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1. 1H HR-MAS NMR Spectroscopy of Tumor-Induced Local Metabolic “Field-Effects” Enables Colorectal Cancer Staging and Prognostication

Author:
Jiménez Beatriz; Mirnezami Reza; Kinross James; Cloarec Olivier; Keun Hector C.; Holmes Elaine; Goldin Robert D.; Ziprin Paul; Darzi Ara; Nicholson Jeremy K.
Source:
Journal of Proteome Research 2013 v.12 no.2 pp. 959-968
ISSN:
1535-3907
Subject:
biomarkers; carcinogenesis; choline; colorectal neoplasms; discriminant analysis; lactic acid; least squares; metabolism; metabolites; metabolomics; models; morbidity; mortality; mucosa; nuclear magnetic resonance spectroscopy; patients; phenylalanine; quantitative analysis; resection; taurine; triacylglycerols; tyrosine
Abstract:
... Colorectal cancer (CRC) is a major cause of morbidity and mortality in developed countries. Despite operative advances and the widespread adoption of combined-modality treatment, the 5-year survival rarely exceeds 60%. Improving our understanding of the biological processes involved in CRC development and progression will help generate new diagnostic and prognostic approaches. Previous studies hav ...
DOI:
10.1021/pr3010106

2. 1H NMR Derived Metabolomic Profile of Neonatal Asphyxia in Umbilical Cord Serum: Implications for Hypoxic Ischemic Encephalopathy

Author:
Reinke Stacey N.; Walsh Brian H.; Boylan Geraldine B.; Sykes Brian D.; Kenny Louise C.; Murray Deirdre M.; Broadhurst David I.
Source:
Journal of Proteome Research 2013 v.12 no.9 pp. 4230-4239
ISSN:
1535-3907
Subject:
3-hydroxybutyric acid; acetone; asphyxia; biochemical pathways; blood serum; disease severity; encephalopathy; energy metabolism; glycerol; hypoxia; hypoxia-inducible factor 1; infants; metabolites; metabolome; multivariate analysis; nuclear magnetic resonance spectroscopy; succinic acid; umbilical cord
Abstract:
... Neonatal hypoxic ischemic encephalopathy (HIE) is a severe consequence of perinatal asphyxia (PA) that can result in life-long neurological disability. Disease mechanisms, including the role and interaction of individual metabolic pathways, remain unclear. As hypoxia is an acute condition, aerobic energy metabolism is central to global metabolic pathways, and these metabolites are detectable using ...
DOI:
10.1021/pr400617m

3. 1H NMR Global Metabolic Phenotyping of Acute Pancreatitis in the Emergency Unit

Author:
Villaseñor Alma; Kinross James M.; Li Jia V.; Penney Nicholas; Barton Richard H.; Nicholson Jeremy K.; Darzi Ara; Barbas Coral; Holmes Elaine
Source:
Journal of Proteome Research 2014 v.13 no.12 pp. 5362-5375
ISSN:
1535-3907
Subject:
alanine; alcohol drinking; biomarkers; cholelithiasis; choline; creatine; decision making; etiology; glucose; guanine; hospitals; inflammation; ketone bodies; lipoproteins; models; nuclear magnetic resonance spectroscopy; pain; pancreatitis; patients; phenotype; urine; valine
Abstract:
... We have investigated the urinary and plasma metabolic phenotype of acute pancreatitis (AP) patients presenting to the emergency room at a single center London teaching hospital with acute abdominal pain using ¹H NMR spectroscopy and multivariate modeling. Patients were allocated to either the AP (n = 15) or non-AP patients group (all other causes of abdominal pain, n = 21) on the basis of the nati ...
DOI:
10.1021/pr500161w

4. 1H NMR Serum Metabonomics for Understanding Metabolic Dysregulation in Women with Idiopathic Recurrent Spontaneous Miscarriage during Implantation Window

Author:
Banerjee Priyanka; Dutta Mainak; Srivastava Sudha; Joshi Mamata; Chakravarty Baidyanath; Chaudhury Koel
Source:
Journal of Proteome Research 2014 v.13 no.6 pp. 3100-3106
ISSN:
1535-3907
Subject:
abortion (animals); arginine; blood serum; data analysis; discriminant analysis; endometrium; glutamine; histidine; inflammation; lysine; metabolites; metabolomics; nuclear magnetic resonance spectroscopy; pathogenesis; phenylalanine; pregnancy; principal component analysis; threonine; tyrosine; women
Abstract:
... In an attempt to find out the association of metabolic dysregulation with poor endometrial receptivity and pregnancy loss, serum metabonomic profiling of women with idiopathic recurrent spontaneous miscarriage (IRSM) is carried out and compared with fertile controls. ¹H nuclear magnetic resonance (NMR)-based metabonomics was used to obtain serum metabolic profiles of 36 women with IRSM and 28 prov ...
DOI:
10.1021/pr500379n

