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CRL2 aids elimination of truncated selenoproteins produced by failed UGA/Sec decoding
Hsiu-Chuan Lin, Szu-Chi Ho, Yi-Yun Chen, et al. Science 2015, 349, 91-95
Transcriptional control of autophagy–lysosome function drives pancreatic cancer metabolism
Rushika M. Perera, Svetlana Stoykova, Brandon N. Nicolay, et al. Nature 524, 361–365, 2015
Structurally Distinct Ca2+ Signaling Domains of Sperm Flagella Orchestrate Tyrosine Phosphorylation and Motility (Proteomics)
Jean-Ju Chung, Sang-Hee Shim, Robert A. Everley, et al. Cell 2014, 157, 808-822
The One Hour Yeast Proteome (Proteomics, peptide ID)
Alexander S. Hebert, Alicia L. Richards, Derek J. Bailey, Arne Ulbrich, Emma E. Coughlin, Michael S. Westphall, and Joshua J. Coon
Molecular & Cellular Proteomics 13, 339–347, 2014.
Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (Proteomics, Neu Code)
Alicia L. Richards, Catherine E. Vincent, Adrian Guthals, Christopher M. Rose, Michael S. Westphall, Nuno Bandeira and Joshua J. Coon
Mol Cell Proteomics 2013 12: 3812-3823
Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates (Proteomics)
Michael W. Senko, Philip M. Remes, Jesse D. Canterbury, Raman Mathur, Qingyu Song,
Shannon M. Eliuk, Chris Mullen, Lee Earley, Mark Hardman, Justin D. Blethrow, Huy Bui,
August Specht, Oliver Lange, Eduard Denisov, Alexander Makarov, Stevan Horning,
and Vlad Zabrouskov
Anal. Chem., 2013, 85 (24), 11710–11714
A novel LC-MS2 product dependent parallel data acquisition function and data analysis workflow for sequencing and identification of intact glycopeptides (Glycoproteomics)
Sz-Wei Wu, Tsung-Hsien Pu, Rosa Viner, and Kay-Hooi Khoo
Anal. Chem., 2014, 86 (11), 5478–5486
Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction
Michael P. Weekes, Peter Tomasec, Edward L. Huttlin, Ceri A. Fielding, David Nusinow, Richard J. Stanton, Eddie C.Y. Wang, Rebecca Aicheler, Isa Murrell, Gavin W.G. Wilkinson, Paul J. Lehner and Steven P. Gygi (Proteomics)
Cell 2014, 157, 1460-1472
O-Glycosylation regulates polarized secretion by modulating Tango1 stability
Liping Zhang, Zulfeqhar Ali Syed, Iris van Dijk Härd, Jae-Min Lim, Lance Wells, and Kelly G. Ten Hagen (Glycoproteomics)
PNAS 2014 111 (20) 7296-7301
In vivo monoubiquitination of anaplerotic phosphoenolpyruvate carboxylase occurs at Lys624 in germinating sorghum seeds
Isabel Ruiz-Ballesta, Ana-Belén Feria, Hong Ni, Yi-Min She, William Charles Plaxton, Cristina Echevarría (Proteomics)
Journal of Experimental Botany, Vol. 65, No. 2, pp. 443–451, 2014
A new high-throughput LC-MS method for the analysis of complex fructan mixtures (Glycomics)
Joran Verspreet, Anders Holmgaard Hansen, Emmie Dornez, Christophe M. Courtin and Scott J. Harrison
Anal Bioanal Chem 2014, 406, 4785-4788
SHANK3 overexpression causes manic-like behavior with unique pharmacogenetic properties.
Han K, Holder Jr JL, Schaaf CP, Lu H, Chen H, Kang H, Tang J, Wu Z, Hao S, Cheung SW, Yu P. Nature. 2013 Nov 7;503(7474):72.
Bacterial inactivation of the anticancer drug doxorubicin.
Westman EL, Canova MJ, Radhi IJ, Koteva K, Kireeva I, Waglechner N, Wright GD. Chemistry & biology. 2012 Oct 26;19(10):1255-64.
Microdose Study of 14C‐Acetaminophen With Accelerator Mass Spectrometry to Examine Pharmacokinetics of Parent Drug and Metabolites in Healthy Subjects.
Tozuka Z, Kusuhara H, Nozawa K, Hamabe Y, Ikushima I, Ikeda T, Sugiyama Y. Clinical Pharmacology & Therapeutics. 2010 Dec 1;88(6):824-30.
Qiao X, Song W, Wang Q, Zhang ZX, Bo T, Li RY, Liang LN, Tzeng YM, Guo DA, Ye M. Comprehensive chemical analysis of triterpenoids and polysaccharides in the medicinal mushroom Antrodia cinnamomea.
RSC Advances. 2015;5(58):47040-52.
Long Z, Guo Z, Liu X, Zhang Q, Liu X, Jin Y, Liang L, Li H, Wei J, Wu N. A sensitive non-derivatization method for apramycin and impurities analysis using hydrophilic interaction liquid chromatography and charged aerosol detection.
Talanta. 2016 Jan 1;146:423-9.
Long Z, Guo Z, Acworth IN, Liu X, Jin Y, Liu X, Liu L, Liang L. A non-derivative method for the quantitative analysis of isosteroidal alkaloids from Fritillaria by high performance liquid chromatography combined with charged aerosol detection.
Talanta. 2016 May 1;151:239-44.
Li Y, Wang H, Si N, Ren W, Han L, Xin S, Zuo R, Wei X, Yang J, Zhao H, Bian B. Metabolic profiling analysis of berberine, palmatine, jatrorrhizine, coptisine and epiberberine in zebrafish by ultra-high performance liquid chromatography coupled with LTQ Orbitrap mass spectrometer.
