Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Meyer, Jesse G.; Schilling, Birgit

doi:10.1080/14789450.2017.1322904

Cited by 131 publications

(115 citation statements)

References 82 publications

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“…The most common example is that untargeted assays which may observe thousands of peptide ions per experiment invariably have a lower limit of detection (LOD) and quantification (LOQ) compared to assays where a smaller number of ions are targeted. [21][22][23] Improvements in each subsequent generation of hardware can mitigate this compromise, but the improvement is limited. Today, the only way to truly offset this rule is to increase the total LCMS run time.…”

Section: Introductionmentioning

confidence: 99%

In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19

Orsburn

Jenkins

Miller

et al. 2020

Preprint

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The novel coronavirus disease first identified in 2019 in Wuhan, has become a serious global public health concern. One current issue is the ability to adequately screen for the virus causing COVID-2 (SARS-CoV-2). Here we demonstrate the feasibility of shotgun proteomics as a SARS-CoV-2 screening method, through the detection of viral peptides in proteolytically digested body fluids. Using in silico methods, we generated trypsin-based shotgun proteomics methods optimized for LCMS systems from 5 commercial instrument vendors (Thermo, SCIEX, Waters, Shimadzu, and Agilent). First, we generated protein FASTA files and their protein digest maps. Second, the FASTA files were used to generate spectral libraries based on experimental data. Third, transition lists were derived from the

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Section: Introductionmentioning

confidence: 99%

In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19

Orsburn

Jenkins

Miller

et al. 2020

Preprint

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“…Mass spectrometry (MS)‐based proteomics has dramatically improved and emerged as a prominent tool in the field of biomarker study. The development of isobaric tagging and targeted quantitative proteomic techniques makes the discovery of novel biomarkers feasible . Many protein biomarkers of IBD have been described and are categorized as primarily blood and fecal biomarkers .…”

Section: Introductionmentioning

confidence: 99%

“…The development of isobaric tagging and targeted quantitative proteomic techniques makes the discovery of novel biomarkers feasible. [9][10][11][12] Many protein biomarkers of IBD have been described and are categorized as primarily blood and fecal biomarkers. [13][14][15] Urine is an attractive resource for biomarker research that has been underutilized.…”

Section: Introductionmentioning

confidence: 99%

Urine Proteome Changes in a TNBS‐Induced Colitis Rat Model

Qin

Wang

et al. 2019

Proteomics Clinical Apps

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Purpose Urine is an important resource for biomarker research. Urine proteins reflect not only renal diseases but also changes in other organs in the body. However, urine has rarely been used to reflect on inflammatory bowel disease. Experimental Design In the present study, a trinitrobenzene sulfonic acid (TNBS)‐induced colitis rat model is used to mimic the human inflammatory bowel disease Crohn's disease (CD). Urine samples are analyzed by label‐free and TMT‐labeled proteomic quantitative methods. Results 77 urinary proteins are significantly changed in the colitis rats compared with that in the controls. These proteins are further validated by parallel reaction monitoring (PRM) targeted proteomic quantitative methods. Based on the human protein tissue atlas, carbonic anhydrase 1, ribonuclease pancreatic gamma type, and neutral and basic amino acid transport protein rBAT are highly enriched in the gastrointestinal tract. Among the nine PRM‐validated proteins, carbonic anhydrase 1, neutrophil collagenase, and neutrophil gelatinase associated lipocalin were previously reported as IBD‐associated proteins (all exhibiting consistent trends with the observation herein), whereas the others are newly discovered by this study. Conclusions and Clinical Relevance The results provide valuable clues for future study of urine biomarker of inflammatory bowel disease and Crohn's disease.

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“…Clinical proteomics mostly relies on the absolute quantification of targeted proteins or on global proteome quantification (Doherty and Whitfield, 2011;Meyer and Schilling, 2017). Although highly successful, this type of analysis does not reveal the synthesis and clearance rates behind the observed abundance.…”

Section: Introductionmentioning

confidence: 99%

In Vivo Large Scale Mapping Of Protein Turnover In The Human Cerebrospinal Fluid

Lehmann

Hirtz

Vialaret

et al. 2019

Preprint

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SummaryThe extraction of accurate physiological parameters from clinical samples provides a unique perspective to understand disease etiology and evolution, including under therapy. We introduce a new proteomics framework to map patient proteome dynamics in vivo, either proteome wide or in large targeted panels. We applied it to ventricular cerebrospinal fluid (CSF) and could determine the turnover parameters of almost 200 proteins, whereas a handful were known previously. We covered a large number of neuron biology- and immune system-related proteins including many biomarkers and drug targets. This first large data set unraveled a significant relationship between turnover and protein origin that relates to our ability to investigate the central nervous system physiology precisely in future studies. Our data constitute a reference in CSF biology as well as a repertoire of peptides for the community to design new proteome dynamics analyses. The disclosed methods apply to other fluids or tissues provided sequential sample collection can be performed.

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Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

Cited by 131 publications

References 82 publications

In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19

In silicoapproach toward the identification of unique peptides from viral protein infection: Application to COVID-19

Urine Proteome Changes in a TNBS‐Induced Colitis Rat Model

In Vivo Large Scale Mapping Of Protein Turnover In The Human Cerebrospinal Fluid

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