医学与生命科学

客户使用赛默飞色谱与质谱仪器发表文章列表（部分）

1 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

2 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

3 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

4 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. 5 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 6 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 7 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 8 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 9 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 10 Low-density lipoprotein receptor class A repeats are O-glycosylated in linker regions Nis Borbye Pedersen, Shengjun Wang, Yoshiki Narimatsu, Zhang Yang, Adnan Halim, Katrine Ter-Borch Gram Schjoldager, Thomas Daugbjerg Madsen, Nabil G. Seidah, Eric Paul Bennett, Steven B. Levery, Henrik Clausen (Glycoproteomics) J. Biol. Chem. 2014 289: 17312-17324 11 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 12 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 13 Immunoprecipitation and mass spectrometry identify non-cell autonomous Otx2 homeoprotein in the granular and supragranular layers of mouse visual cortex (Proteomics) Namsuk Kim, Dario Acampora, Florent Dingli, Damarys Loew, Antonio Simeone, Alain Prochiantz and Ariel A. Di Nardo F1000Research 2014, 3:178 Last updated: 15 AUG 2014 14 B4GAT1 is the Priming Enzyme 1 for the LARGE-dependent Functional Glycosylation of -Dystroglycan (Glycomics) Jeremy L. Praissman, David H. Live, Shuo Wang, Annapoorani Ramiah, Zoeisha S. Chinoy, Geert-Jan Boons, Kelley W. Moremen and Lance Wells eLife 2014;3:e03943 15 Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex (Proteomics)

Yi Shi, Javier Fernandez-Martinez, Elina Tjioe, Riccardo Pellarin, Seung Joong Kim, Rosemary Williams, Dina Schneidman-Duhovny, Andrej Sali, Michael P. Rout and Brian T. Chait Mol Cell Proteomics 2014, 13 (11), 2927-2943 16 Reliable Identification of Cross-Linked Products in Protein Interaction Studies by 13C-Labeled p-Benzoylphenylalanine (Proteomics) Jens Pettelkau, Christian H. Ihling, Petra Frohberg, Lars van Werven, Olaf Jahn and Andrea Sinz J Am Soc Mass Spectrom. 2014, 25, 1628-1641 17 Liquid chromatography/mass spectrometry analysis of branched fructans produced in vitro with 13C-labeled substrates (Glycomics) Joran Verspreet, Anders Holmgaard Hansen, Emmie Dornez, Jan A. Delcour, Scott J. Harrison and Christophe M. Courtin Rapid Commun. Mass Spectrom. 2014, 28, 1–10 18 Integrated solid phase extraction – capillary liquid chromatography (speLC) interfaced to ESI-MS/MS for fast characterization and quantification of protein and proteomes (Proteomics) Lasse Gaarde Falkenby, Gerard Such-Sanmartín, Martin R. Larsen, Ole Vorm, Nicolai Bache, and Ole Nørregaard Jensen J. Proteome Res. 2014, 13(12), 6169-6175 19 Over 10000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry (Proteomics) Liangliang Sun, Alexander S. Hebert, Xiaojing Yan, Yimeng Zhao, Michael S. Westphall, Matthew J. P. Rush, Guijie Zhu, Matthew M. Champion, Joshua J. Coon, and Norman J. Dovichi Angew. Chem. 2014, 126, 1 – 4 20 The complete and ubiquitinated proteome of the Legionella-containing vacuole within human macrophages (Proteomics) William M. Bruckert and Yousef Abu Kwaik J. Proteome Res., Just Accepted 21 Human Serum Proteins Recognized by CA215 and Cancerous Immunoglobulins and Implications in Cancer Immunology (Proteomics) Gregory Lee, Suefay Liu and Cheng-Yuan Huang Cancer and Clinical Oncology; Vol. 3, No. 2; 2014 22 CRISPR-Cas9-Based Knockout of the Prion Protein and Its Effect on the Proteome

(Proteomics) Mohadeseh Mehrabian, Dylan Brethour, Sarah MacIsaac, Jin Kyu Kim, C. Geeth Gunawardana, Hansen Wang and Gerold Schmitt-Ulms PLOS ONE | DOI:10.1371/journal.pone.0114594 23 Quantitative Analysis of Targeted Proteins in Complex Sample Using Novel Data Independent Acquisition (Proteomics) ZHANG Wei, Reiko Kiyonami, JIANG Zheng, CHEN Wei CHINESE JOURNAL OF ANALYTICAL CHEMISTRY, Volume 42, Issue 12, December 2014 24 SIRT1 Deacetylates TopBP1 and Modulates Intra-S-Phase Checkpoint and DNA Replication Origin Firing (Proteomics) Rui-Hong Wang, Tyler J. Lahusen, Qiang Chen, Xiaoling Xu, Lisa M. Miller Jenkins, Elisabetta Leo, Haiqing Fu, Mirit Aladjem, Yves Pommier, Ettore Appella, Chu-Xia Deng Int J Biol Sci 2014; 10(10):1193-1202 25 Blau Syndrome–Associated Nod2 Mutation Alters Expression of Full-Length NOD2 and Limits Responses to Muramyl Dipeptide in Knock-in Mice (Proteomics) Jae Dugan, Eric Griffiths, Paige Snow, Holly Rosenzweig, Ellen Lee, Brieanna Brown, Daniel W. Carr, Carlos Rose, James Rosenbaum, Michael P. Davey J Immunol 2015 194:349-357 26 Cortical Tubers: Windows into Dysregulation of Epilepsy Risk and Synaptic Signaling Genes by MicroRNAs (Proteomics) Alan A. Dombkowski, Carlos E. Batista, Daniela Cukovic,Nicholas J. Carruthers, Ramya Ranganathan, Upasana Shukla, Paul M. Stemmer, Harry T. Chugani and Diane C. Chugani Cerebral Cortex, 2014, 1–13 27 Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/Orbitrap mass spectrometer (Proteomics) Brian K Erickson, Mark P Jedrychowski, Graeme C. McAlister, Robert A. Everley, Ryan C Kunz, and Steven P. Gygi Anal. Chem., Just Accepted Manuscript, Publication Date (Web): 18 Dec 2014 28 Versatile characterization of glycosylation modification in CTLA4-Ig fusion proteins by liquid chromatography mass spectrometry (Glycoproteomics) Lei Zhu, Qingcheng Guo, Huaizu Guo, Tao Liu, Yingxin Zheng, Peiming Gu, Xi Chen, Hao Wang, Sheng Hou and Yajun Guo mAbs 6:6, 1474—1485, 2014 29 LC-MS analysis reveals the presence of graminan- and neo-type fructans 1 in wheat grains (Glycomics) Joran Verspreet, Anders Holmgaard Hansen, Emmie Dornez, Jan A. Delcour, Wim Van den Ende, Scott J. Harrison and Christophe M. Courtin

Journal of Cereal Science, In Press, Accepted Manuscript, Available online 27 December 2014 30 Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis (Proteomics) Capucine Van Rechem, Joshua C. Black, Myriam Boukhali, Martin J. Aryee, Susanne Gräslund, