Pleural effusion lipoproteins measured by NMR spectroscopy for diagnosis of exudative pleural effusions: a novel tool for pore-size estimation.

Abstract:

:High-resolution proton nuclear magnetic resonance (NMR) spectrometry of biofluids has been increasingly used in laboratory diagnosis of various diseases. In this study, we extended the use of (1)H NMR spectroscopy for laboratory diagnosis of exudative pleural effusions using pleural fluids. We compared this new NMR-based test with Light's criteria, the current gold standard for laboratory diagnosis of exudative pleural effusions. We analyzed 67 samples of pleural effusions from patients with pulmonary malignancy (N = 32), pulmonary tuberculosis (N = 18), and congestive heart failure (N = 17). The metabolomes of pleural effusions were analyzed using (1)H NMR spectroscopy on a Bruker 600 MHz spectrometer. Through a metabolome-wide association approach with filtering of insignificant markers (p value <4 × 10(-6)) and multivariate analysis (principal component analysis and orthogonal partial least squares-discriminant analysis), lipoprotein was found to be the best biomarker that distinguished exudates from transudates. Using NMR-based lipoprotein profiling to classify exudative pleural effusions from transudates, the area-under-receiver operating characteristic (ROC) curve was 0.96 with sensitivity of 98%, specificity of 88%, and accuracy of 98%. In contrast, the current gold standard, Light's criteria, give a specificity of only 65% at the same sensitivity level of 98%. Using the principle of size exclusion, NMR-based lipoprotein profiling of pleural fluids has an unprecedented diagnostic performance superiority over the Light's criteria. The capillary leaks secondary to inflammation result in a larger pleural pore-size, which allows the large-sized lipoproteins to accumulate in exudative pleural effusions. In contrast, the pleural permeability is intact in transudates, which allow only small-sized lipoproteins to pass into the pleural effusions. The average capillary pore-size of the pleura can therefore be determined by using NMR-based lipoprotein profiling of pleural fluids. We believe this new test will change the current clinical practice for management of pleural effusions and will become a new standard for clinical practice.

journal_name

J Proteome Res

authors

Lam CW,Law CY

doi

10.1021/pr5004856

subject

Has Abstract

pub_date

2014-09-05 00:00:00

pages

4104-12

issue

9

eissn

1535-3893

issn

1535-3907

journal_volume

13

pub_type

杂志文章
  • S-nitrosoproteome in endothelial cells revealed by a modified biotin switch approach coupled with Western blot-based two-dimensional gel electrophoresis.

    abstract::NO-mediated S-nitrosation of cysteine residues has been recognized as a fundamental post-translational modification. S-Nitrosation of endothelial cell (EC) proteins can alter function and affect vascular homeostasis. Trace amounts of S-nitrosoproteins in endothelial cells (ECs) in vivo coupled with lability of the S-n...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr9005662

    authors: Huang B,Liao CL,Lin YP,Chen SC,Wang DL

    更新日期:2009-10-01 00:00:00

  • Detergent-based but gel-free method allows identification of several hundred membrane proteins in single LC-MS runs.

    abstract::Detergents are indispensable solubilizing agents in the purification and analysis of membrane proteins. For mass spectrometric identification of proteins, it is essential that detergents are removed prior to analysis, necessitating an in-gel digestion step. Here, we report a procedure that allows use of detergents and...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800412j

    authors: Nagaraj N,Lu A,Mann M,Wiśniewski JR

    更新日期:2008-11-01 00:00:00

  • Proteomic Analysis of Peripheral Blood Mononuclear Cells after a High-Fat, High-Carbohydrate Meal with Orange Juice.

    abstract::Oxidative stress and inflammation play a role in the physiopathology of insulin resistance, diabetes and cardiovascular disease. A single high-fat, high-carbohydrate (HFHC) meal induces an increase in inflammatory and oxidative stress markers in peripheral blood mononuclear cells (PBMC). Previous studies have shown th...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00476

    authors: Chaves DFS,Carvalho PC,Brasili E,Rogero MM,Hassimotto NA,Diedrich JK,Moresco JJ,Yates JR 3rd,Lajolo FM

    更新日期:2017-11-03 00:00:00

  • Worker honeybee sterility: a proteomic analysis of suppressed ovary activation.

    abstract::Eusocial behavior is extensively studied in the honeybee, Apis mellifera, as it displays an extreme form of altruism. Honeybee workers are generally obligatory sterile in a bee colony headed by a queen, but the inhibition of ovary activation is lifted upon the absence of queen and larvae. Worker bees are then able to ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201222s

    authors: Cardoen D,Ernst UR,Boerjan B,Bogaerts A,Formesyn E,de Graaf DC,Wenseleers T,Schoofs L,Verleyen P

    更新日期:2012-05-04 00:00:00

  • Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches.

