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Progenesis QI

The next generation in LC-MS data analysis software.
Discover the significantly changing compounds in your samples.

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Progenesis QI is the new name for Progenesis CoMet

Progenesis QI software references

2017

Abdelrazig S, Ortori CA, Davey G, Deressa W, Mulleta D, Barrett DA, Amberbir A, Fogarty AW (2017) A metabolomic analytical approach permits identification of urinary biomarkers for Plasmodium falciparum infection: a case-control study. Malar J 16:229

Artegoitia VM, Foote AP, Lewis RM, Freetly HC (2017) Rumen Fluid Metabolomics Analysis Associated with Feed Efficiency on Crossbred Steers. Sci Rep 7:2864

Bao W, Cao C, Li S, Bo L, Zhang M, Zhao X, Liu Y, Sun C (2017) Metabonomic analysis of quercetin against the toxicity of acrylamide in rat urine. Food Funct 8:1204-1214

Bozek K, Khrameeva EE, Reznick J, Omerbasic D, Bennett NC, Lewin GR, Azpurua J, Gorbunova V, Seluanov A, Regnard P, Wanert F, Marchal J, Pifferi F, Aujard F, Liu Z, Shi P, Paabo S, Schroeder F, Willmitzer L, Giavalisco P, Khaitovich P (2017) Lipidome determinants of maximal lifespan in mammals. Sci Rep 7:5

Cao J, Li M, Chen J, Liu P, Li Z (2016) Effects of MeJA on Arabidopsis metabolome under endogenous JA deficiency. Sci Rep 6:37674

Carey AN, Zhang W, Setchell KDR, Simmons JR, Shi T, Lages CS, Mullen M, Carroll K, Karns R, Bessho K, Sheridan R, Zhao X, Weber SN, Miethke AG (2017) Hepatic MDR3 expression impacts lipid homeostasis and susceptibility to inflammatory bile duct obstruction in neonates. Pediatr Res 82:122-132

Charkoftaki G, Chen Y, Han M, Sandoval M, Yu X, Zhao H, Orlicky DJ, Thompson DC, Vasiliou V (2017) Transcriptomic analysis and plasma metabolomics in Aldh16a1-null mice reveals a potential role of ALDH16A1 in renal function. Chem Biol Interact (In press)

Chen DQ, Cao G, Chen H, Liu D, Su W, Yu XY, Vaziri ND, Liu XH, Bai X, Zhang L, Zhao YY (2017) Gene and protein expressions and metabolomics exhibit activated redox signaling and wnt/beta-catenin pathway are associated with metabolite dysfunction in patients with chronic kidney disease. Redox Biol 12:505-521

Chen H, Chen L, Liu D, Chen DQ, Vaziri ND, Yu XY, Zhang L, Su W, Bai X, Zhao YY (2017) Combined Clinical Phenotype and Lipidomic Analysis Reveals the Impact of Chronic Kidney Disease on Lipid Metabolism. J Proteome Res 16:1566-1578

Chen XQ, Zhou CX, Elsheikha HM, He S, Hu GX, Zhu XQ (2017) Profiling of the perturbed metabolomic state of mouse spleen during acute and chronic toxoplasmosis. Parasit Vectors 10:339

Choo JM, Trim PJ, Leong LEX, Abell GCJ, Brune C, Jeffries N, Wesselingh S, Dear TN, Snel MF, Rogers GB (2017) Inbred Mouse Populations Exhibit Intergenerational Changes in Intestinal Microbiota Composition and Function Following Introduction to a Facility. Front Microbiol 8:608

Dorival-Garcia N, Larsson I, Bones J (2017) Non-volatile extractable analysis of prefilled syringes for parenteral administration of drug products. J Pharm Biomed Anal 142:337-342

Einarsdottir E, Magnusdottir M, Astarita G, Kock M, Ogmundsdottir HM, Thorsteinsdottir M, Rapp HT, Omarsdottir S, Paglia G (2017) Metabolic Profiling as a Screening Tool for Cytotoxic Compounds: Identification of 3-Alkyl Pyridine Alkaloids from Sponges Collected at a Shallow Water Hydrothermal Vent Site North of Iceland. Mar Drugs 15 (In press)

Eloy NB, Voorend W, Lan W, Saleme ML, Cesarino I, Vanholme R, Smith RA, Goeminne G, Pallidis A, Morreel K, Nicomedes J, Jr., Ralph J, Boerjan W (2017) Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content. Plant Physiol 173:998-1016

Fluck M, Ruoss S, Mohl CB, Valdivieso P, Benn MC, von Rechenberg B, Laczko E, Hu J, Wieser K, Meyer DC, Gerber C (2017) Genomic and lipidomic actions of nandrolone on detached rotator cuff muscle in sheep. J Steroid Biochem Mol Biol 165:382-395

Gagnebin Y, Tonoli D, Lescuyer P, Ponte B, de Seigneux S, Martin PY, Schappler J, Boccard J, Rudaz S (2017) Metabolomic analysis of urine samples by UHPLC-QTOF-MS: Impact of normalization strategies. Anal Chim Acta 955:27-35

Gethings LA, Richardson K, Wildgoose J, Lennon S, Jarvis S, Bevan CL, Vissers JPC, Langridge JI (2017) Lipid Profiling of Complex Biological Mixtures by Liquid Chromatography Mass Spectrometry Using a Novel Scanning Quadrupole Data Independent Acquisition Strategy. Rapid Commun Mass Spectrom (In press)

Guzman MK, Parween S, Butardo VM, Alhambra CM, Anacleto R, Seiler C, Bird AR, Chow CP, Sreenivasulu N (2017) Investigating glycemic potential of rice by unraveling compositional variations in mature grain and starch mobilization patterns during seed germination. Sci Rep 7:5854