Xenobiotica. 2015 Apr 3;45(4):302-11.
Jin Y, Wu CS, Zhang JL, Li YF. A new strategy for the discovery of epimedium metabolites using high-performance liquid chromatography with high resolution mass spectrometry.
Analytica chimica acta. 2013 Mar 20;768:111-7.
Wang Q, Jiang P, Ye FY, Shi R, Ma YM, Zhong J, Wu JS, Liu P, Liu CH, Jia YQ. Identification and pharmacokinetics of multiple constituents in rat plasma after oral administration of Yinchenzhufu decoction.
Journal of ethnopharmacology. 2014 May 14;153(3):714-24.
Zhang JY, Wang ZJ, Zhang Q, Wang F, Ma Q, Lin ZZ, Lu JQ, Qiao YJ. Rapid screening and identification of target constituents using full scan-parent ions list-dynamic exclusion acquisition coupled to diagnostic product ions analysis on a hybrid LTQ-Orbitrap mass spectrometer.
Talanta. 2014 Jun 15;124:111-22.
Lu C, Deng J, Li L, Wang D, Li G. Application of metabolomics on diagnosis and treatment of patients with psoriasis in traditional Chinese medicine.
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics. 2014 Jan 31;1844(1):280-8.
Yan B, Deng Y, Hou J, Bi Q, Yang M, Jiang B, Liu X, Wu W, Guo D. UHPLC-LTQ-Orbitrap MS combined with spike-in method for plasma metabonomics analysis of acute myocardial ischemia rats and pretreatment effect of Danqi Tongmai tablet.
Molecular BioSystems. 2015;11(2):486-96.
Cao S, Zhang Z, Ye Y, Chen L, Li Y, Yu X, Yang Y, Wang L, Li Z, Li L. Metabolic transformation evidence of caffeic acid derivatives in male rats after the oral administration of functional food by UPLC coupled with a hybrid quadrupole-orbitrap mass spectrometer.
RSC Advances. 2015;5(22):16960-7.
Chen G, Pramanik BN, Liu YH, Mirza UA. Applications of LC/MS in structure identifications of small molecules and proteins in drug discovery.
Journal of mass spectrometry. 2007 Mar 1;42(3):279-87.
Light-dependent chlorophyll f synthase is a highly divergent paralog of PsbA of photosystem II
Ming-Yang Ho, Gaozhong Shen, Daniel P. Canniffe, et al. Science. 2016 Aug 26;353(6302)
A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti
Harald Marx, Catherine E Minogue, Dhileepkumar Jayaraman, et al. Nature Biotechnology (2016) doi:10.1038/nbt.3681
High-throughput metabolic screening of microalgae genetic variation in response to nutrient limitation.
Bajhaiya, Amit K., Andrew P. Dean, Thomas Driver, et al.Metabolomics 12.1 (2016): 9.
OsMOGS is required for N-glycan formation and auxin-mediated root development in rice (Oryza sativa L.) (Glycomics)
SuiKang Wang, YanXia Xu, ZhiLan Li, SaiNa Zhang, Jae-Min Lim, Kyun Oh Lee, ChuanYou Li, Qian Qian, De An Jiang and YanHua Qi
Plant J. 2014, 78, 632-645
In vivo monoubiquitination of anaplerotic phosphoenolpyruvate carboxylase occurs at Lys624 in germinating sorghum seeds (Proteomics, plant proteomics, peptide ID, UBIQUITYLATION)
Isabel Ruiz-Ballesta, Ana-Belén Feria, Hong Ni, Yi-Min She, William Charles Plaxton, Cristina Echevarría
Journal of Experimental Botany, Vol. 65, No. 2, pp. 443–451, 2014
Two-dimensional phos-tag zymograms for tracing phosphoproteins by activity in-gel staining (Proteomics, peptide ID, PHOSPHORYLATION)
Claudia-Nicole Meisrimler, Alexandra Schwendke and Sabine Lüthje
Frontiers in Plants 2015
Identification of regulatory and cargo proteins of endosomal and secretory pathways in Arabidopsis thaliana by proteomic dissection (Proteomics, peptide ID, plant proteomics)
William Heard, Jan Sklenar, Daniel F. A. Tome, Silke Robatzek, and Alexandra M. E. Jones
Mol Cell Proteomics mcp.M115.050286. First Published on April 21, 2015
Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study (Proteomics, peptide ID, plant proteomics)
Felipe Bastida, Carlos García, Martin von Bergen, José L. Moreno, Hans H. Richnow, Nico Jehmlich
Applied Soil Ecology 93 (2015) 65–67
Two serine residues in Pseudomonas syringae effector HopZ1a are required for acetyltransferase activity and association with the host co-factor (Proteomics, peptide IDs, plant proteomics)
Ka-Wai Ma, Shushu Jiang, Eva Hawara, DongHyuk Lee, Songqin Pan, Gitta Coaker, Jikui Song and Wenbo Ma
New Phytologist 2015
S-Nitrosation of Conserved Cysteines Modulates Activity and Stability of S-Nitrosoglutathione Reductase (GSNOR) (proteomics, plants, Intact)
Damian Guerra, Keith Ballard, Ian Truebridge, and Elizabeth Vierling
Biochemistry, 2016, 55 (17), pp 2452–2464
Molecular cloning of plane pollen allergen Pla a 3 and its utility as diagnostic marker for peach associated plane pollen allergy biotransformation (proteomics, plants peptide ID)
Wangorsch, H. Larsson, M. Messmer, A. Garcıa-Moral, I. Lauer, S. Wolfheimer, S. Schulke, J. Bartra , S. Vieths, J. Lidholm and S. Scheurer
Clinical & Experimental Allergy, 46, 764–774, 2016
