quantification of bile acids are disclosed. Bile acids in plasma, serum and/or blood such as a dried blood spot are used to identify subjects with a Niemann-Pick disease. The methods include measuring levels of a bile acid, such as 3β,5α,6β-trihydroxycholanic acid, N-(3β,5α,6β-trihydroxy-cholan-24-oyl)glycine, N-(3β,5α,6β-trihydroxy-cholan-24-oyl)taurine, or a combination thereof. Detection of bile acids involve mass spectroscopy and/or a combination of mass spectroscopy and liquid chromatography such as a LC-MS/MS assay. The methods can be used with sphingomyelinase assays to detect, diagnose and differentiate between Niemann-Pick A/B and Niemann-Pick C (NPC) disease.

Disclosed herein are methods for identifying novel drug candidates.

The present invention encompasses filamin A (FLNA) binding proteins. Specifically, the invention relates to antibodies to FLNA. An antibody of the invention can be a full-length antibody or an antigen-binding portion thereof. Methods of making and methods of using the antibodies of the invention in methods of diagnosis, monitoring and prognosis or prostate cancer are also provided.

This invention relates to a method of determining ligands of macromolecules, said method comprising or consisting of (a) subjecting a sample comprising (i) complexes formed by said macromolecules and said ligands and (ii) unbound ligands to a method which separates said complexes from said unbound ligands; (b) releasing ligands from complexes obtained in step (a); and (c) subjecting the released ligands obtained in step (b) to a chemical analysis method, thereby determining said ligands of said macromolecules.

This invention provides methods for the screening and identification of antigenic components in a tissue or organ of interest.

The invention provides an unbiased method to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells by applying the unbiased determination technique of SWATH-MS or the biased technique of SRM-MS to a thermal shift assay to evaluate drug target interactions. In addition, the results created by SWATH-MS can be analyzed by SRM-MS in a biased manner to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells.

The present invention provides specific peptide biomarkers and sets of peptide biomarkers for use in methods of detecting or identifying bacterial biomarkers in a sample, wherein said bacterial biomarkers can be used to detect Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, and/or Moraxella catarrhalis in a sample. Kits and diagnostic methods are also provided.

Methods and systems to perform genetically variant protein analysis and related marker genetic protein variations and databases, which in several embodiments allow performing a reliable genetic variation protein analysis in biological samples of different types and conditions taking into account the features of the biological sample where the analysis is performed.