Holt GS, Lodge JK, McCarthy AJ, Graham AK, Young G, Bridge SH, Brown AK, Veses-Garcia M, Lanyon CV, Sails A, Allison HE, Smith DL (2017) Shigatoxin encoding Bacteriophage varphi24B modulates bacterial metabolism to raise antimicrobial tolerance. Sci Rep 7:40424

Huang W, Robert CA, Herve MR, Hu L, Bont Z, Erb M (2017) A mechanism for sequence specificity in plant-mediated interactions between herbivores. New Phytol 214:169-179

Imasawa T, Obre E, Bellance N, Lavie J, Rigothier C, Delmas Y, Combe C, Lacombe D, Benard G, Claverol S, Bonneu M, Rossignol R (2017) High glucose repatterns human podocyte energy metabolism during differentiation and diabetic nephropathy. Faseb J 31:294-307

Jiang L, Gu H, Lin Y, Xu W, Zhu R, Kong J, Luo L, Long H, Liu B, Chen B, Zhao Y, Cen X (2017) Remodeling of brain lipidome in methamphetamine-sensitized mice. Toxicol Lett 279:67-76

Jing J, Shi Y, Zhang Q, Wang J, Ruan J (2017) Prediction of Chinese green tea ranking by metabolite profiling using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS). Food Chem 221:311-316

Jones JW, Carter CL, Li F, Yu J, Pierzchalski K, Jackson IL, Vujaskovic Z, Kane MA (2017) Ultraperformance convergence chromatography-high resolution tandem mass spectrometry for lipid biomarker profiling and identification. Biomed Chromatogr 31 (In press)

Kang LP, Huang YY, Zhan ZL, Liu DH, Peng HS, Nan TG, Zhang Y, Hao QX, Tang JF, Zhu SD, Yang G, Guo LP, Chen M, Huang LQ (2017) Structural characterization and discrimination of the Paris polyphylla var. yunnanensis and Paris vietnamensis based on metabolite profiling analysis. J Pharm Biomed Anal 142:252-261

Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O (2017) Identification of small molecules using accurate mass MS/MS search. Mass Spectrom Rev (In press)

Law KP, Han TL, Mao X, Zhang H (2017) Tryptophan and purine metabolites are consistently upregulated in the urinary metabolome of patients diagnosed with gestational diabetes mellitus throughout pregnancy: A longitudinal metabolomics study of Chinese pregnant women part 2. Clin Chim Acta 468:126-139

Law KP, Mao X, Han TL, Zhang H (2017) Unsaturated plasma phospholipids are consistently lower in the patients diagnosed with gestational diabetes mellitus throughout pregnancy: A longitudinal metabolomics study of Chinese pregnant women part 1. Clin Chim Acta 465:53-71

Law KP, Zhang H (2017) The pathogenesis and pathophysiology of gestational diabetes mellitus: Deductions from a three-part longitudinal metabolomics study in China. Clin Chim Acta 468:60-70

Li XN, Zhang A, Wang M, Sun H, Liu Z, Qiu S, Zhang T, Wang X (2017) Screening the active compounds of Phellodendri Amurensis cortex for treating prostate cancer by high-throughput chinmedomics. Sci Rep 7:46234

Lin L, Li H, Lin H, Zhang M, Qu C, Yan L, Yin X, Ni J (2017) A New Perspective on Liver Injury by Traditional Chinese Herbs Such As Polygonum multiflorum: The Geographical Area of Harvest As an Important Contributory Factor. Front Pharmacol 8:349

Lindner S, Gruhle K, Schmidt R, Garamus VM, Ramsbeck D, Hause G, Meister A, Sinz A, Drescher S (2017) Azide-Modified Membrane Lipids: Synthesis, Properties, and Reactivity. Langmuir 33:4960-4973

Lu S, Han Y, Chu H, Kong L, Zhang A, Yan G, Sun H, Wang P, Wang X (2017) Characterizing serum metabolic alterations of Alzheimer's disease and intervention of Shengmai-San by ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry. Food Funct 8:1660-1671

Mansfeld BN, Colle M, Kang Y, Jones AD, Grumet R (2017) Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici. Hortic Res 4:17022

Mnich E, Vanholme R, Oyarce P, Liu S, Lu F, Goeminne G, Jorgensen B, Motawie MS, Boerjan W, Ralph J, Ulvskov P, Moller BL, Bjarnholt N, Harholt J (2017) Degradation of lignin beta-aryl ether units in Arabidopsis thaliana expressing LigD, LigF and LigG from Sphingomonas paucimobilis SYK-6. Plant Biotechnol J 15:581-593

Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD (2017) Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics. Anal Chem 89:3517-3523

Noratto GD, Chew BP, Atienza LM (2017) Red raspberry (Rubus idaeus L.) intake decreases oxidative stress in obese diabetic (db/db) mice. Food Chem 227:305-314

O'Connor A, Brasher CJ, Slatter DA, Meckelmann SW, Hawksworth JI, Allen SM, O'Donnell VB (2017) LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets. JCI Insight 2:e91634

Pabst T, Kortz L, Fiedler GM, Ceglarek U, Idle JR, Beyoglu D (2017) The plasma lipidome in acute myeloid leukemia at diagnosis in relation to clinical disease features. BBA Clin 7:105-114

Paglia G, Astarita G (2017) Metabolomics and lipidomics using traveling-wave ion mobility mass spectrometry. Nat Protoc 12:797-813

Patel D, Thompson MD, Manna SK, Krausz KW, Zhang L, Nilubol N, Gonzalez FJ, Kebebew E (2017) Unique and Novel Urinary Metabolomic Features in Malignant versus Benign Adrenal Neoplasms. Clin Cancer Res (In press)

Pickens CA, Vazquez AI, Jones AD, Fenton JI (2017) Obesity, adipokines, and C-peptide are associated with distinct plasma phospholipid profiles in adult males, an untargeted lipidomic approach. Sci Rep 7:6335

Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I (2017) Integrated mass spectrometry imaging and omics workflows on the same tissue section using grid-aided, parafilm-assisted microdissection. Biochim Biophys Acta 1861:1702-1714

Randazzo GM, Tonoli D, Strajhar P, Xenarios I, Odermatt A, Boccard J, Rudaz S (2017) Enhanced metabolite annotation via dynamic retention time prediction: Steroidogenesis alterations as a case study. J Chromatogr B Analyt Technol Biomed Life Sci (In press)

Ribeiro MAS, Murgu M, Silva VM, Sawaya A, Ribeiro LF, Justi A, Meurer EC (2017) The screening of organic matter in mineral and tap water by UHPLC-HRMS. Talanta 174:581-586

Rochat B (2017) Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data. J Am Soc Mass Spectrom 28:709-723

Rosenmai AK, Bengtstrom L, Taxvig C, Trier X, Petersen JH, Svingen T, Binderup ML, Barbara Medea Alice VV, Dybdahl M, Granby K, Vinggaard AM (2017) An effect-directed strategy for characterizing emerging chemicals in food contact materials made from paper and board. Food Chem Toxicol 106:250-259

Salazar C, Jones MD, Sturtevant D, Horn PJ, Crossley J, Zaman K, Chapman KD, Wrona M, Isaac G, Smith NW, Shulaev V (2017) Development and application of sub-2-mum particle CO2 -based chromatography coupled to mass spectrometry for comprehensive analysis of lipids in cottonseed extracts. Rapid Commun Mass Spectrom 31:591-605

Sethi S, Brietzke E (2017) Recent advances in lipidomics: Analytical and clinical perspectives. Prostaglandins Other Lipid Mediat 128-129:8-16

Shang J, Castro-Perez JM, Shen X, Zhu Y, Liu H, Qian Y, Previs S, Howard AD, Erion M, Kelley DE, Wang L (2017) Duodenal-jejunal bypass surgery induces hepatic lipidomic alterations associated with ameliorated hepatic steatosis in mice. Obesity (Silver Spring) 24:1938-1945

Som NF, Heine D, Holmes NA, Munnoch JT, Chandra G, Seipke RF, Hoskisson PA, Wilkinson B, Hutchings MI (2017) The Conserved Actinobacterial Two-Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B-65442. Front Microbiol 8:1145

Steenackers W, Klima P, Quareshy M, Cesarino I, Kumpf RP, Corneillie S, Araujo P, Viaene T, Goeminne G, Nowack MK, Ljung K, Friml J, Blakeslee JJ, Novak O, Zazimalova E, Napier R, Boerjan W, Vanholme B (2017) cis-Cinnamic Acid Is a Novel, Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation. Plant Physiol 173:552-565

Tam ZY, Ng SP, Tan LQ, Lin CH, Rothenbacher D, Klenk J, Boehm BO (2017) Metabolite profiling in identifying metabolic biomarkers in older people with late-onset type 2 diabetes mellitus. Sci Rep 7:4392

Tipthara P, Kunacheva C, Soh YN, Wong SC, Pin NS, Stuckey DC, Boehm BO (2017) Global Profiling of Metabolite and Lipid Soluble Microbial Products in Anaerobic Wastewater Reactor Supernatant Using UPLC-MSE. J Proteome Res 16:559-570

Verplanken K, Stead S, Jandova R, Poucke CV, Claereboudt J, Bussche JV, Saeger S, Takats Z, Wauters J, Vanhaecke L (2017) Rapid evaporative ionization mass spectrometry for high-throughput screening in food analysis: The case of boar taint. Talanta 169:30-36

Wang J, Qi P, Hou J, Shen Y, Yang M, Bi Q, Deng Y, Shi X, Feng R, Feng Z, Wu W, Guo D (2017) The profiling of the metabolites of hirsutine in rat by ultra-high performance liquid chromatography coupled with linear ion trap Orbitrap mass spectrometry: An improved strategy for the systematic screening and identification of metabolites in multi-samples in vivo. J Pharm Biomed Anal 134:149-157

Wen B, Mei Z, Zeng C, Liu S (2017) metaX: a flexible and comprehensive software for processing metabolomics data. BMC Bioinformatics 18:183

Wu JL, Zhou CX, Wu PJ, Xu J, Guo YQ, Xue F, Getachew A, Xu SF (2017) Brain metabolomic profiling of eastern honey bee (Apis cerana) infested with the mite Varroa destructor. PLoS One 12:e0175573

Xi X, Kwok LY, Wang Y, Ma C, Mi Z, Zhang H (2017) Ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry MSE-based untargeted milk metabolomics in dairy cows with subclinical or clinical mastitis. J Dairy Sci 100:4884-4896

Yang BY, Tan JY, Liu Y, Liu B, Jin S, Guo HW, Kuang HX (2017) A UPLC-TOF/MS-based metabolomics study of rattan stems of Schisandra. chinensis effects on Alzheimer's disease rats model. Biomed Chromatogr (In press)

Yao C, Yang W, Zhang J, Qiu S, Chen M, Shi X, Pan H, Wu W, Guo D (2017) UHPLC-Q-TOF-MS-based metabolomics approach to compare the saponin compositions of Xueshuantong injection and Xuesaitong injection. J Sep Sci 40:834-841

Yoshitomi T, Oshima N, Goto Y, Nakamori S, Wakana D, Anjiki N, Sugimura K, Kawano N, Fuchino H, Iida O, Kagawa T, Jinno H, Kawahara N, Kobayashi Y, Maruyama T (2017) Construction of Prediction Models for the Transient Receptor Potential Vanilloid Subtype 1 (TRPV1)-Stimulating Activity of Ginger and Processed Ginger Based on LC-HRMS Data and PLS Regression Analyses. J Agric Food Chem 65:3581-3588

