The present invention provides glycated Amadori products of the CD59 peptide and fragments thereof to be used as tools and among methods for the diagnosis and prognosis of pre-diabetes and diabetes. Certain aspects of the invention include glycated Amadori products of CD59 and fragments thereof to be used for the generation of antibodies and antibody fragments. Still other aspects of the invention include methodologies for the preparation of glycated Amadori products of CD59, fragments thereof, the inventive antibodies, and antibody fragments.

Provided herein are methods of preparing a protein sample for proteomic analysis. In exemplary embodiments, the method comprises (a) contacting a blood sample comprising proteins with a protective agent comprising an anticoagulant (AC) and an aldehyde releaser (AR), to obtain a mixture, optionally, wherein the blood sample is added to a blood collection tube (BCT) comprising the protective agent, and (b) isolating a fraction comprising proteins or a source of proteins from the mixture to yield a protein sample or a source of a protein sample, wherein steps of the method are carried out in the absence of exogenous proteolytic enzyme inhibitors, wherein the protein sample is suitable for proteomic and peptidomic analysis.

The invention relates to the measurement and profiling of proteins including phosphoproteins from cells in particular the measurement and profiling of phosphoproteins involved in cancer.

This disclosure relates to methods of preparing re-usable and dry-able cartridges comprising matrices comprising a detection molecule such as an antibody, for detection or enrichment of an analyte in a sample, such as an antigen recognized by an antibody. In some embodiments, the cartridge comprises a tube or well that holds the matrix. In some embodiments, the matrix or associated cartridges may be stored wet or dry. The disclosure also relates to the cartridges and methods of their use.

Methods are provided for making rapid labeled dextran ladders and other calibrants useful in liquid chromatography. The methodologies include a two-step process comprising a reductive amination step of providing a reducing glycan and reacting it with a compound having a primary amine to produce an intermediate compound. The intermediate compound is then rapidly tagged with a rapid tagging reagent to produce the rapid labeled dextran ladder.

Methods for peptide and/or protein quantification by mass spectrometry using labeled peptides, wherein multiple labels lead to distinct fragments for the labeled peptides and their unlabeled variant, thus facilitating data analysis and enhancing the potential for quantification. Methods for selecting the label and label position are further given, as well as sets of labeled peptides resulting from or for use in the above-mentioned methods. The methods and substances are especially useful for data-independent or multiplexed parallel reaction monitoring proteomics applications involving peptide quantification.

Provided herein are methods, assays and devices for the differential diagnosis and detection of disease progression of autoimmune diseases. The methods, assays and devices provided herein produce and analyze binding patterns of peripheral-blood antibodies on mimetic peptide arrays that differentiate autoimmune diseases, and identify patients progressing to internal organ complications such as interstitial lung disease (ILD), and gastric antral vascular ectasia (GAVE), or renal involvement.

It is provided a reversible streptavidin based analyte enrichment system for use in crosslinking mass spectrometry analysis, in particular for enriching at least parts of crosslinked peptides pairs in mass spectrometry analysis, and a method of enriching at least parts of crosslinked peptides pairs, in particular for use in crosslinking mass spectroscopy analysis.

Systems and methods for determining amino acid sequences of peptides that bind to MHC-I or HLA-I complex or MHC-II or HLA-II complex are provided. One embodiment includes isolating peptides from MHC or HLA class I or class II-peptide complexes and adding one or more known labeled peptides of interest to form a sample containing labeled peptides and unlabeled isolated peptides. The method also includes analyzing the sample with an LC-MS/MS system to obtain sequence data of the peptides, and increasing the sensitivity of the LC-MS/MS system when the labeled peptide is detected by the LC-MS/MS system. The method then concludes with determining the amino acid sequence of the unlabeled peptides in an m/z range that includes the m/z of the labeled peptide. The system can be triggered to increase the sensitivity in or near the m/z of the labeled peptide using an algorithm or computer program.

A detection system for the interaction between known molecules and proteins based on covalent connection and an identification or verification method thereof are disclosed. The detection system comprises: a) streptavidin-short peptide tetramer; b) PafA enzyme; and c) Biotin-modified known molecules. After a known molecule interacts with a protein, streptavidin-short peptide tetramer can efficiently capture interacting proteins of known molecules under mild conditions. Then, under the catalysis of PafA enzyme, the interaction between short peptides and known molecules is made into protein covalent binding, so that the non-covalent binding between known molecules and proteins is converted into covalent binding between streptavidin and protein, and then analysis, separation and identification are carried out. This method can capture weak interaction and instantaneous interaction on the basis of keeping the natural structure of known molecules, which can be used to verify and discover known molecules and interacting proteins.