Methods for derivatization of biomolecules including glycans or other biopolymers with one or more fluorescent, MS active compounds by reductive amination or rapid tagging in order to produce derivatized glycan having a pKa >7 and between about 200 Å and about 1000 Å of nonpolar surface area are described.

Provided is a method for analyzing a sample containing a sialic-acid-containing glycan including a sialic-acid-linkage specific modification, based on mass spectrum data of the sample, including steps of: detecting, from the mass spectrum data, a representative peak for each isotope peak cluster; detecting, from the representative peaks, an isomer peak cluster including multiple ion peaks estimated to be identical in the number of sialic acids and the glycan composition exclusive of the sialic acids; estimating a glycan composition for each representative peak according to predetermined glycan search conditions; creating a mass spectrum with an annotation added for each isomer peak cluster to indicate a correspondence between each peak in one cluster and a peak in a mass spectrum, and displaying the annotated mass spectrum on a display section; and creating a table relating each estimated glycan-composition candidate to an isomer peak cluster, and displaying the table on the display section.

The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the ALK, Ros, Ron, Ret, TS, and/or FGFR1 proteins that are particularly advantageous for quantifying the ALK, Ros, Ron, Ret, TS, and/or FGFR1 proteins directly in biological samples that have been fixed in formalin by the methods of Selected Reaction Monitoring (SRM) mass spectrometry, or as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein the biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from the biological sample using the Liquid Tissue™ reagents and protocol and the ALK, Ros, Ron, Ret, TS, and/or FGFR1 proteins are quantitated in the Liquid Tissue™ sample by the method of SRM/MRM mass spectrometry, by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of an ALK, Ros, Ron, Ret, TS, and/or FGFR1 fragment peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.

Detecting glycosaminoglycans (GAGs) and/or determining the level of one or more glycosaminoglycans can be useful, e.g., in identifying or monitoring various medical conditions, the status of patients having various medical conditions, and/or the response to treatment of individuals having various medical conditions. The present invention provides methods for detecting glycosaminoglycans and/or determining the level of glycosaminoglycans through the use of, e.g., mass spectrometry.

Provided are methods of detecting the presence or amount of a vitamin D metabolite in a sample using mass spectrometry. The methods generally directed to ionizing a vitamin D metabolite in a sample and detecting the amount of the ion to determine the presence or amount of the vitamin D metabolite in the sample. Also provided are methods to detect the presence or amount of two or more vitamin D metabolites in a single assay.

Disclosed herein are methods for tracking solutions, (e.g., reaction conditions in solutions). In some embodiments, the method comprises: contacting a first lanthanide-chelator complex to a first solution to generate a first barcoded solution, wherein the first lanthanide-chelator complex comprises a first lanthanide chelated by a first chelator; contacting a second lanthanide-chelator complex to a second solution to generate a second barcoded solution, wherein the second lanthanide-chelator complex comprises a second lanthanide chelated by a second chelator; mixing the first barcoded solution and the second barcoded solution to form one or more mixtures; and identifying the first lanthanide ions in the mass spectrum and the second lanthanide ions in the mass spectrum to track the condition of each of the one or more mixtures.

Provided herein is synthesis of a novel acidic acid residue targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker. The novel mass spectrometry-cleavable cross-linking agents can be used in mass spectrometry to facilitate structural analysis of intra-protein interactions in proteins and inter-protein interactions in protein complexes. Also disclosed herein are data based on the novel MS-cleavable homobifunctional cross-linker that are complimentary to amine-reactive sulfoxide-containing MS-cleavable reagents.

Peptide and/or protein quantitation methods, kits, and compositions, particularly useful for mass spectrometry, are provided herein based on a bathocuproine-based composition complex such as bathocuproinedisulfonic acid disodium salt hydrate complex. The methods are one-step rapid absorbance methods using small sample volumes. They produce a robust signal with high signal to background ratio and accurately quantitate even complex peptide mixtures with low variability and high sensitivity.

Provided is a high-accuracy analysis method utilizing an enzyme-lined immunoassay. The presence of an analyte 3 can be detected or the abundance of the analyte 3 can be analyzed by: bonding an antibody 5 that is capable of specifically bonding to the analyte 3 immobilized on a solid phase 1 and has an enzyme 7 bonded thereto; then decomposing an enzyme substrate 8, which can generate decomposition products capable of being detected easily with a mass spectrometry, with the enzyme 7 bonded to the antibody 5; and then analyzing the decomposition products 9 and 10 with a mass spectrometry.

Described herein are sets of metabolite and lipid (e.g., fatty acid) markers that can be used in the detection of early stage colorectal cancer and/or early development of adenomatous polyps. Presented herein are illustrative pathology-linked panels. In certain embodiments, the markers presented herein (or subsets thereof) are used as a panel for detecting either colorectal cancer or adenomatous polyps at the same time. The markers presented herein include metabolites and lipids (e.g., fatty acid) freely detectable and accurately quantifiable in human serum. In certain embodiments, the sample may be plasma, urine, saliva, whole blood, dried blood spot or dried serum spot.