Yu Z, Miller HC, Puzon GJ, Clowers BH (2017) Development of Untargeted Metabolomics Methods for the Rapid Detection of Pathogenic Naegleria fowleri. Environ Sci Technol 51:4210-4219


2016

Ali MR, Wu Y, Han T, Zang X, Xiao H, Tang Y, Wu R, Fernandez FM, El-Sayed MA (2016) Simultaneous Time-Dependent Surface-Enhanced Raman Spectroscopy, Metabolomics, and Proteomics Reveal Cancer Cell Death Mechanisms Associated with Gold Nanorod Photothermal Therapy. J Am Chem Soc 138:15434-15442

Alwarawrah Y, Hughes P, Loiselle D, Carlson DA, Darr DB, Jordan JL, Xiong J, Hunter LM, Dubois LG, Thompson JW, Kulkarni MM, Ratcliff AN, Kwiek JJ, Haystead TA (2016) Fasnall, a Selective FASN Inhibitor, Shows Potent Anti-tumor Activity in the MMTV-Neu Model of HER2(+) Breast Cancer. Cell Chem Biol 23:678-688

Arias M, Chevallier OP, Graham SF, Gasull-Gimenez A, Fodey T, Cooper KM, Crooks SR, Danaher M, Elliott CT (2016) Metabolomics reveals novel biomarkers of illegal 5-nitromimidazole treatment in pigs. Further evidence of drug toxicity uncovered. Food Chem 199:876-884

Black C, Haughey SA, Chevallier OP, Galvin-King P, Elliott CT (2016) A comprehensive strategy to detect the fraudulent adulteration of herbs: The oregano approach. Food Chem 210:551-557

Blaise BJ, Correia G, Tin A, Young JH, Vergnaud AC, Lewis M, Pearce JT, Elliott P, Nicholson JK, Holmes E, Ebbels TM (2016) Power Analysis and Sample Size Determination in Metabolic Phenotyping. Anal Chem 88:5179-5188

Brown JA, Codreanu SG, Shi M, Sherrod SD, Markov DA, Neely MD, Britt CM, Hoilett OS, Reiserer RS, Samson PC, McCawley LJ, Webb DJ, Bowman AB, McLean JA, Wikswo JP (2016) Metabolic consequences of inflammatory disruption of the blood-brain barrier in an organ-on-chip model of the human neurovascular unit. J Neuroinflammation 13:306

Cao J, Li M, Chen J, Liu P, Li Z (2016) Effects of MeJA on Arabidopsis metabolome under endogenous JA deficiency. Sci Rep 6:37674

Carrizo D, Chevallier OP, Woodside JV, Brennan SF, Cantwell MM, Cuskelly G, Elliott CT (2016) Untargeted metabolomic analysis of human serum samples associated with exposure levels of Persistent organic pollutants indicate important perturbations in Sphingolipids and Glycerophospholipids levels. Chemosphere 168:731-738

Chen H, Cao G, Chen DQ, Wang M, Vaziri ND, Zhang ZH, Mao JR, Bai X, Zhao YY (2016) Metabolomics insights into activated redox signaling and lipid metabolism dysfunction in chronic kidney disease progression. Redox Biol 10:168-178

Chen WW, Freinkman E, Wang T, Birsoy K, Sabatini DM (2016) Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism. Cell 166:1324-1337 e1311

Chen YX, Zhang XJ, Huang J, Zhou SJ, Liu F, Jiang LL, Chen M, Jian-Bo W, Yang DZ (2016) UHPLC/Q-TOFMS-based plasma metabolomics of polycystic ovary syndrome patients with and without insulin resistance. J Pharm Biomed Anal 121:141-150

Chen Z, Xu X, Zhang J, Liu Y, Li L, Wang W, Xu H, Jiang W, Wang Y (2016) Application of LC-MS-Based Global Metabolomic Profiling Methods to Human Mental Fatigue. Anal Chem 88:11293-11296

Chu H, Zhang A, Han Y, Lu S, Kong L, Han J, Liu Z, Sun H, Wang X (2016) Metabolomics approach to explore the effects of Kai-Xin-San on Alzheimer's disease using UPLC/ESI-Q-TOF mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 1015-1016:50-61

Cowan E, Kumar P, Burch KJ, Grieve DJ, Green BD, Graham SF (2016) Treatment of lean and diet-induced obesity (DIO) mice with a novel stable obestatin analogue alters plasma metabolite levels as detected by untargeted LC-MS metabolomics. Metabolomics 12:124

Dhungana S, Carlson JE, Pathmasiri W, McRitchie S, Davis M, Sumner S, Appt SE (2016) Impact of a western diet on the ovarian and serum metabolome. Maturitas 92:134-142

Fang H, Zhang A, Yu J, Wang L, Liu C, Zhou X, Sun H, Song Q, Wang X (2016) Insight into the metabolic mechanism of scoparone on biomarkers for inhibiting Yanghuang syndrome. Sci Rep 6:37519

Gray N, Adesina-Georgiadis K, Chekmeneva E, Plumb RS, Wilson ID, Nicholson JK (2016) Development of a Rapid Microbore Metabolic Profiling Ultraperformance Liquid Chromatography-Mass Spectrometry Approach for High-Throughput Phenotyping Studies. Anal Chem 88:5742-5751

Huang W, Robert CA, Herve MR, Hu L, Bont Z, Erb M (2016) A mechanism for sequence specificity in plant-mediated interactions between herbivores. New Phytol 214:169-179

Jang C, Oh SF, Wada S, Rowe GC, Liu L, Chan MC, Rhee J, Hoshino A, Kim B, Ibrahim A, Baca LG, Kim E, Ghosh CC, Parikh SM, Jiang A, Chu Q, Forman DE, Lecker SH, Krishnaiah S, Rabinowitz JD, Weljie AM, Baur JA, Kasper DL, Arany Z (2016) A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance. Nat Med 22:421-426