Application of wide selected-ion monitoring (WiSIM)-data independent acquisition (DIA) to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor (Proteomics, WiSIM-DIA, PLANT)
Laetitia B.B. Martin, Robert W. Sherwood, Joshua J. Nicklay, Yong Yang, Tara L. Muratore-Schroeder, Elizabeth T. Anderson, Theodore. W. Thannhauser, Jocelyn K.C. Rose, Sheng Zhang
Proteomics
New insights into the post-translational modification of multiple phosphoenolpyruvate carboxylase isoenzymes by phosphorylation and monoubiquitination during sorghum seed development and germination (Proteomics, UBIQUITYLATION, PLANTS)
Isabel Ruiz-Ballesta, Guillermo Baena, Jacinto Gandullo, Liqun Wang, Yi-Min She, William Charles Plaxton and Cristina Echevarría
Journal of Experimental Botany, Vol. 67, No. 11 pp. 3523–3536, 2016
Selenium promotes sulfur accumulation and plant growth in wheat (Triticum aestivum) (Proteomics, LFQ, Plants)
Paulo F. Boldrin, Marislaine A. de Figueiredo, Yong Yang, Hongmei Luo, Shree Giri, Jonathan J. Hart, Valdemar Faquin, Luiz R.G. Guilherme, Theorodore W. Thannhauser and Li Li
Physiologia Plantarum 2016
Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis(Glycoproteomics, N-Glycopeptide, Plants)
Jun Ma, Dinghe Wang, Jessica She, Jianming Li, Jian-Kang Zhu and Yi-Min She
NEW PHYTOLOGIST
Development of a laser capture microscope-based single-cell-type proteomics tool for studying proteomes of individual cell layers of plant roots (Proteomics, Peptide IDs, Plants)
Yingde Zhu, Hui Li, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish, and Theodore W Thannhauser
Hortic Res. 2016; 3: 16026
Development of a laser capture microscope-based single-cell-type proteomics tool for studying proteomes of individual cell layers of plant roots (Proteomics, peptide ID, Plant proteomics)
Yingde Zhu, Hui Li, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish and Theodore W Thannhauser
Horticulture Research (2016) 3, 16026; doi:10.1038/hortres.2016.26
Insight into enzymatic degradation of corn, wheat, and soybean cell wall cellulose using quantitative secretome analysis of Aspergillus fumigatus (Proteomics, iTRAQ MS2, plants)
Prakriti Sharma Ghimire, Haomiao Ouyang, Qian Wang, Yuanming Luo, Bo Shi, Jinghua Yang, Yang Lu, and Cheng Jin
J. Proteome Res., Just Accepted Manuscript
Mapping the Triticum aestivum proteome (Proteomics, peptide ID, Triticum aestivum proteome)
Owen Duncan, Josua Trösch, Ricarda Fenske, Nicolas L. Taylor and A Harvey Millar
THE PLANT JOURNAL Accepted manuscript online: 24 OCT 2016
Effects of the Herbicide Imazethapyr on Photosynthesis in PGR5- and NDH-Deficient Arabidopsis thaliana at the Biochemical, Transcriptomic, and Proteomic Levels (Proteomics, iTRAQ, Photosynthesis, Plants)
Chongchong Sun, Si Chen, Yujian Jin, Hao Song, Songlin Ruan, Zhengwei Fu, Muhammad Asad Ullah Asad, and Haifeng Qian
J. Agric. Food Chem., 2016, 64 (22), pp 4497–4504
Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2–MND1 (Proteomics, crosslinking, complex conformations in solution of the plant HOP2–MND1 complex)
Evelyn Rampler, Thomas Stranzl, Zsuzsanna Orban-Nemeth, David Maria Hollenstein, Otto Hudecz, Peter Schlögelhofer, and Karl Mechtler
J. Proteome Res., 2015, 14 (12), pp 5048–5062
Protein Dynamics in Young Maize Root Hairs in Response to Macro- and Micronutrient Deprivation (Proteomics, Phosphopeptides, LFQ, Young Maize Root Hairs, Plants)
Zhi Li, Daniel Phillip, Benjamin Neuhäuser, Waltraud X. Schulze, and Uwe Ludewig
J. Proteome Res., 2015, 14 (8), pp 3362–3371
New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants (Proteomics, iTRAQ, Plants)
Islam Mostafa, Ning Zhu, Mi-Jeong Yoo, Kelly M. Balmant, Biswapriya B. Misra, Craig Dufresne, Maged Abou-Hashem, Sixue Chen, Maher El-Domiaty
Journal of Proteomics, Volume 138, 14 April 2016, Pages 1-19
PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity (Proteomics, ADP-ribosylation, Plants)
Baomin Feng, Shisong Ma, Sixue Chen, Ning Zhu, Shuxin Zhang, Bin Yu, Yu Yu, Brandon Le, Xuemei Chen, Savithramma P Dinesh-Kumar, Libo Shan and Ping He
EMBO Rep. 2016 Oct 18. pii: e201642486. [Epub ahead of print]
Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition (Proteomics, Phosphorylation, LFQ, roots)
Jochen Menz, Zhi Li, Waltraud X. Schulze and Uwe Ludewig
THE PLANT JOURNAL 2106
Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling (Proteomics, peptide ID, plants, heat stress)
Krzysztof Brzezinka, Simone Altmann, Hjördis Czesnick, Philippe Nicolas, Michal Gorka, Eileen Benke, Tina Kabelitz, Felix Jähne, Alexander Graf, Christian Kappel, Isabel Bäurle
Elife. 2016 Sep 28;5. pii: e17061
Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease (Proteomics, TMT, Huanglongbing disease)