5. 1H NMR Spectroscopy of Fecal Extracts Enables Detection of Advanced Colorectal Neoplasia

Author:
Amiot Aurelien; Dona Anthony C.; Wijeyesekera Anisha; Tournigand Christophe; Baumgaertner Isabelle; Lebaleur Yann; Sobhani Iradj; Holmes Elaine
Source:
Journal of Proteome Research 2015 v.14 no.9 pp. 3871-3881
ISSN:
1535-3907
Subject:
Clostridium leptum; acetates; blood serum; butyrates; colorectal neoplasms; correlation; developing countries; fatty acid composition; glucose; glutamic acid; glutamine; hematologic tests; intestinal microorganisms; magnetism; metabolites; metabolomics; methylation; models; mortality; nuclear magnetic resonance spectroscopy; patients; phenotype; prediction; propionic acid; proteome; quantitative polymerase chain reaction; screening; short chain fatty acids; urine; variance
Abstract:
... Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its etiopathogenesis and earlier diagnosis. Here, we investigated the fecal metabolic phenotype of patients with advanced colorectal neoplasia and controls using ¹H-nuclear magnetic resonance (NMR) spectroscopy and multivariate modeling. The fecal microbiota composition was assessed by qu ...
DOI:
10.1021/acs.jproteome.5b00277

6. 1H NMR Spectroscopy of Serum Reveals Unique Metabolic Fingerprints Associated with Subtypes of Surgically Induced Osteoarthritis in Sheep

Author:
Maher Anthony D.; Coles Chantal; White Jason; Bateman John F.; Fuller Emily S.; Burkhardt Dan; Little Christopher B.; Cake Martin; Read Richard; McDonagh Matthew B.; Rochfort Simone Jane
Source:
Journal of Proteome Research 2012 v.11 no.8 pp. 4261-4268
ISSN:
1535-3907
Subject:
animal models; animals; anterior cruciate ligament; biochemical pathways; biomarkers; blood serum; branched chain amino acids; data analysis; data collection; discriminant analysis; experimental design; human diseases; least squares; metabolomics; nuclear magnetic resonance spectroscopy; osteoarthritis; principal component analysis; proteome; spectral analysis; surgery
Abstract:
... Osteoarthritis (OA) is a highly prevalent joint disease. Its slow progressive nature and the correlation between pathological changes and clinical symptoms mean that OA is often well advanced by the time of diagnosis. In the absence of any specific pharmacological treatments, there is a pressing need to develop robust biomarkers for OA. We have adopted a nuclear magnetic resonance (NMR)-based meta ...
DOI:
10.1021/pr300368h

7. 1H NMR Study on the Short- and Long-Term Impact of Two Training Programs of Sprint Running on the Metabolic Fingerprint of Human Serum

Author:
Pechlivanis Alexandros; Kostidis Sarantos; Saraslanidis Ploutarchos; Petridou Anatoli; Tsalis George; Veselkov Kirill; Mikros Emmanuel; Mougios Vassilis; Theodoridis Georgios A.
Source:
Journal of Proteome Research 2013 v.12 no.1 pp. 470-480
ISSN:
1535-3907
Subject:
acetoacetic acid; acetone; alanine; arginine; blood serum; citrates; exercise; glucose; glycoproteins; histidine; humans; isoleucine; lactic acid; leucine; lipids; long term effects; lysine; men; metabolism; metabolites; metabolomics; models; nuclear magnetic resonance spectroscopy; proteome; pyruvic acid; sports; taurine; trimethylamine; valine
Abstract:
... Metabonomics is an established strategy in the exploration of the effects of various stimuli on the metabolic fingerprint of biofluids. Here, we present an application of ¹H NMR-based metabonomics on the field of exercise biochemistry. Fourteen men were assigned to either of two training programs, which lasted 8 weeks and involved sets of 80-m maximal runs separated by either 10 s or 1 min of rest ...
DOI:
10.1021/pr300846x

8. 1H NMR To Evaluate the Metabolome of Bronchoalveolar Lavage Fluid (BALf) in Bronchiolitis Obliterans Syndrome (BOS): Toward the Development of a New Approach for Biomarker Identification