Jones JW, Carter CL, Li F, Yu J, Pierzchalski K, Jackson IL, Vujaskovic Z, Kane MA (2016) Ultraperformance convergence chromatography-high resolution tandem mass spectrometry for lipid biomarker profiling and identification. Biomed Chromatogr (In press)

Kaakoush NO, Pickford R, Jaffe A, Ooi CY (2016) Is there a role for stool metabolomics in cystic fibrosis? Pediatr Int 58:808-811

Kim MS, Jin JS, Kwak YS, Hwang GS (2016) Metabolic Response of Strawberry (Fragaria x ananassa) Leaves Exposed to the Angular Leaf Spot Bacterium (Xanthomonas fragariae). J Agric Food Chem 64:1889-1898

Kim W, Peever TL, Park JJ, Park CM, Gang DR, Xian M, Davidson JA, Infantino A, Kaiser WJ, Chen W (2016) Use of metabolomics for the chemotaxonomy of legume-associated Ascochyta and allied genera. Sci Rep 6:20192

Kong Z, Li M, An J, Chen J, Bao Y, Francis F, Dai X (2016) The fungicide triadimefon affects beer flavor and composition by influencing Saccharomyces cerevisiae metabolism. Sci Rep 6:33552

Lai CJ, Zha L, Liu DH, Kang L, Ma X, Zhan ZL, Nan TG, Yang J, Li F, Yuan Y, Huang LQ (2016) Global profiling and rapid matching of natural products using diagnostic product ion network and in silico analogue database: Gastrodia elata as a case study. J Chromatogr A 1456:187-195

Laiakis EC, Pannkuk EL, Diaz-Rubio ME, Wang YW, Mak TD, Simbulan-Rosenthal CM, Brenner DJ, Fornace AJ, Jr. (2016) Implications of genotypic differences in the generation of a urinary metabolomics radiation signature. Mutat Res 788:41-49

Lesche D, Geyer R, Lienhard D, Nakas CT, Diserens G, Vermathen P, Leichtle AB (2016) Does centrifugation matter? Centrifugal force and spinning time alter the plasma metabolome. Metabolomics 12:159

Lewis MR, Pearce JT, Spagou K, Green M, Dona AC, Yuen AH, David M, Berry DJ, Chappell K, Horneffer-van der Sluis V, Shaw R, Lovestone S, Elliott P, Shockcor J, Lindon JC, Cloarec O, Takats Z, Holmes E, Nicholson JK (2016) Development and Application of Ultra-Performance Liquid Chromatography-TOF MS for Precision Large Scale Urinary Metabolic Phenotyping. Anal Chem 88:9004-9013

McIlroy GD, Tammireddy SR, Maskrey BH, Grant L, Doherty MK, Watson DG, Delibegovic M, Whitfield PD, Mody N (2016) Fenretinide mediated retinoic acid receptor signalling and inhibition of ceramide biosynthesis regulates adipogenesis, lipid accumulation, mitochondrial function and nutrient stress signalling in adipocytes and adipose tissue. Biochem Pharmacol 100:86-97

Mnich E, Vanholme R, Oyarce P, Liu S, Lu F, Goeminne G, Jorgensen B, Motawie MS, Boerjan W, Ralph J, Ulvskov P, Moller BL, Bjarnholt N, Harholt J (2016) Degradation of lignin beta-aryl ether units in Arabidopsis thaliana expressing LigD, LigF and LigG from Sphingomonas paucimobilis SYK-6. Plant Biotechnol J 15:581-593

Nakabayashi R, Sawada Y, Aoyagi M, Yamada Y, Hirai MY, Sakurai T, Kamoi T, Rowan DD, Saito K (2016) Chemical Assignment of Structural Isomers of Sulfur-Containing Metabolites in Garlic by Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry. J Nutr 146:397S-402S

Paglia G, Stocchero M, Cacciatore S, Lai S, Angel P, Alam MT, Keller M, Ralser M, Astarita G (2016) Unbiased Metabolomic Investigation of Alzheimer's Disease Brain Points to Dysregulation of Mitochondrial Aspartate Metabolism. J Proteome Res 15:608-618

Pirhaji L, Milani P, Leidl M, Curran T, Avila-Pacheco J, Clish CB, White FM, Saghatelian A, Fraenkel E (2016) Revealing disease-associated pathways by network integration of untargeted metabolomics. Nat Methods 13:770-776

Plucinska K, Dekeryte R, Koss D, Shearer K, Mody N, Whitfield PD, Doherty MK, Mingarelli M, Welch A, Riedel G, Delibegovic M, Platt B (2016) Neuronal human BACE1 knockin induces systemic diabetes in mice. Diabetologia 59:1513-1523

Prudent M, Stauber F, Rapin A, Hallen S, Pham N, Abonnenc M, Marvin L, Rochat B, Tissot JD, Lion N (2016) Small-Scale Perfusion Bioreactor of Red Blood Cells for Dynamic Studies of Cellular Pathways: Proof-of-Concept. Front Mol Biosci 3:11

Rusilowicz M, Dickinson M, Charlton A, O'Keefe S, Wilson J (2016) A batch correction method for liquid chromatography-mass spectrometry data that does not depend on quality control samples. Metabolomics 12:56

Saigusa D, Okamura Y, Motoike IN, Katoh Y, Kurosawa Y, Saijyo R, Koshiba S, Yasuda J, Motohashi H, Sugawara J, Tanabe O, Kinoshita K, Yamamoto M (2016) Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery. PLoS One 11:e0160555

Salem MA, Juppner J, Bajdzienko K, Giavalisco P (2016) Protocol: a fast, comprehensive and reproducible one-step extraction method for the rapid preparation of polar and semi-polar metabolites, lipids, proteins, starch and cell wall polymers from a single sample. Plant Methods 12:45