Federico Martinelli, Russell L. Reagan, David Dolan, Veronica Fileccia and Abhaya M. Dandekar
BMC Plant Biology (2016) 16:167 https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0858-5
Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.) (Proteomics, Phosphorylation, rice)
Jiehua Qiu, Yuxuan Hou, Xiaohong Tong, Yifeng Wang, Haiyan Lin, Qing Liu, Wen Zhang, Zhiyong Li, Babi R. Nallamilli, Jian Zhang
Plant Mol Biol (2016) 90:249–265
From Phosphoproteome to Modeling of Plant Signaling Pathways (proteomics, Phosphoproteomics, Protocols)
Maksim Zakhartsev , Heidi Pertl-Obermeyer, Waltraud X. Schulze
Proteomics in Systems Biology Volume 1394 of the series Methods in Molecular Biology pp 245-259
A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight (Proteomics, Phosphoproteomics, RICE, BACTERIAL BLIGHT)
Yuxuan Hou, Jiehua Qiu, Xiaohong Tong, Xiangjin Wei, Babi R. Nallamilli, Weihuai Wu, Shiwen Huang and Jian Zhang
BMC Plant Biology (2015) 15:163
Phosphopeptide Profiling of Receptor Kinase Mutants (proteomics, Phosphoproteomics, Protocols, Receptor Kinase Mutants)
Xu Na Wu and Waltraud X. Schulze
Plant Phosphoproteomics Volume 1306 of the series Methods in Molecular Biology pp 71-79
Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed (Proteomics, Acetylation, Succinylation, Rice seed)
Dongli He, Qiong Wang, Ming Li, Rebecca Njeri Damaris, Xingling Yi, Zhongyi Cheng, and Pingfang Yang
J. Proteome Res., 2016, 15 (3), pp 879–890
The SAGA complex in the rice pathogen Fusarium fujikuroi: structure and functional characterization (Proteomics, LFQ, iBAQ, rice pathogen)
Sarah M. Rösler, Katharina Kramer, Iris Finkemeier, Hans-Ulrich Humpf and Bettina Tudzynski
MOLECULAR MICROBIOLOGY 2016
Biosynthesis of Chlorophyll a in a Purple Bacterial Phototroph and Assembly into a Plant Chlorophyll−Protein Complex (Proteomics, peptide ID, Photosynthesis)
Andrew Hitchcock, Philip J. Jackson, Jack W. Chidgey, Mark J. Dickman, C. Neil Hunter and Daniel P. Canniffe
ACS Synth. Biol., Article ASAP
A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions (Proteomics, rice proteomics, Peptide ID, spectral counting)
Joohyun Lee, Wondo Lee and Soon-Wook Kwon
Proteome Science (2015) 13:27
Systemic cold stress adaptation of Chlamydomonas reinhardtii.
Valledor L, Furuhashi T, Hanak AM, Weckwerth W. Molecular & Cellular Proteomics. 2013 Aug 1;12(8):2032-47.
Possible role of nutritional priming for early salt and drought stress responses in Medicago truncatula.
Staudinger C, Mehmeti V, Turetschek R, Lyon D, Egelhofer V, Wienkoop S. Frontiers in plant science. 2012;3.
Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques.
Komatsu S, Yamamoto A, Nakamura T, Nouri MZ, Nanjo Y, Nishizawa K, Furukawa K. Journal of proteome research. 2011 Aug 2;10(9):3993-4004.
Stress responses to Tomato yellow leaf curl virus (TYLCV) infection of resistant and susceptible tomato plants are different.
Moshe A, Pfannstiel J, Brotman Y, Kolot M, Sobol I, Czosnek H, Gorovits R. Metabolomics S1. 2012;6(10.4172):2153-0769.
Influence of sodium salicylate on rosmarinic acid, carnosol and carnosic acid accumulation by Salvia officinalis L. shoots grown in vitro.
Kračun-Kolarević M, Dmitrović S, Filipović B, Perić M, Mišić D, Simonović A, Todorović S. Biotechnology letters. 2015 Aug 1;37(8):1693-701.
Mass spectrometry‐based metabolomics application to identify quantitative resistance‐related metabolites in barley against Fusarium head blight.
Bollina V, Kumaraswamy GK, Kushalappa AC, Choo TM, Dion Y, Rioux S, Faubert D, Hamzehzarghani H. Molecular plant pathology.2010 Nov 1;11(6):769-82.
Metabolomic analysis of wild and transgenic Nicotiana langsdorffii plants exposed to abiotic stresses: unraveling metabolic responses.
Scalabrin E, Radaelli M, Rizzato G, Bogani P, Buiatti M, Gambaro A, Capodaglio G. Analytical and bioanalytical chemistry. 2015 Aug 1;407(21):6357-68.
Transglutaminase-catalyzed glycosylation of natural actomyosin (NAM) using glucosamine as amine donor: Functionality and gel microstructure.
Hrynets Y, Ndagijimana M, Betti M. Food Hydrocolloids. 2014 May 31;36:26-36.
A comprehensive characterisation of beer polyphenols by high resolution mass spectrometry (LC–ESI-LTQ-Orbitrap-MS).
Quifer-Rada P, Vallverdú-Queralt A, Martínez-Huélamo M, Chiva-Blanch G, Jáuregui O, Estruch R, Lamuela-Raventós R. Food chemistry. 2015 Feb 15;169:336-43.
Profiling the metabolome changes caused by cranberry procyanidins in plasma of female rats using 1H NMR and UHPLC‐Q‐Orbitrap‐HRMS global metabolomics approaches.
Liu H, Garrett TJ, Tayyari F, Gu L. Molecular nutrition & food research. 2015 Nov 1;59(11):2107-18.
Comprehensive identification of walnut polyphenols by liquid chromatography coupled to linear ion trap–Orbitrap mass spectrometry.
