Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification

Ren, Annie; Diamandis, Eleftherios P.; Kulasingam, Vathany

doi:10.1016/j.mcpro.2021.100155

Cited by 46 publications

(59 citation statements)

References 167 publications

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“…Proteins play a role in determining the identity of a cell [ 13 ]. Cell function can be affected by abnormal polypeptide sequences, altered protein expression, or abnormal post-translational modifications.…”

Section: Proteomicsmentioning

confidence: 99%

“…The development of proteomics technologies has made it easier to identify protein biomarkers applied to tumor diagnosis. Current proteomics technologies can be categorized into antibody-, mass-spectrometry- (MS), and aptamer-based techniques [ 13 ]. In this chapter, we describe current proteomic technologies identifying bladder cancer biomarkers, including NMIBC.…”

Section: Proteomicsmentioning

confidence: 99%

“…Some proteins are much more abundant in some biological samples than others, leading to less abundant protein peaks that are almost invisible compared to the enormous peaks from the highly abundant ones. Therefore, there is inevitably a bias towards large amounts of protein in MS [ 13 ]. Several methods, such as nanoparticle-based methods, have been developed to remove the interfering proteins [ 32 ].…”

Section: Proteomicsmentioning

confidence: 99%

See 2 more Smart Citations

Proteomics for Early Detection of Non-Muscle-Invasive Bladder Cancer: Clinically Useful Urine Protein Biomarkers

Ahn

Kang

Kim

et al. 2022

Life

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Bladder cancer is the fourth most common cancer in men, and most cases are non-muscle-invasive. A high recurrence rate is a critical problem in non-muscle-invasive bladder cancer. The availability of few urine tests hinders the effective detection of superficial and small bladder tumors. Cystoscopy is the gold standard for diagnosis; however, it is associated with urinary tract infections, hematuria, and pain. Early detection is imperative, as intervention influences recurrence. Therefore, urinary biomarkers need to be developed to detect these bladder cancers. Recently, several protein candidates in the urine have been identified as biomarkers. In the present narrative review, the current status of the development of urinary protein biomarkers, including FDA-approved biomarkers, is summarized. Additionally, contemporary proteomic technologies, such as antibody-based methods, mass-spectrometry-based methods, and machine-learning-based diagnosis, are reported. Furthermore, new strategies for the rapid and correct profiling of potential biomarkers of bladder cancer in urine are introduced, along with their limitations. The advantages of urinary protein biomarkers and the development of several related technologies are highlighted in this review. Moreover, an in-depth understanding of the scientific background and available protocols in research and clinical applications of the surveillance of non-muscle bladder cancer is provided.

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Section: Proteomicsmentioning

confidence: 99%

Section: Proteomicsmentioning

confidence: 99%

Section: Proteomicsmentioning

confidence: 99%

See 1 more Smart Citation

Proteomics for Early Detection of Non-Muscle-Invasive Bladder Cancer: Clinically Useful Urine Protein Biomarkers

Ahn

Kang

Kim

et al. 2022

Life

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“… 2 Last but not least, it estimates the protein expression levels in cells and tissues serving as a quantitative denominator common to all omics sciences. In contrast to popular immunodetection methods (e.g., enzyme-linked immunosorbent assay (ELISA) or Western blotting), 3 mass spectrometry quantifies proteins by comparing the abundance of endogenous quantotypic (Q)-peptides with corresponding synthetic peptide standards having the exactly known concentration. The protein concentration is then inferred from the concentrations of Q-peptides.…”

Section: Introductionmentioning

confidence: 99%

FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards

et al. 2022

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Absolute (molar) quantification of clinically relevant proteins determines their reference values in liquid and solid biopsies. The FastCAT (for Fast-track QconCAT) method employs multiple short (<50 kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated quantotypic (Q)-peptides representing the quantified proteins. Each CP also comprises scrambled sequences of reference (R)-peptides that relate its abundance to a single protein standard (bovine serum albumin, BSA). FastCAT not only alleviates the need to purify CP or use sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but also improves the accuracy, precision, and dynamic range of the absolute quantification by grouping Q-peptides according to the expected abundance of the target proteins. We benchmarked FastCAT against the reference method of MS Western and tested it in the direct molar quantification of neurological markers in human cerebrospinal fluid at the low ng/mL level.

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“…2 Last but not least, it estimates the proteins expression level in cells and tissues serving as a quantitative denominator common to all omics sciences. In contrast to popular immunodetection methods (e.g., ELISA or Western blotting), 3 mass spectrometry quantifies proteins by comparing the abundance of endogenous quantotypic (Q-)peptides with corresponding synthetic peptide standards having the exactly known concentration. The protein concentration is then inferred from the concentrations of Q-peptides.…”

Section: Introductionmentioning

confidence: 99%

FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standards

Rzagalinski

Bogdanova

Raghuraman

et al. 2021

Preprint

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Absolute (molar) quantification of proteins provides the analytical rationale for system-level modelling of diverse molecular mechanisms. FastCAT method employs multiple short (<50 kDa) stable-isotope labeled chimeric proteins (CPs) composed of concatenated quantotypic (Q-) peptides representing the quantified proteins. Each CP also comprises scrambled sequences of reference (R-) peptides that relate its abundance to a single protein standard (BSA). FastCAT not only alleviates the need in purifying CP or using SDS-PAGE, but also improves the accuracy, precision and dynamic range of the absolute quantifications by grouping Q-peptides according to the expected abundance of target proteins. We benchmarked FastCAT against the reference method of MS Western and tested it in the direct molar quantifications of neurological markers in human cerebrospinal fluid at the low ng/mL level.

show abstract

Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification

Cited by 46 publications

References 167 publications

Proteomics for Early Detection of Non-Muscle-Invasive Bladder Cancer: Clinically Useful Urine Protein Biomarkers

Proteomics for Early Detection of Non-Muscle-Invasive Bladder Cancer: Clinically Useful Urine Protein Biomarkers

FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards

FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standards

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