Author:
Ciaramelli Carlotta; Fumagalli Marco; Viglio Simona; Bardoni Anna Maria; Piloni Davide; Meloni Federica; Iadarola Paolo; Airoldi Cristina
Source:
Journal of Proteome Research 2017 v.16 no.4 pp. 1669-1682
ISSN:
1535-3907
Subject:
amino acids; biomarkers; bronchiolitis; disaccharides; inflammation; lungs; metabolites; metabolome; models; monitoring; nuclear magnetic resonance spectroscopy; nucleotides; patients; phospholipids; prediction; proteome; screening; statistical analysis; tricarboxylic acid cycle
Abstract:
... This report describes the application of NMR spectroscopy to the profiling of metabolites in bronchoalveolar lavage fluid (BALf) of lung transplant recipients without bronchiolitis obliterans syndrome (BOS) (stable, S, n = 10), and with BOS at different degrees of severity (BOS 0p, n = 10; BOS I, n = 10). Through the fine-tuning of a number of parameters concerning both sample preparation/processi ...
DOI:
10.1021/acs.jproteome.6b01038

9. 1H NMR To Explore the Metabolome of Exhaled Breath Condensate in α1-Antitrypsin Deficient Patients: A Pilot Study

Author:
Airoldi Cristina; Ciaramelli Carlotta; Fumagalli Marco; Bussei Rita; Mazzoni Valeria; Viglio Simona; Iadarola Paolo; Stolk Jan
Source:
Journal of Proteome Research 2016 v.15 no.12 pp. 4569-4578
ISSN:
1535-3907
Subject:
acetates; acetoin; condensates; discriminant analysis; least squares; metabolism; metabolites; metabolome; metabolomics; nuclear magnetic resonance spectroscopy; patients; principal component analysis; propionic acid; proteome; pulmonary emphysema; pyruvic acid; therapeutics
Abstract:
... The metabolomic analysis of exhaled breath condensate (EBC) may provide insights on both the pathology of pulmonary disorders and the response to therapy. This pilot study describes the ability of nuclear magnetic resonance (NMR)-based metabolomics to discriminate α1-antitrypsin deficient (AATD)-patients, who were diagnosed with moderate to severe emphysema, from healthy individuals. Comparative a ...
DOI:
10.1021/acs.jproteome.6b00648

10. 1H NMR-Based Global Metabolic Studies of Pseudomonas aeruginosa upon Exposure of the Quorum Sensing Inhibitor Resveratrol

Author:
Chen Tongtong; Sheng Jiyang; Fu Yonghong; Li Minghui; Wang Junsong; Jia Ai-Qun
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 824-830
ISSN:
1535-3907
Subject:
Pseudomonas aeruginosa; amino acids; anaerobiosis; antioxidant activity; cytotoxicity; drugs; energy; gene expression; gene expression regulation; metabolic studies; metabolites; nuclear magnetic resonance spectroscopy; oxidative stress; protein synthesis; proteome; pyocyanin; quorum sensing; resveratrol; tricarboxylic acid cycle; virulence
Abstract:
... Quorum sensing (QS) is a process of bacterial communication that has been a novel target for drug discovery. Pyocyanin quantification assay confirmed that resveratrol was an effective quorum sensing inhibitor (QSI) against Pseudomonas aeruginosa PAO1. In this study, the global metabolite changes of P. aeruginosa PAO1 exposed to QSI resveratrol were investigated by ¹H NMR spectroscopy. A total of 4 ...
DOI:
10.1021/acs.jproteome.6b00800

11. 1H NMR-Based Urinary Metabolic Profiling Reveals Changes in Nicotinamide Pathway Intermediates Due to Postnatal Stress Model in Rat

Author:
Tomassini Alberta; Vitalone Annabella; Marini Federico; Praticò Giulia; Sciubba Fabio; Bevilacqua Marta; Delfini Maurizio; Di Sotto Antonella; Di Giacomo Silvia; Mariani Paola; Mammola Caterina L.; Gaudio Eugenio; Miccheli Alfredo; Mazzanti Gabriela
Source:
Journal of Proteome Research 2014 v.13 no.12 pp. 5848-5859
ISSN:
1535-3907
Subject:
NAD (coenzyme); adulthood; analysis of variance; digestive system; females; lactulose; mannitol; metabolomics; models; nicotinamide; nuclear magnetic resonance spectroscopy; permeability; proteome; pups; rats; tryptophan; urinalysis; weaning
Abstract:
... The maternal separation protocol in rodents is a widely recognized model of early life stress allowing acute and chronic physiological consequences to be studied. An ¹H NMR-based metabolomic approach was applied to urines to evaluate the systemic metabolic consequences of maternal separation stress in female rats after the beginning of weaning and 4 weeks later when the rats were reaching adulthoo ...
DOI:
10.1021/pr500748r

