In this protocol we describe the separation of collagen crosslinks in biological tissues and samples including skin, tendon, cartilage, bone and urine. The existing methods use either cation exchange chromatography followed by post-column derivatization with ninhydrin or reverse phase chromatography with mass spectrometry detection. The cation exchange chromatography method has limited sensitivity and long run times while reverse phase chromatography requires strong ion-pairing. In this method, the sample containing crosslinks is applied on a diamond hydride column using water and acetonitrile solvents containing 0.1% (w/v) formic acid. Eight crosslinks are eluted separately from the column and detected by mass spectrometry in the sub-pmol range. By using this method, it is possible to separate all crosslinks of collagen in several biological samples without the need for ion-pairing agent or derivatization for detection.
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http://dx.doi.org/10.21769/BioProtoc.3224 | DOI Listing |
J Proteome Res
January 2025
The First Affiliated Hospital of Ningbo University, Ningbo315010, P.R. China.
Lung adenocarcinoma (LUAD) is the most common histological subtype of nonsmall-cell lung cancer. Herein, a multiomics method, which combined proteomic and N-glycoproteomic analyses, was developed to analyze the normal and cancerous bronchoalveolar lavage fluids (BALFs) from six LUAD patients to identify potential biomarkers of LUAD. The data-independent acquisition proteomic analysis was first used to analyze BALFs, which identified 59 differentially expressed proteins (DEPs).
View Article and Find Full Text PDFKidney360
November 2024
The Departments of Medicine, Veterans Affairs Palo Alto Healthcare System and Stanford University, Palo Alto, CA, USA 94304.
Background: Hemodialysis may excessively remove valuable solutes. Untargeted metabolomics data from a prior study suggested that ergothioneine was depleted in the plasma of hemodialysis subjects. Ergothioneine is a dietary-derived solute with antioxidant properties.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
January 2025
Department of Chemistry, Center for Innovative Technology, Vanderbilt University, Nashville, Tennessee 37235, United States.
Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this "Fast-Pass" DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ∼40 s per sample.
View Article and Find Full Text PDFPLoS One
January 2025
Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
Non-covalent protein-protein interactions are one of the most fundamental building blocks in cellular signalling pathways. Despite this, they have been historically hard to identify using conventional methods due to their often weak and transient nature. Using genetic code expansion and incorporation of commercially available unnatural amino acids, we have developed a highly accessible method whereby interactions between biotinylated ubiquitin-like protein (UBL) probes and their binding partners can be stabilised using ultraviolet (UV) light-induced crosslinks.
View Article and Find Full Text PDFEnviron Sci Technol
January 2025
National High Magnetic Field Laboratory Geochemistry Group and Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida 32306, United States.
Intensification of wastewater treatment residual (i.e., biosolid) applications to watersheds can alter the amount and composition of organic matter (OM) mobilized into waterways.
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