Regueiro J, Sánchez-González C, Vallverdú-Queralt A, Simal-Gándara J, Lamuela-Raventós R, Izquierdo-Pulido M. Food chemistry. 2014 Jun 1;152:340-8.
Identification of phenolic compounds in red wine extract samples and zebrafish embryos by HPLC-ESI-LTQ-Orbitrap-MS.
Vallverdú-Queralt A, Boix N, Piqué E, Gómez-Catalan J, Medina-Remon A, Sasot G, Mercader-Martí M, Llobet JM, Lamuela-Raventos RM. Food chemistry. 2015 Aug 15;181:146-51.
Identification and quantification of phytochemicals in nutraceutical products from green tea by UHPLC–Orbitrap-MS.
López-Gutiérrez N, Romero-González R, Plaza-Bolaños P, Vidal JL, Frenich AG. Food chemistry. 2015 Apr 15;173:607-18.
Molecular signatures of transgenerational response to ocean acidification in a species of reef fish.
Schunter C, Welch MJ, Ryu T, Zhang H, Berumen ML, Nilsson GE, Munday PL, Ravasi T. Nat Clim Change. 2016 Nov 1;6:1014-8.
Photoinduced Hydrodefluorination Mechanisms of Perfluorooctanoic Acid by the SiC/Graphene Catalyst.
Huang D, Yin L, Niu J. Environ. Sci. Technol. 2016 May 9;50(11):5857-63.
Use of stable isotope signatures to determine mercury sources in the Great Lakes.
Lepak RF, Yin R, Krabbenhoft DP, Ogorek JM, DeWild JF, Holsen TM, Hurley JP. Environmental Science & Technology Letters. 2015 Nov 25;2(12):335-41.
Degradation of the cytostatic etoposide in chlorinated water by liquid chromatography coupled to quadrupole-Orbitrap mass spectrometry: Identification and quantification of by-products in real water samples.
Negreira N, de Alda ML, Barceló D. Science of The Total Environment. 2015 Feb 15;506:36-45.
Quantitative performance of liquid chromatography coupled to Q-Exactive high resolution mass spectrometry (HRMS) for the analysis of tetracyclines in a complex matrix.
Solliec M, Roy-Lachapelle A, Sauvé S. Analytica chimica acta. 2015 Jan 1;853:415-24.
High resolution/accurate mass (HRMS) detection of anatoxin-a in lake water using LDTD–APCI coupled to a Q-Exactive mass spectrometer.
Roy-Lachapelle A, Solliec M, Sinotte M, Deblois C, Sauvé S. Talanta. 2015 Jan 15;132:836-44.
Ultrasonic or accelerated solvent extraction followed by U-HPLC-high mass accuracy MS for screening of pharmaceuticals and fungicides in soil and plant samples.
Chitescu CL, Oosterink E, de Jong J, Stolker AA. Talanta. 2012 Jan 15;88:653-62.
Broad target chemical screening approach used as tool for rapid assessment of groundwater quality.
ter Laak TL, Puijker LM, van Leerdam JA, Raat KJ, Kolkman A, de Voogt P, van Wezel AP. Science of the Total Environment. 2012 Jun 15;427:308-13.
Lead isotope characterization of petroleum fuels in Taipei, Taiwan.
Yao PH, Shyu GS, Chang YF, Chou YC, Shen CC, Chou CS, Chang TK. International journal of environmental research and public health. 2015 Apr 24;12(5):4602-16.
A precise analytical method for bromine stable isotopes in natural waters by GasBench II-IRMS.
Du Y, Ma T, Yang J, Liu L, Shan H, Cai H, Liu C, Chen L. International Journal of Mass Spectrometry. 2013 Mar 15;338:50-6.
High spatial resolution in situ U–Pb dating using laser ablation multiple ion counting inductively coupled plasma mass spectrometry (LA-MIC-ICP-MS).
Xie LW, Yang JH, Yin QZ, Yang YH, Liu JB, Huang C. Journal of Analytical Atomic Spectrometry. 2017;32(5):975-86.
High-precision zircon U/Pb geochronology by ID-TIMS using new 10 13 ohm resistors.
von Quadt A, Wotzlaw JF, Buret Y, Large SJ, Peytcheva I, Trinquier A. Journal of Analytical Atomic Spectrometry. 2016;31(3):658-65.
Investigation of the effect of ammonium sulfate on populations of ambient methane oxidising bacteria by 13 C-labelling and GC/C/IRMS analysis of phospholipid fatty acids.
Crossman ZM, Wang ZP, Ineson P, Evershed RP. Soil Biology and Biochemistry. 2006 May 31;38(5):983-90.
Precise δ13C analysis of dissolved inorganic carbon in natural waters using automated headspace sampling and continuous‐flow mass spectrometry.
Torres ME, Mix AC, Rugh WD. Limnology and Oceanography: Methods. 2005 Aug 1;3(8):349-60.
Real-time measurements of δ 13 C, CO 2 concentration, and CO 2/SO 2 in volcanic plume gases at Mount Etna, Italy, over 5 consecutive days.
Rizzo AL, Liuzzo M, Ancellin MA, Jost HJ. Chemical Geology. 2015 Sep 14;411:182-91.
The Asian monsoon over the past 640,000 years and ice age terminations.
Wang X, Li X, Kong X, Wang Y, Ning Y, Zhang H. Nature. 2016 Jun;534:30.
The δ30Si peak value discovered in middle Proterozoic chert and its implication for environmental variations in the ancient ocean.
Ding TP, Gao JF, Tian SH, Fan CF, Zhao Y, Wan DF, Zhou JX. Scientific Reports. 2017;7.