Schmidt R, Ostorhazi E, Wende E, Knappe D, Hoffmann R (2016) Pharmacokinetics and in vivo efficacy of optimized oncocin derivatives. J Antimicrob Chemother 71:1003-1011

Shahaf N, Rogachev I, Heinig U, Meir S, Malitsky S, Battat M, Wyner H, Zheng S, Wehrens R, Aharoni A (2016) The WEIZMASS spectral library for high-confidence metabolite identification. Nat Commun 7:12423

Shen S, Weng R, Li L, Xu X, Bai Y, Liu H (2016) Metabolomic Analysis of Mouse Embryonic Fibroblast Cells in Response to Autophagy Induced by Acute Starvation. Sci Rep 6:34075

Shi H, Hu L, Chen S, Bao W, Yang S, Zhao X, Sun C (2016) Metabolomics analysis of urine from rats administered with long-term, low-dose acrylamide by ultra-performance liquid chromatography-mass spectrometry. Xenobiotica:1-11

Steenackers W, Cesarino I, Klima P, Quareshy M, Vanholme R, Corneillie S, Kumpf RP, Van de Wouwer D, Ljung K, Goeminne G, Novak O, Zazimalova E, Napier R, Boerjan W, Vanholme B (2016) The Allelochemical MDCA Inhibits Lignification and Affects Auxin Homeostasis. Plant Physiol 172:874-888

Vaughan D, Brogioli M, Maier T, White A, Waldron S, Rittweger J, Toigo M, Wettstein J, Laczko E, Fluck M (2016) The Angiotensin Converting Enzyme Insertion/Deletion Polymorphism Modifies Exercise-Induced Muscle Metabolism. PLoS One 11:e0149046

Wali S, Gupta R, Yu JJ, Mfuh A, Gao X, Guentzel MN, Chambers JP, Abu Bakar S, Zhong G, Arulanandam BP (2016) Guinea pig genital tract lipidome reveals in vivo and in vitro regulation of phosphatidylcholine 16:0/18:1 and contribution to Chlamydia trachomatis serovar D infectivity. Metabolomics 12 (In press)

Walton A, Stes E, Goeminne G, Braem L, Vuylsteke M, Matthys C, De Cuyper C, Staes A, Vandenbussche J, Boyer FD, Vanholme R, Fromentin J, Boerjan W, Gevaert K, Goormachtig S (2016) The Response of the Root Proteome to the Synthetic Strigolactone GR24 in Arabidopsis. Mol Cell Proteomics 15:2744-2755

Wang J, Qi P, Hou J, Shen Y, Yang M, Bi Q, Deng Y, Shi X, Feng R, Feng Z, Wu W, Guo D (2016) The profiling of the metabolites of hirsutine in rat by ultra-high performance liquid chromatography coupled with linear ion trap Orbitrap mass spectrometry: An improved strategy for the systematic screening and identification of metabolites in multi-samples in vivo. J Pharm Biomed Anal 134:149-157

Yang Z, Hou JJ, Qi P, Yang M, Yan BP, Bi QR, Feng RH, Yang WZ, Wu WY, Guo DA (2016) Colon-derived uremic biomarkers induced by the acute toxicity of Kansui radix: A metabolomics study of rat plasma and intestinal contents by UPLC-QTOF-MS(E). J Chromatogr B Analyt Technol Biomed Life Sci 1026:193-203

Zhang A, Liu Q, Zhao H, Zhou X, Sun H, Nan Y, Zou S, Ma CW, Wang X (2016) Phenotypic characterization of nanshi oral liquid alters metabolic signatures during disease prevention. Sci Rep 6:19333

Zhang J, Yang W, Li S, Yao S, Qi P, Yang Z, Feng Z, Hou J, Cai L, Yang M, Wu W, Guo DA (2016) An intelligentized strategy for endogenous small molecules characterization and quality evaluation of earthworm from two geographic origins by ultra-high performance HILIC/QTOF MS(E) and Progenesis QI. Anal Bioanal Chem 408:3881-3890


2015

Ashraf-Khorassani M, Yang J, Rainville P, Jones MD, Fountain KJ, Isaac G, Taylor LT (2015) Ultrahigh performance supercritical fluid chromatography of lipophilic compounds with application to synthetic and commercial biodiesel. J Chromatogr B Analyt Technol Biomed Life Sci 983-984:94-100

Avin-Wittenberg T, Bajdzienko K, Wittenberg G, Alseekh S, Tohge T, Bock R, Giavalisco P, Fernie AR (2015) Global Analysis of the Role of Autophagy in Cellular Metabolism and Energy Homeostasis in Arabidopsis Seedlings under Carbon Starvation. Plant Cell 27:306-322

Boulard C, Bardet M, Chardot T, Dubreucq B, Gromova M, Guillermo A, Miquel M, Nesi N, Yen-Nicolay S, Jolivet P (2015) The structural organization of seed oil bodies could explain the contrasted oil extractability observed in two rapeseed genotypes. Planta 242:53-68

Burch TC, Isaac G, Booher CL, Rhim JS, Rainville P, Langridge J, Baker A, Nyalwidhe JO (2015) Comparative Metabolomic and Lipidomic Analysis of Phenotype Stratified Prostate Cells. PLoS One 10:e0134206

Chetwynd AJ, Abdul-Sada A, Holt SG, Hill EM (2015) Use of a pre-analysis osmolality normalisation method to correct for variable urine concentrations and for improved metabolomic analyses. J Chromatogr A (In press)

Chevallier OP, Graham SF, Alonso E, Duffy C, Silke J, Campbell K, Botana LM, Elliott CT (2015) New insights into the causes of human illness due to consumption of azaspiracid contaminated shellfish. Sci Rep 5:9818

Dai W, Qi D, Yang T, Lv H, Guo L, Zhang Y, Zhu Y, Peng Q, Xie D, Tan J, Lin Z (2015) Nontargeted Analysis Using Ultraperformance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry Uncovers the Effects of Harvest Season on the Metabolites and Taste Quality of Tea (Camellia sinensis L.). J Agric Food Chem 63:9869-9878