12. 1H NMR-Linked Metabolomics Analysis of Liver from a Mouse Model of NP-C1 Disease

Author:
Ruiz-Rodado Victor; Nicoli Elena-Raluca; Probert Fay; Smith David A.; Morris Lauren; Wassif Christopher A.; Platt Frances M.; Grootveld Martin
Source:
Journal of Proteome Research 2016 v.15 no.10 pp. 3511-3527
ISSN:
1535-3907
Subject:
animal models; biochemical pathways; biomarkers; biosynthesis; data collection; fibrosis; glutamic acid; glutamine; heterozygosity; inosine; liver; lysine; metabolomics; methionine; mice; mutants; nicotinamide; nuclear magnetic resonance spectroscopy; ornithine; pathogenesis; patients; phenylalanine; proteome; threonine; topology; tyrosine; valine
Abstract:
... Clinical manifestations of Niemann–Pick type C1 (NP-C1) disease include neonatal hepatosplenomegaly and in some patients progressive liver dysfunction and failure. This study involved a ¹H NMR-linked metabolomics analysis of liver samples collected from a NP-C1 disease mutant mouse model in order to explore time-dependent imbalances in metabolic pathways associated with NP-C1 liver dysfunction, in ...
DOI:
10.1021/acs.jproteome.6b00238

13. IL- 6 Linkage to Exercise-Induced Shifts in Lipid-Related Metabolites: A Metabolomics-Based Analysis

Author:
Nieman David C.; Sha Wei; Pappan Kirk L.
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 970-977
ISSN:
1535-3907
Subject:
adipose tissue; beta oxidation; bioinformatics; biopsy; blood sampling; carnitine; cortisol; dicarboxylic acids; epinephrine; equations; exercise; exercise equipment; glycogen; interleukin-6; interleukin-8; ketone bodies; lipolysis; males; medium chain fatty acids; metabolomics; models; muscles; proteome
Abstract:
... Metabolomics profiling and bioinformatics technologies were used to determine the relationship between exercise-induced increases in IL-6 and lipid-related metabolites. Twenty-four male runners (age 36.5 ± 1.8 y) ran on treadmills to exhaustion (2.26 ± 0.01 h, 24.9 ± 1.3 km, 69.7 ± 1.9% VO₂ₘₐₓ). Vastus lateralis muscle biopsy and blood samples were collected before and immediately after running an ...
DOI:
10.1021/acs.jproteome.6b00892

14. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

Author:
Choi Meena; Eren-Dogu Zeynep F.; Colangelo Christopher; Cottrell John; Hoopmann Michael R.; Kapp Eugene A.; Kim Sangtae; Lam Henry; Neubert Thomas A.; Palmblad Magnus; Phinney Brett S.; Weintraub Susan T.; MacLean Brendan; Vitek Olga
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 945-957
ISSN:
1535-3907
Subject:
computer software; data collection; liquid chromatography; proteins; proteome; statistical analysis; tandem mass spectrometry; uncertainty
Abstract:
... Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography–tandem mass spectrometry (LC–MS/MS) experiments requires a series of computational steps that identify and quantify LC–MS features. It also requires statistical analyses that distinguish systematic changes in abundance between conditions from artifacts of biological and technical variation. The 2 ...
DOI:
10.1021/acs.jproteome.6b00881

15. AFFIRMA Multiplexed Immunoaffinity Platform That Combines Recombinant Antibody Fragments and LC-SRM Analysis

Author:
Säll Anna; Carlsson Fredrika; Olsson Niclas; Wingren Christer; Ohlin Mats; Persson Helena; Waldemarson Sofia
Source:
Journal of Proteome Research 2014 v.13 no.12 pp. 5837-5847
ISSN:
1535-3907
Subject:
automation; biomarkers; blood serum; proteins; proteome; recombinant antibodies
Abstract:
... Targeted measurements of low abundance proteins in complex mixtures are in high demand in many areas, not the least in clinical applications measuring biomarkers. We here present the novel platform AFFIRM (AFFInity sRM) that utilizes the power of antibody fragments (scFv) to efficiently enrich for target proteins from a complex background and the exquisite specificity of SRM-MS based detection. To ...
DOI:
10.1021/pr500757s