CRL2 aids elimination of truncated selenoproteins produced by failed UGA/Sec decoding
Hsiu-Chuan Lin, Szu-Chi Ho, Yi-Yun Chen, et al. Science 2015, 349, 91-95
Transcriptional control of autophagy–lysosome function drives pancreatic cancer metabolism
Rushika M. Perera, Svetlana Stoykova, Brandon N. Nicolay, et al. Nature 524, 361–365, 2015
Structurally Distinct Ca2+ Signaling Domains of Sperm Flagella Orchestrate Tyrosine Phosphorylation and Motility (Proteomics)
Jean-Ju Chung, Sang-Hee Shim, Robert A. Everley, et al. Cell 2014, 157, 808-822
The One Hour Yeast Proteome (Proteomics, peptide ID)
Alexander S. Hebert, Alicia L. Richards, Derek J. Bailey, Arne Ulbrich, Emma E. Coughlin, Michael S. Westphall, and Joshua J. Coon
Molecular & Cellular Proteomics 13, 339–347, 2014.
Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (Proteomics, Neu Code)
Alicia L. Richards, Catherine E. Vincent, Adrian Guthals, Christopher M. Rose, Michael S. Westphall, Nuno Bandeira and Joshua J. Coon
Mol Cell Proteomics 2013 12: 3812-3823
Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates (Proteomics)
Michael W. Senko, Philip M. Remes, Jesse D. Canterbury, Raman Mathur, Qingyu Song,
Shannon M. Eliuk, Chris Mullen, Lee Earley, Mark Hardman, Justin D. Blethrow, Huy Bui,
August Specht, Oliver Lange, Eduard Denisov, Alexander Makarov, Stevan Horning,
and Vlad Zabrouskov
Anal. Chem., 2013, 85 (24), 11710–11714
A novel LC-MS2 product dependent parallel data acquisition function and data analysis workflow for sequencing and identification of intact glycopeptides (Glycoproteomics)
Sz-Wei Wu, Tsung-Hsien Pu, Rosa Viner, and Kay-Hooi Khoo
Anal. Chem., 2014, 86 (11), 5478–5486
Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction
Michael P. Weekes, Peter Tomasec, Edward L. Huttlin, Ceri A. Fielding, David Nusinow, Richard J. Stanton, Eddie C.Y. Wang, Rebecca Aicheler, Isa Murrell, Gavin W.G. Wilkinson, Paul J. Lehner and Steven P. Gygi (Proteomics)
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O-Glycosylation regulates polarized secretion by modulating Tango1 stability
Liping Zhang, Zulfeqhar Ali Syed, Iris van Dijk Härd, Jae-Min Lim, Lance Wells, and Kelly G. Ten Hagen (Glycoproteomics)
PNAS 2014 111 (20) 7296-7301
In vivo monoubiquitination of anaplerotic phosphoenolpyruvate carboxylase occurs at Lys624 in germinating sorghum seeds
Isabel Ruiz-Ballesta, Ana-Belén Feria, Hong Ni, Yi-Min She, William Charles Plaxton, Cristina Echevarría (Proteomics)
Journal of Experimental Botany, Vol. 65, No. 2, pp. 443–451, 2014
A new high-throughput LC-MS method for the analysis of complex fructan mixtures (Glycomics)
Joran Verspreet, Anders Holmgaard Hansen, Emmie Dornez, Christophe M. Courtin and Scott J. Harrison
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Light-dependent chlorophyll f synthase is a highly divergent paralog of PsbA of photosystem II
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A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti
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OsMOGS is required for N-glycan formation and auxin-mediated root development in rice (Oryza sativa L.) (Glycomics)
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In vivo monoubiquitination of anaplerotic phosphoenolpyruvate carboxylase occurs at Lys624 in germinating sorghum seeds (Proteomics, plant proteomics, peptide ID, UBIQUITYLATION)
Isabel Ruiz-Ballesta, Ana-Belén Feria, Hong Ni, Yi-Min She, William Charles Plaxton, Cristina Echevarría
Journal of Experimental Botany, Vol. 65, No. 2, pp. 443–451, 2014
Two-dimensional phos-tag zymograms for tracing phosphoproteins by activity in-gel staining (Proteomics, peptide ID, PHOSPHORYLATION)
Claudia-Nicole Meisrimler, Alexandra Schwendke and Sabine Lüthje
Frontiers in Plants 2015
Identification of regulatory and cargo proteins of endosomal and secretory pathways in Arabidopsis thaliana by proteomic dissection (Proteomics, peptide ID, plant proteomics)
William Heard, Jan Sklenar, Daniel F. A. Tome, Silke Robatzek, and Alexandra M. E. Jones
Mol Cell Proteomics mcp.M115.050286. First Published on April 21, 2015
Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study (Proteomics, peptide ID, plant proteomics)
Felipe Bastida, Carlos García, Martin von Bergen, José L. Moreno, Hans H. Richnow, Nico Jehmlich
Applied Soil Ecology 93 (2015) 65–67
Two serine residues in Pseudomonas syringae effector HopZ1a are required for acetyltransferase activity and association with the host co-factor (Proteomics, peptide IDs, plant proteomics)
Ka-Wai Ma, Shushu Jiang, Eva Hawara, DongHyuk Lee, Songqin Pan, Gitta Coaker, Jikui Song and Wenbo Ma
New Phytologist 2015
S-Nitrosation of Conserved Cysteines Modulates Activity and Stability of S-Nitrosoglutathione Reductase (GSNOR) (proteomics, plants, Intact)
Damian Guerra, Keith Ballard, Ian Truebridge, and Elizabeth Vierling
Biochemistry, 2016, 55 (17), pp 2452–2464
Molecular cloning of plane pollen allergen Pla a 3 and its utility as diagnostic marker for peach associated plane pollen allergy biotransformation (proteomics, plants peptide ID)
Wangorsch, H. Larsson, M. Messmer, A. Garcıa-Moral, I. Lauer, S. Wolfheimer, S. Schulke, J. Bartra , S. Vieths, J. Lidholm and S. Scheurer
Clinical & Experimental Allergy, 46, 764–774, 2016
