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Areas covered: Recent advances have developed methodologies to reduce the large protein concentration dynamic range of SF and subsequently allow deeper exploration of the SF proteome. This review concentrates on methods to overcome biofluid complexity, mass spectrometry proteomics methodologies, extracellular vesicles proteomics and the application of advances within the field in clinical disease, including osteoarthritis, rheumatoid arthritis, spondyloarthritis and juvenile arthritis. A narrative review was conducted with articles searched using PubMed, 1991–2018.
Expert opinion: The SF proteomics field faces various challenges, including the requirement for rigorous and standardised methods of sample collection/storage, the sensitivity and specificity of proteomic assays, techniques to combat the large protein concentration dynamic range and comprehensive data analysis to reduce falsely identified markers. Additionally, there are challenges in developing multi ‘omic’ integration techniques, with computational integration enhancing analysis. 相似文献
- •Targeted mass spectrometry assay to quantify prion protein (PrP) in spinal fluid.
- •Precise measurement of PrP peptide concentration across protein domains.
- •Peptides are uniformly decreased in symptomatic prion disease patients.
- •Assay applicable to humans and preclinical species for drug development.
- •Fast and culture-free method for the identification of the 15 bacterial species causing UTIs.
- •Combination of DIA analysis and machine learning algorithms to define a peptide signature.
- •High accuracy, good linearity and reproducibility, sensitivity below standard threshold.
- •Transferability to other laboratories and other mass spectrometers.
- •Method for the analysis of response curves from thermal proteome profiling (TPP).
- •NPARC uses nonparametric statistics and provides false discovery-rate (FDR) control.
- •Increased proteome coverage and sensitivity to identify drug-binding proteins.
- •Multiplex epitope mapping/antigenic determinant identification in the gas phase.
- •Intact transition and controlled dissociation of immune complexes by MS.
- •Simultaneous identification and amino acid sequence determination of epitopes.
- •Simplified in-solution sample handling because of ion manipulation and filtering by MS.
- •Retention time shift can lead to inversion of elution order of peptides.
- •Global alignment methods are suboptimal for alignment of distant runs.
- •DIAlignR employs hybrid (global + local) RT alignment approach.
- •DIAlignR can align swapped peaks accurately across distant runs.