    abstract::Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200092z

    authors: Zarei M,Sprenger A,Metzger F,Gretzmeier C,Dengjel J

    更新日期:2011-08-05 00:00:00

  • Circulating Lamin B1 (LMNB1) biomarker detects early stages of liver cancer in patients.

    abstract::Hepatocellular carcinoma (HCC) is a major liver malignancy possessing a high mortality rate and is particularly prevalent in China and Asia. While surgery is the most effective treatment for liver tumor, about 80% of HCC patients are inoperable at presentation and die early due to late diagnosis. For early cancer dete...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr9002118

    authors: Sun S,Xu MZ,Poon RT,Day PJ,Luk JM

    更新日期:2010-01-01 00:00:00

  • Analysis of detergent-insoluble and whole cell lysate fractions of resting neutrophils using high-resolution mass spectrometry.

    abstract::Neutrophilic granulocytes play a major role in the initiation and resolution of the inflammatory response, and demonstrate significant transcriptional and translational activity. Although much was known about neutrophils prior to the introduction of proteomics, the use of MS-based methodologies has provided an unprece...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1000253

    authors: Tomazella GG,daSilva I,Thomé CH,Greene LJ,Koehler CJ,Thiede B,Wiker HG,de Souza GA

    更新日期:2010-04-05 00:00:00

  • Identification of Api88 Binding Partners in Escherichia coli Using a Photoaffinity-Cross-Link Strategy and Label-Free Quantification.

    abstract::Gene-encoded antimicrobial peptides (AMPs) kill bacteria very efficiently by either lytic mechanisms or inhibition of specific bacterial targets. Proline-rich AMPs (PrAMPs), for example, produced in insects and mammals rely on the second mechanism. They bind to the 70 kDa bacterial heat shock protein DnaK and the 60 k...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00283

    authors: Volke D,Krizsan A,Berthold N,Knappe D,Hoffmann R

    更新日期:2015-08-07 00:00:00

  • Analysis of genomic and proteomic data using advanced literature mining.

    abstract::High-throughput technologies, such as proteomic screening and DNA micro-arrays, produce vast amounts of data requiring comprehensive analytical methods to decipher the biologically relevant results. One approach would be to manually search the biomedical literature; however, this would be an arduous task. We developed...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0340227

    authors: Hu Y,Hines LM,Weng H,Zuo D,Rivera M,Richardson A,LaBaer J

    更新日期:2003-07-01 00:00:00

  • In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.

    abstract::Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. H...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500196b

    authors: Beck DB,Narendra V,Drury WJ 3rd,Casey R,Jansen PW,Yuan ZF,Garcia BA,Vermeulen M,Bonasio R

    更新日期:2014-12-05 00:00:00

  • Proteomic analysis of high-grade dysplastic cervical cells obtained from ThinPrep slides using laser capture microdissection and mass spectrometry.

    abstract::The purpose of this discovery phase study was to identify candidate protein biomarkers for high-grade dysplastic cervical cells using mass spectrometry. Laser Capture Microdissection (LCM) was utilized to isolate high-grade dysplastic and normal cells from ThinPrep slides prepared from cervical cytological specimens. ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070319j

    authors: Gu Y,Wu SL,Meyer JL,Hancock WS,Burg LJ,Linder J,Hanlon DW,Karger BL

    更新日期:2007-11-01 00:00:00

  • Characterization of amyloid beta peptides in cerebrospinal fluid by an automated immunoprecipitation procedure followed by mass spectrometry.

    abstract::Pathogenic events in Alzheimer's disease are believed to involve an imbalance between the production and clearance of the neurotoxic 42 amino acid form of the beta-amyloid peptide (Abeta1-42). Although much is known about the production of Abeta1-42, many questions remain about its degradation. Here, we describe an op...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0703627

    authors: Portelius E,Tran AJ,Andreasson U,Persson R,Brinkmalm G,Zetterberg H,Blennow K,Westman-Brinkmalm A

    更新日期:2007-11-01 00:00:00

  • A new form of crystalline rubisco and the conversion to its common dodecahedral form.

    abstract::In this paper, we present a new purification procedure that yields a new crystalline form of rubisco and has enabled us to completely remove this most abundant protein from tobacco leaf extract. The crystals formed within 48 h after refrigeration at 4 degrees C at pH 5.6. However, these crystals were not well-ordered ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr025548e

    authors: Kwanyuen P,Allina SM,Weissinger AK,Wilson RF

    更新日期:2002-09-01 00:00:00

  • Phosphoproteome exploration reveals a reformatting of cellular processes in response to low sterol biosynthetic capacity in Arabidopsis.