Application of wide selected-ion monitoring (WiSIM)-data independent acquisition (DIA) to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor (Proteomics, WiSIM-DIA, PLANT)
Laetitia B.B. Martin, Robert W. Sherwood, Joshua J. Nicklay, Yong Yang, Tara L. Muratore-Schroeder, Elizabeth T. Anderson, Theodore. W. Thannhauser, Jocelyn K.C. Rose, Sheng Zhang
Proteomics
New insights into the post-translational modification of multiple phosphoenolpyruvate carboxylase isoenzymes by phosphorylation and monoubiquitination during sorghum seed development and germination (Proteomics, UBIQUITYLATION, PLANTS)
Isabel Ruiz-Ballesta, Guillermo Baena, Jacinto Gandullo, Liqun Wang, Yi-Min She, William Charles Plaxton and Cristina Echevarría
Journal of Experimental Botany, Vol. 67, No. 11 pp. 3523–3536, 2016
Selenium promotes sulfur accumulation and plant growth in wheat (Triticum aestivum) (Proteomics, LFQ, Plants)
Paulo F. Boldrin, Marislaine A. de Figueiredo, Yong Yang, Hongmei Luo, Shree Giri, Jonathan J. Hart, Valdemar Faquin, Luiz R.G. Guilherme, Theorodore W. Thannhauser and Li Li
Physiologia Plantarum 2016
Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis(Glycoproteomics, N-Glycopeptide, Plants)
Jun Ma, Dinghe Wang, Jessica She, Jianming Li, Jian-Kang Zhu and Yi-Min She
NEW PHYTOLOGIST
Development of a laser capture microscope-based single-cell-type proteomics tool for studying proteomes of individual cell layers of plant roots (Proteomics, Peptide IDs, Plants)
Yingde Zhu, Hui Li, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish, and Theodore W Thannhauser
Hortic Res. 2016; 3: 16026
Development of a laser capture microscope-based single-cell-type proteomics tool for studying proteomes of individual cell layers of plant roots (Proteomics, peptide ID, Plant proteomics)
Yingde Zhu, Hui Li, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish and Theodore W Thannhauser
Horticulture Research (2016) 3, 16026; doi:10.1038/hortres.2016.26
Insight into enzymatic degradation of corn, wheat, and soybean cell wall cellulose using quantitative secretome analysis of Aspergillus fumigatus (Proteomics, iTRAQ MS2, plants)
Prakriti Sharma Ghimire, Haomiao Ouyang, Qian Wang, Yuanming Luo, Bo Shi, Jinghua Yang, Yang Lu, and Cheng Jin
J. Proteome Res., Just Accepted Manuscript
Mapping the Triticum aestivum proteome (Proteomics, peptide ID, Triticum aestivum proteome)
Owen Duncan, Josua Trösch, Ricarda Fenske, Nicolas L. Taylor and A Harvey Millar
THE PLANT JOURNAL Accepted manuscript online: 24 OCT 2016
Effects of the Herbicide Imazethapyr on Photosynthesis in PGR5- and NDH-Deficient Arabidopsis thaliana at the Biochemical, Transcriptomic, and Proteomic Levels (Proteomics, iTRAQ, Photosynthesis, Plants)
Chongchong Sun, Si Chen, Yujian Jin, Hao Song, Songlin Ruan, Zhengwei Fu, Muhammad Asad Ullah Asad, and Haifeng Qian
J. Agric. Food Chem., 2016, 64 (22), pp 4497–4504
Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2–MND1 (Proteomics, crosslinking, complex conformations in solution of the plant HOP2–MND1 complex)
Evelyn Rampler, Thomas Stranzl, Zsuzsanna Orban-Nemeth, David Maria Hollenstein, Otto Hudecz, Peter Schlögelhofer, and Karl Mechtler
J. Proteome Res., 2015, 14 (12), pp 5048–5062
Protein Dynamics in Young Maize Root Hairs in Response to Macro- and Micronutrient Deprivation (Proteomics, Phosphopeptides, LFQ, Young Maize Root Hairs, Plants)
Zhi Li, Daniel Phillip, Benjamin Neuhäuser, Waltraud X. Schulze, and Uwe Ludewig
J. Proteome Res., 2015, 14 (8), pp 3362–3371
New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants (Proteomics, iTRAQ, Plants)
Islam Mostafa, Ning Zhu, Mi-Jeong Yoo, Kelly M. Balmant, Biswapriya B. Misra, Craig Dufresne, Maged Abou-Hashem, Sixue Chen, Maher El-Domiaty
Journal of Proteomics, Volume 138, 14 April 2016, Pages 1-19
PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity (Proteomics, ADP-ribosylation, Plants)
Baomin Feng, Shisong Ma, Sixue Chen, Ning Zhu, Shuxin Zhang, Bin Yu, Yu Yu, Brandon Le, Xuemei Chen, Savithramma P Dinesh-Kumar, Libo Shan and Ping He
EMBO Rep. 2016 Oct 18. pii: e201642486. [Epub ahead of print]
Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition (Proteomics, Phosphorylation, LFQ, roots)
Jochen Menz, Zhi Li, Waltraud X. Schulze and Uwe Ludewig
THE PLANT JOURNAL 2106
Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling (Proteomics, peptide ID, plants, heat stress)
Krzysztof Brzezinka, Simone Altmann, Hjördis Czesnick, Philippe Nicolas, Michal Gorka, Eileen Benke, Tina Kabelitz, Felix Jähne, Alexander Graf, Christian Kappel, Isabel Bäurle
Elife. 2016 Sep 28;5. pii: e17061
Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease (Proteomics, TMT, Huanglongbing disease)
Federico Martinelli, Russell L. Reagan, David Dolan, Veronica Fileccia and Abhaya M. Dandekar
BMC Plant Biology (2016) 16:167 https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0858-5
Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.) (Proteomics, Phosphorylation, rice)
Jiehua Qiu, Yuxuan Hou, Xiaohong Tong, Yifeng Wang, Haiyan Lin, Qing Liu, Wen Zhang, Zhiyong Li, Babi R. Nallamilli, Jian Zhang
Plant Mol Biol (2016) 90:249–265
From Phosphoproteome to Modeling of Plant Signaling Pathways (proteomics, Phosphoproteomics, Protocols)
Maksim Zakhartsev , Heidi Pertl-Obermeyer, Waltraud X. Schulze
Proteomics in Systems Biology Volume 1394 of the series Methods in Molecular Biology pp 245-259
