New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report. (Q47203339)

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5 April 2020

title

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report (English)

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5 April 2020

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5 April 2020

Jessica Lasky-Su

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5 April 2020

Angela J Rogers

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5 April 2020

Brent W Winston

series ordinal

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American Thoracic Society Workgroup on Metabolomics and Proteomics

series ordinal

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publication date

1 December 2017

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Proceedings of the American Thoracic Society

5 April 2020

published in

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volume

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issue

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page(s)

1721-1743

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Profiling of ARDS pulmonary edema fluid identifies a metabolically distinct subset.

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26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Personal omics profiling reveals dynamic molecular and medical phenotypes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Using control genes to correct for unwanted variation in microarray data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MetSign: a computational platform for high-resolution mass spectrometry-based metabolomics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MetaboLab--advanced NMR data processing and analysis for metabolomics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Proteomic profiling of S-acylated macrophage proteins identifies a role for palmitoylation in mitochondrial targeting of phospholipid scramblase 3.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Identification of novel diagnostic biomarkers for asthma and chronic obstructive pulmonary disease.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Metabolomics applied to urine samples in childhood asthma; differentiation between asthma phenotypes and identification of relevant metabolites.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

AStream: an R package for annotating LC/MS metabolomic data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Metabolomic profiling of asthma: Diagnostic utility of urine nuclear magnetic resonance spectroscopy

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

A tissue-specific atlas of mouse protein phosphorylation and expression

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Metabolomic Analysis and Visualization Engine for LC−MS Data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma 1H-nuclear magnetic resonance quantitative metabolomics and computational analysis

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

An integrative systems biology approach to understanding pulmonary diseases

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

(1)H nuclear magnetic resonance metabolomics analysis identifies novel urinary biomarkers for lung function

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Identification of lipocalin and apolipoprotein A1 as biomarkers of chronic obstructive pulmonary disease

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

rNMR: open source software for identifying and quantifying metabolites in NMR spectra

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

apLCMS--adaptive processing of high-resolution LC/MS data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Mass spectrometric analysis of biomarkers and dilution markers in exhaled breath condensate reveals elevated purines in asthma and cystic fibrosis

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Quantitative proteomics analysis of macrophage rafts reveals compartmentalized activation of the proteasome and of proteasome-mediated ERK activation in response to lipopolysaccharide.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Calgranulin B (S100A9) levels in bronchoalveolar lavage fluid of patients with interstitial lung diseases.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Proteomic analysis in lung tissue of smokers and COPD patients

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Significance analysis of spectral count data in label-free shotgun proteomics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Serum amyloid a is a biomarker of acute exacerbations of chronic obstructive pulmonary disease

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Chemometrics in metabonomics.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Adjusting batch effects in microarray expression data using empirical Bayes methods

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Exhaled breath condensate: methodological recommendations and unresolved questions.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorption/ionization-mass spectrometry profiling with mass spectrometric protein identification

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Proteomic analysis of pulmonary edema fluid and plasma in patients with acute lung injury.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Can we discover novel pathways using metabolomic analysis?

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

A genomic and proteomic analysis of activation of the human neutrophil by lipopolysaccharide and its mediation by p38 mitogen-activated protein kinase.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Determination of low-molecular-mass antioxidant concentrations in human respiratory tract lining fluids

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Application of a new method for analysis of exhaled gas in critically ill patients.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Metabolic regulation of gene transcription in mammals

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5946579

Accurate, fully-automated NMR spectral profiling for metabolomics

26 August 2018

1 reference

https://api.crossref.org/works/10.1513%2FANNALSATS.201710-770WS

Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1513%2FANNALSATS.201710-770WS

Targeted metabolomics identifies perturbations in amino acid metabolism that sub-classify patients with COPD

21 January 2018

1 reference

https://api.crossref.org/works/10.1513%2FANNALSATS.201710-770WS

Metabolic profiling detects biomarkers of protein degradation in COPD patients

21 January 2018

1 reference

https://api.crossref.org/works/10.1513%2FANNALSATS.201710-770WS

Estimation of volume of epithelial lining fluid recovered by lavage using urea as marker of dilution

21 January 2018

1 reference

12 December 2020

Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis

1 reference

12 December 2020

Proteomic studies on receptor for advanced glycation end product variants in idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease

1 reference

12 December 2020

Metabolites as global regulators: a new view of protein regulation: systematic investigation of metabolite-protein interactions may help bridge the gap between genome-wide association studies and small molecule screening studies

1 reference

12 December 2020

Heat shock protein 27 and cyclophilin A associate with the pathogenesis of COPD

1 reference

12 December 2020

Separating smoking-related diseases using NMR-based metabolomics of exhaled breath condensate

1 reference

12 December 2020

Metabolomics pilot study to identify volatile organic compound markers of childhood asthma in exhaled breath

1 reference

12 December 2020

Imaging mass spectrometry: Molecular microscopy for the new age of biology and medicine

1 reference

12 December 2020

10.1513/ANNALSATS.201710-770WS

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29192815%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29192815%20AND%20SRC:MED&resulttype=core&format=json

5 April 2020

PubMed publication ID

29192815

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29192815%20AND%20SRC:MED&resulttype=core&format=json