    abstract::Sterols are membrane-bound isoprenoid lipids that are required for cell viability and growth. In plants, it is generally assumed that 3-hydroxy-3-methylglutaryl-CoA-reductase (HMGR) is a key element of their biosynthesis, but the molecular regulation of that pathway is largely unknown. In an attempt to identify regula...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201127u

    authors: Heintz D,Gallien S,Compagnon V,Berna A,Suzuki M,Yoshida S,Muranaka T,Van Dorsselaer A,Schaeffer C,Bach TJ,Schaller H

    更新日期:2012-02-03 00:00:00

  • Proteomic analysis of hearts from Akita mice suggests that increases in soluble epoxide hydrolase and antioxidative programming are key changes in early stages of diabetic cardiomyopathy.

    abstract::Cardiovascular disease is the leading cause of diabetic morbidity with more than 10% of type 1 diabetes mellitus (T1DM) patients dying before they are 40 years old. This study utilized Akita mice, a murine model with T1DM progression analogous to that of humans. Diabetic cardiomyopathy in Akita mice presents as cardia...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr4004739

    authors: Dewey S,Lai X,Witzmann FA,Sohal M,Gomes AV

    更新日期:2013-09-06 00:00:00

  • AKT1 and AKT2 induce distinct phosphorylation patterns in HL-1 cardiac myocytes.

    abstract::The protein kinase AKT is a central kinase in the heart and has a major impact on growth/hypertrophy, survival/apoptosis, and metabolism. To gain more insight into AKT isoform-specific signaling at the molecular level, we investigated the phosphoproteome of HL-1 cardiomyocytes carrying AKT1 or AKT2 isoform-specific kn...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500131g

    authors: Reinartz M,Raupach A,Kaisers W,Gödecke A

    更新日期:2014-10-03 00:00:00

  • Elucidation of glycoprotein structures by unspecific proteolysis and direct nanoESI mass spectrometric analysis of ZIC-HILIC-enriched glycopeptides.

    abstract::Protein glycosylation was explored by direct nanoESI MS and MS/MS analysis of ZIC-HILIC-enriched proteolytic glycopeptides without further separation or purification. In a previous publication, we demonstrated that a direct MS-based analysis of proteolytic glycopeptides is feasible for a number of proteins (Henning , ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101082c

    authors: Neue K,Mormann M,Peter-Katalinić J,Pohlentz G

    更新日期:2011-05-06 00:00:00

  • Characterization of the Interactome of the Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 2 Reveals the Hyper Variable Region as a Binding Platform for Association with 14-3-3 Proteins.

    abstract::Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to the swine industry worldwide and hence global food security, exacerbated by a newly emerged highly pathogenic (HP-PRRSV) strain from China. PRRSV nonstructural protein 2 (nsp2) is a multifunctional polypeptide with strain-dependent influe...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00396

    authors: Xiao Y,Wu W,Gao J,Smith N,Burkard C,Xia D,Zhang M,Wang C,Archibald A,Digard P,Zhou EM,Hiscox JA

    更新日期:2016-05-06 00:00:00

  • Integrative Genomic and Proteomic Analysis of the Response of Lactobacillus casei Zhang to Glucose Restriction.

    abstract::Nutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. As next-generation sequencing technology has greatly advanced, we performed proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00886

    authors: Yu J,Hui W,Cao C,Pan L,Zhang H,Zhang W

    更新日期:2018-03-02 00:00:00

  • Acute phencyclidine treatment induces extensive and distinct protein phosphorylation in rat frontal cortex.

    abstract::Phencyclidine (PCP), a noncompetitive N-methyl-D-aspartate receptor antagonist, induces psychotomimetic effects in humans and animals. Administration of PCP to rodents is used as a preclinical model for schizophrenia; however, the molecular mechanisms underlying the symptoms remain largely unknown. Acute PCP treatment...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr4010794

    authors: Palmowski P,Rogowska-Wrzesinska A,Williamson J,Beck HC,Mikkelsen JD,Hansen HH,Jensen ON

    更新日期:2014-03-07 00:00:00

  • Primary cell cultures arising from normal kidney and renal cell carcinoma retain the proteomic profile of corresponding tissues.

    abstract::Renal cell carcinoma (RCC) tissue is composed of a mixture of neoplastic and normal cells, which complicate proteome analysis. The aim of our study was to investigate whether it is feasible to establish primary cell cultures of RCC and of renal cortex maintaining the tissue phenotype along with a more homogeneous and ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050002o

    authors: Perego RA,Bianchi C,Corizzato M,Eroini B,Torsello B,Valsecchi C,Di Fonzo A,Cordani N,Favini P,Ferrero S,Pitto M,Sarto C,Magni F,Rocco F,Mocarelli P

    更新日期:2005-09-01 00:00:00

  • Investigating the dynamic nature of the interactions between nuclear proteins and histones upon DNA damage using an immobilized peptide chemical proteomics approach.