A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight (Proteomics, Phosphoproteomics, RICE, BACTERIAL BLIGHT)
Yuxuan Hou, Jiehua Qiu, Xiaohong Tong, Xiangjin Wei, Babi R. Nallamilli, Weihuai Wu, Shiwen Huang and Jian Zhang
BMC Plant Biology (2015) 15:163
Phosphopeptide Profiling of Receptor Kinase Mutants (proteomics, Phosphoproteomics, Protocols, Receptor Kinase Mutants)
Xu Na Wu and Waltraud X. Schulze
Plant Phosphoproteomics Volume 1306 of the series Methods in Molecular Biology pp 71-79
Global Proteome Analyses of Lysine Acetylation and Succinylation Reveal the Widespread Involvement of both Modification in Metabolism in the Embryo of Germinating Rice Seed (Proteomics, Acetylation, Succinylation, Rice seed)
Dongli He, Qiong Wang, Ming Li, Rebecca Njeri Damaris, Xingling Yi, Zhongyi Cheng, and Pingfang Yang
J. Proteome Res., 2016, 15 (3), pp 879–890
The SAGA complex in the rice pathogen Fusarium fujikuroi: structure and functional characterization (Proteomics, LFQ, iBAQ, rice pathogen)
Sarah M. Rösler, Katharina Kramer, Iris Finkemeier, Hans-Ulrich Humpf and Bettina Tudzynski
MOLECULAR MICROBIOLOGY 2016
Biosynthesis of Chlorophyll a in a Purple Bacterial Phototroph and Assembly into a Plant Chlorophyll−Protein Complex (Proteomics, peptide ID, Photosynthesis)
Andrew Hitchcock, Philip J. Jackson, Jack W. Chidgey, Mark J. Dickman, C. Neil Hunter and Daniel P. Canniffe
ACS Synth. Biol., Article ASAP
A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions (Proteomics, rice proteomics, Peptide ID, spectral counting)
Joohyun Lee, Wondo Lee and Soon-Wook Kwon
Proteome Science (2015) 13:27
Systemic cold stress adaptation of Chlamydomonas reinhardtii.
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Possible role of nutritional priming for early salt and drought stress responses in Medicago truncatula.
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Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques.
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Stress responses to Tomato yellow leaf curl virus (TYLCV) infection of resistant and susceptible tomato plants are different.
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Mass spectrometry‐based metabolomics application to identify quantitative resistance‐related metabolites in barley against Fusarium head blight.
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Metabolomic analysis of wild and transgenic Nicotiana langsdorffii plants exposed to abiotic stresses: unraveling metabolic responses.
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A comprehensive characterisation of beer polyphenols by high resolution mass spectrometry (LC–ESI-LTQ-Orbitrap-MS).
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Profiling the metabolome changes caused by cranberry procyanidins in plasma of female rats using 1H NMR and UHPLC‐Q‐Orbitrap‐HRMS global metabolomics approaches.
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Comprehensive identification of walnut polyphenols by liquid chromatography coupled to linear ion trap–Orbitrap mass spectrometry.
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Identification of phenolic compounds in red wine extract samples and zebrafish embryos by HPLC-ESI-LTQ-Orbitrap-MS.
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Identification and quantification of phytochemicals in nutraceutical products from green tea by UHPLC–Orbitrap-MS.
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Photoinduced Hydrodefluorination Mechanisms of Perfluorooctanoic Acid by the SiC/Graphene Catalyst.
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Use of stable isotope signatures to determine mercury sources in the Great Lakes.
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Degradation of the cytostatic etoposide in chlorinated water by liquid chromatography coupled to quadrupole-Orbitrap mass spectrometry: Identification and quantification of by-products in real water samples.
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Quantitative performance of liquid chromatography coupled to Q-Exactive high resolution mass spectrometry (HRMS) for the analysis of tetracyclines in a complex matrix.
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High resolution/accurate mass (HRMS) detection of anatoxin-a in lake water using LDTD–APCI coupled to a Q-Exactive mass spectrometer.
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Ultrasonic or accelerated solvent extraction followed by U-HPLC-high mass accuracy MS for screening of pharmaceuticals and fungicides in soil and plant samples.
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Broad target chemical screening approach used as tool for rapid assessment of groundwater quality.
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Lead isotope characterization of petroleum fuels in Taipei, Taiwan.
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A precise analytical method for bromine stable isotopes in natural waters by GasBench II-IRMS.
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High spatial resolution in situ U–Pb dating using laser ablation multiple ion counting inductively coupled plasma mass spectrometry (LA-MIC-ICP-MS).
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High-precision zircon U/Pb geochronology by ID-TIMS using new 10 13 ohm resistors.
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