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL (2015) Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl 9:745-754 (in press)

Graham SF, Chevallier OP, Elliott CT, Holscher C, Johnston J, McGuinness B, Kehoe PG, Passmore AP, Green BD (2015) Untargeted metabolomic analysis of human plasma indicates differentially affected polyamine and L-arginine metabolism in mild cognitive impairment subjects converting to Alzheimer's disease. PLoS One 10:e0119452

Gray N, Lewis MR, Plumb RS, Wilson ID, Nicholson JK (2015) High-Throughput Microbore UPLC-MS Metabolic Phenotyping of Urine for Large-Scale Epidemiology Studies. J Proteome Res 14:2714-2721

Haoula Z, Ravipati S, Stekel DJ, Ortori CA, Hodgman C, Daykin C, Raine-Fenning N, Barrett DA, Atiomo W (2015) Lipidomic analysis of plasma samples from women with polycystic ovary syndrome. Metabolomics 11:657-666

Holcapek M, Cervena B, Cifkova E, Lisa M, Chagovets V, Vostalova J, Bancirova M, Galuszka J, Hill M (2015) Lipidomic analysis of plasma, erythrocytes and lipoprotein fractions of cardiovascular disease patients using UHPLC/MS, MALDI-MS and multivariate data analysis. J Chromatogr B Analyt Technol Biomed Life Sci 990:52-63

Kim D, Fiske BP, Birsoy K, Freinkman E, Kami K, Possemato RL, Chudnovsky Y, Pacold ME, Chen WW, Cantor JR, Shelton LM, Gui DY, Kwon M, Ramkissoon SH, Ligon KL, Kang SW, Snuderl M, Vander Heiden MG, Sabatini DM (2015) SHMT2 drives glioma cell survival in ischaemia but imposes a dependence on glycine clearance. Nature 520:363-367

Lin L, Lin H, Zhang M, Ni B, Yin X, Qu C, Ni J (2015) A novel method to analyze hepatotoxic components in Polygonum multiflorum using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. J Hazard Mater 299:249-259

Liu F, Bai X, Ding RB, Hu YJ, Su H, Wan JB (2015) UPLC/Q-TOFMS-Based Metabolomics Studies on the Protective Effect of Panax notoginseng Saponins on Alcoholic Liver Injury. Am J Chin Med 43:695-714

Liu H, Zhang L, Zhao B, Zhang Z, Qin L, Zhang Q, Wang Q, Lu Z, Gao X (2015) Hypothalamus metabolomic profiling to elucidate the tissue-targeted biochemical basis of febrile response in yeast-induced pyrexia rats. Chem Biol Interact 231:61-70

Maldini M, Natella F, Baima S, Morelli G, Scaccini C, Langridge J, Astarita G (2015) Untargeted Metabolomics Reveals Predominant Alterations in Lipid Metabolism Following Light Exposure in Broccoli Sprouts. Int J Mol Sci 16:13678-13691

McIlroy GD, Tammireddy SR, Maskrey BH, Grant L, Doherty MK, Watson DG, Delibegovic M, Whitfield PD, Mody N (2015) Fenretinide mediated retinoic acid receptor signalling and inhibition of ceramide biosynthesis regulates adipogenesis, lipid accumulation, mitochondrial function and nutrient stress signalling in adipocytes and adipose tissue. Biochem Pharmacol (In press)

Mertens J, Pollier J, Vanden Bossche R, Lopez-Vidriero I, Franco-Zorrilla JM, Goossens A (2015) The bHLH Transcription Factors TSAR1 and TSAR2 Regulate Triterpene Saponin Biosynthesis in Medicago truncatula. Plant Physiol 170:194-210

Milner JJ, Rebeles J, Dhungana S, Stewart DA, Sumner SC, Meyers MH, Mancuso P, Beck MA (2015) Obesity Increases Mortality and Modulates the Lung Metabolome during Pandemic H1N1 Influenza Virus Infection in Mice. J Immunol 194:4846-4859

Mulek M, Fekete A, Wiest J, Holzgrabe U, Mueller MJ, Hogger P (2015) Profiling a gut microbiota-generated catechin metabolite's fate in human blood cells using a metabolomic approach. J Pharm Biomed Anal 114:71-81

Nakabayashi R, Yang Z, Nishizawa T, Mori T, Saito K (2015) Top-down Targeted Metabolomics Reveals a Sulfur-Containing Metabolite with Inhibitory Activity against Angiotensin-Converting Enzyme in Asparagus officinalis. J Nat Prod 78:1179-1183

Neubauer C, Dalleska NF, Cowley ES, Shikuma NJ, Wu CH, Sessions AL, Newman DK (2015) Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation. Geobiology 13:443-453

Pacini T, Fu W, Gudmundsson S, Chiaravalle AE, Brynjolfson S, Palsson BO, Astarita G, Paglia G (2015) Multidimensional analytical approach based on UHPLC-UV-ion mobility-MS for the screening of natural pigments. Anal Chem 87:2593-2599

Passos-Castilho AM, Carvalho VM, Cardozo KH, Kikuchi L, Chagas AL, Gomes-Gouvea MS, Malta F, de Seixas-Santos Nastri AC, Pinho JR, Carrilho FJ, Granato CF (2015) Serum lipidomic profiling as a useful tool for screening potential biomarkers of hepatitis B-related hepatocellular carcinoma by ultraperformance liquid chromatography-mass spectrometry. BMC Cancer 15:985

Stark TD, Losch S, Wakamatsu J, Balemba OB, Frank O, Hofmann T (2015) UPLC-ESI-TOF MS-Based Metabolite Profiling of the Antioxidative Food Supplement Garcinia buchananii. J Agric Food Chem 63:7169-7179