    abstract::As a result of the complexity and dynamic range of the cellular proteome, including mutual interactions and interactions with other molecules, focused proteomic approaches are important to study subsets of physiologically important proteins. In one such approach, a small molecule or part of a protein is immobilized on...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060278b

    authors: Dirksen EH,Pinkse MW,Rijkers DT,Cloos J,Liskamp RM,Slijper M,Heck AJ

    更新日期:2006-09-01 00:00:00

  • MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.

    abstract::Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most wide...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500202e

    authors: Dorfer V,Pichler P,Stranzl T,Stadlmann J,Taus T,Winkler S,Mechtler K

    更新日期:2014-08-01 00:00:00

  • Speeding Up Percolator.

    abstract::The processing of peptide tandem mass spectrometry data involves matching observed spectra against a sequence database. The ranking and calibration of these peptide-spectrum matches can be improved substantially using a machine learning postprocessor. Here, we describe our efforts to speed up one widely used postproce...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00288

    authors: Halloran JT,Zhang H,Kara K,Renggli C,The M,Zhang C,Rocke DM,Käll L,Noble WS

    更新日期:2019-09-06 00:00:00

  • Phospho-iTRAQ: assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry.

    abstract::The ability to distinguish between phosphopeptides of high and low stoichiometry is essential to discover the true extent of protein phosphorylation. We here extend the strategy whereby a peptide sample is briefly split in two identical parts and differentially labeled preceding the phosphatase treatment of one part. ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500889v

    authors: Glibert P,Meert P,Van Steendam K,Van Nieuwerburgh F,De Coninck D,Martens L,Dhaenens M,Deforce D

    更新日期:2015-02-06 00:00:00

  • Global Analysis of Protein Lysine Succinylation Profiles and Their Overlap with Lysine Acetylation in the Marine Bacterium Vibrio parahemolyticus.

    abstract::Protein lysine acylation, including acetylation and succinylation, has been found to be a major post-translational modification (PTM) and is associated with the regulation of cellular processes that are widespread in bacteria. Vibrio parahemolyticus is a model marine bacterium that causes seafood-borne illness in huma...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00485

    authors: Pan J,Chen R,Li C,Li W,Ye Z

    更新日期:2015-10-02 00:00:00

  • Pilot phase I/II personalized therapy trial for metastatic colorectal cancer: evaluating the feasibility of protein pathway activation mapping for stratifying patients to therapy with imatinib and panitumumab.

    abstract::This nonrandomized phase I/II trial assessed the efficacy/tolerability of imatinib plus panitumumab in patients affected by metastatic colorectal cancer (mCRC) after stratification to treatment by selection of activated imatinib drug targets using reverse-phase protein array (RPPA). mCRC patients presenting with a bio...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr401267m

    authors: Pierobon M,Silvestri A,Spira A,Reeder A,Pin E,Banks S,Parasido E,Edmiston K,Liotta L,Petricoin E

    更新日期:2014-06-06 00:00:00

  • Two-dimensional liquid chromatography-tandem mass spectrometry coupled with isobaric tags for relative and absolute quantification (iTRAQ) labeling approach revealed first proteome profiles of pulmonary alveolar macrophages infected with porcine reproduct

    abstract::Porcine reproductive and respiratory syndrome (PRRS) has devastated the pig industry worldwide for almost 25 years, and its virus (PRRSV) preferentially infects and replicates in pulmonary alveolar macrophages (PAMs). To discover cellular protein responses in PRRSV-infected PAMs, two-dimensional liquid chromatography-...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201266z

    authors: Lu Q,Bai J,Zhang L,Liu J,Jiang Z,Michal JJ,He Q,Jiang P

    更新日期:2012-05-04 00:00:00

  • Imaging mass spectrometry-based molecular histology differentiates microscopically identical and heterogeneous tumors.

    abstract::Many tumors display significant cellular heterogeneity as well as molecular heterogeneity. Sensitive biomarkers that differentiate between diagnostically challenging tumors must contend with this heterogeneity. Mass spectrometry-based molecular histology of a patient series of heterogeneous, microscopically identical ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr301190g

    authors: Jones EA,Schmitz N,Waaijer CJ,Frese CK,van Remoortere A,van Zeijl RJ,Heck AJ,Hogendoorn PC,Deelder AM,Altelaar AF,Bovée JV,McDonnell LA

    更新日期:2013-04-05 00:00:00

  • Beyond linker histones and high mobility group proteins: global profiling of perchloric acid soluble proteins.

    abstract::Extraction with HClO(4) provides an easy method for efficient enrichment of both histone H1 and HMG proteins from a variety of tissues. Usually, the histone and the HMG proteins are the most abundant components of the extracts, however, other proteins have frequently been observed but only seldom studied in more detai...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050415p

    authors: Zougman A,Wiśniewski JR

    更新日期:2006-04-01 00:00:00