16. AKT1 and AKT2 Induce Distinct Phosphorylation Patterns in HL-1 Cardiac Myocytes

Author:
Reinartz Michael; Raupach Annika; Kaisers Wolfgang; Gödecke Axel
Source:
Journal of Proteome Research 2014 v.13 no.10 pp. 4232-4245
ISSN:
1535-3907
Subject:
apoptosis; calcium channels; calcium-binding proteins; cardiomyocytes; heat shock proteins; hypertrophy; insulin; isotope labeling; mammals; mass spectrometry; metabolism; phosphopeptides; phosphoproteins; phosphorylation; protein kinases; proteome; proteomics; rapamycin; stable isotopes
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 knock down, respectively. We combined stable isotope labeling with high resolution ...
DOI:
10.1021/pr500131g

17. The Absence of Heat Shock Protein HSP101 Affects the Proteome of Mature and Germinating Maize Embryos

Author:
Lázaro-Mixteco Pedro E.; Nieto-Sotelo Jorge; Swatek Kirby N.; Houston Norma L.; Mendoza-Hernández Guillermo; Thelen Jay J.; Dinkova Tzvetanka D.
Source:
Journal of Proteome Research 2012 v.11 no.6 pp. 3246-3258
ISSN:
1535-3907
Subject:
enzymes; seedlings; mass spectrometry; proteome; heat stress; actin; molecular weight; imbibition; Zea mays; messenger RNA; corn; root growth; proteomics; heat shock proteins; seed germination; translation (genetics); protein synthesis; embryo (plant); cytokinins; mutants
Abstract:
... Maize heat shock protein HSP101 accumulates during embryo maturation and desiccation and persists at high levels during the first 24 h following kernel imbibition in the absence of heat stress. This protein has a known function in disaggregation of high molecular weight complexes and has been proposed to be a translational regulator of specific mRNAs. Here, a global proteomic approach was used to ...
DOI:
10.1021/pr3000046

18. Absolute Proteome Analysis of Colorectal Mucosa, Adenoma, and Cancer Reveals Drastic Changes in Fatty Acid Metabolism and Plasma Membrane Transporters

Author:
Wiśniewski Jacek R.; Duś-Szachniewicz Kamila; Ostasiewicz Paweł; Ziółkowski Piotr; Rakus Dariusz; Mann Matthias
Source:
Journal of Proteome Research 2015 v.14 no.9 pp. 4005-4018
ISSN:
1535-3907
Subject:
DNA replication; adenoma; colorectal neoplasms; death; energy metabolism; enterocytes; enzymes; fatty acid metabolism; metastasis; patients; physiological transport; plasma membrane; principal component analysis; proteome; proteomics; transporters
Abstract:
... Colorectal cancer is a leading cause of cancer-related death. It develops from normal enterocytes, through a benign adenoma stage, into the cancer and finally into the metastatic form. We previously compared the proteomes of normal colorectal enterocytes, cancer and nodal metastasis to a depth of 8100 proteins and found extensive quantitative remodeling between normal and cancer tissues but not ca ...
DOI:
10.1021/acs.jproteome.5b00523

19. Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation

Author:
Liao Yalin; Weber Darren; Xu Wei; Durbin-Johnson Blythe P.; Phinney Brett S.; Lönnerdal Bo
Source:
Journal of Proteome Research 2017 v.16 no.11 pp. 4113-4121
ISSN:
1535-3907
Subject:
alpha-casein; amino acid composition; beta-casein; bioactive properties; breast milk; cattle; infant formulas; kappa-casein; lactation; protein content; proteome; quantitative analysis; regression analysis; whey; whey protein
Abstract:
... Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analys ...
DOI:
10.1021/acs.jproteome.7b00486

20. Absolute Quantitation of Low Abundance Plasma APL1β peptides at Sub-fmol/mL Level by SRM/MRM without Immunoaffinity Enrichment

Author:
Sano Shozo; Tagami Shinji; Hashimoto Yuuki; Yoshizawa-Kumagaye Kumiko; Tsunemi Masahiko; Okochi Masayasu; Tomonaga Takeshi
Source:
Journal of Proteome Research 2014 v.13 no.2 pp. 1012-1020
ISSN:
1535-3907
Subject:
Alzheimer disease; acetonitrile; albumins; antibodies; blood proteins; blood serum; cation exchange; chromatography; ions; monitoring; peptides; precipitin tests; proteome; spectrometers
Abstract:
... Selected/multiple reaction monitoring (SRM/MRM) has been widely used for the quantification of specific proteins/peptides, although it is still challenging to quantitate low abundant proteins/peptides in complex samples such as plasma/serum. To overcome this problem, enrichment of target proteins/peptides is needed, such as immunoprecipitation; however, this is labor-intense and generation of anti ...
DOI:
10.1021/pr4010103