Stewart CJ, Nelson A, Treumann A, Skeath T, Cummings SP, Embleton ND, Berrington JE (2015) Metabolomic and proteomic analysis of serum from preterm infants with necrotising entercolitis and late-onset sepsis. Pediatr Res (In press)

Tonoli D, Furstenberger C, Boccard J, Hochstrasser D, Jeanneret F, Odermatt A, Rudaz S (2015) Steroidomic Footprinting Based on Ultra-High Performance Liquid Chromatography Coupled with Qualitative and Quantitative High-Resolution Mass Spectrometry for the Evaluation of Endocrine Disrupting Chemicals in H295R Cells. Chem Res Toxicol 28:955-966

Wang_XK (2015) Identification of particulate organosulfates in three megacities at the middle and lower reaches of the Yangtze River. Atmos Chem Phys Discuss 15:21415–21448

Watschinger K, Keller MA, McNeill E, Alam MT, Lai S, Sailer S, Rauch V, Patel J, Hermetter A, Golderer G, Geley S, Werner-Felmayer G, Plumb RS, Astarita G, Ralser M, Channon KM, Werner ER (2015) Tetrahydrobiopterin and alkylglycerol monooxygenase substantially alter the murine macrophage lipidome. Proc Natl Acad Sci U S A 112:2431-2436

Yang Z, Hou JJ, Qi P, Yang M, Yan BP, Bi QR, Feng RH, Yang WZ, Wu WY, Guo DA (2015) Colon-derived uremic biomarkers induced by the acute toxicity of Kansui radix: A metabolomics study of rat plasma and intestinal contents by UPLC-QTOF-MS. J Chromatogr B Analyt Technol Biomed Life Sci (in press)

Zhang ZH, Wei F, Vaziri ND, Cheng XL, Bai X, Lin RC, Zhao YY (2015) Metabolomics insights into chronic kidney disease and modulatory effect of rhubarb against tubulointerstitial fibrosis. Sci Rep 5:14472

Zhao YY, Wang HL, Cheng XL, Wei F, Bai X, Lin RC, Vaziri ND (2015) Metabolomics analysis reveals the association between lipid abnormalities and oxidative stress, inflammation, fibrosis, and Nrf2 dysfunction in aristolochic acid-induced nephropathy. Sci Rep 5:12936

Zhao Y, Liu T, Luo J, Zhang Q, Xu S, Han C, Xu J, Chen M, Chen Y, Kong L (2015) Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport. Front Plant Sci 6:996

Zhou T, Wang M, Cheng H, Cui C, Su S, Xu P, Xue M (2015) UPLC-HRMS based metabolomics reveals the sphingolipids with long fatty chains and olefinic bonds up-regulated in metabolic pathway for hypoxia preconditioning. Chem Biol Interact 242:145-152


2014

Astarita G, McKenzie JH, Wang B, Strassburg K, Doneanu A, Johnson J, Baker A, Hankemeier T, Murphy J, Vreeken RJ, Langridge J, Kang JX (2014) A protective lipidomic biosignature associated with a balanced omega-6/omega-3 ratio in fat-1 transgenic mice. PLoS One 9:e96221

Avanesov AS, Ma S, Pierce KA, Yim SH, Lee BC, Clish CB, Gladyshev VN (2014) Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation. Elife 3:e02077

Damen CW, Isaac G, Langridge J, Hankemeier T, Vreeken RJ (2014) Enhanced lipid isomer separation in human plasma using reversed-phase UPLC with ion-mobility/high-resolution MS detection. J Lipid Res 55:1772-1783

Laiakis EC, Strassburg K, Bogumil R, Lai S, Vreeken RJ, Hankemeier T, Langridge J, Plumb RS, Fornace AJ, Jr., Astarita G (2014) Metabolic phenotyping reveals a lipid mediator response to ionizing radiation. J Proteome Res 13:4143-4154

Paglia G, Angel PM, Williams JP, Richardson K, Olivos HJ, Thompson JW, Menikarachchi LC, Lai S, Walsh C, Moseley MA, Plumb RS, Grant DF, Palsson BO, Langridge JI, Geromanos SJ, Astarita G (2014) Ion-Mobility-Derived Collision Cross Section as an Additional Measure for Lipid Fingerprinting and Identification. Anal Chem

Paglia G, Williams JP, Menikarachchi L, Thompson JW, Tyldesley-Worster R, Halldorsson S, Rolfsson O, Moseley A, Grant D, Langridge J, Palsson BO, Astarita G (2014) Ion mobility derived collision cross sections to support metabolomics applications. Anal Chem 86:3985-3993

Sedic M, Gethings LA, Vissers JP, Shockcor JP, McDonald S, Vasieva O, Lemac M, Langridge JI, Batinic D, Pavelic SK (2014) Label-free mass spectrometric profiling of urinary proteins and metabolites from paediatric idiopathic nephrotic syndrome. Biochem Biophys Res Commun 452:21-26

Sundin L, Vanholme R, Geerinck J, Goeminne G, Hofer R, Kim H, Ralph J, Boerjan W (2014) Mutation of the Inducible ARABIDOPSIS THALIANA CYTOCHROME P450 REDUCTASE2 Alters Lignin Composition and Improves Saccharification. Plant Physiol 166:1956-1971

Van Acker R, Leple JC, Aerts D, Storme V, Goeminne G, Ivens B, Legee F, Lapierre C, Piens K, Van Montagu MC, Santoro N, Foster CE, Ralph J, Soetaert W, Pilate G, Boerjan W (2014) Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase. Proc Natl Acad Sci U S A 111:845-850

Zhang A, Zhou X, Zhao H, Guan Y, Zhou S, Yan GL, Ma Z, Liu Q, Wang X (2014) Rapidly improved determination of metabolites from biological data sets using the high-efficient TransOmics tool. Mol Biosyst 10:2160-2165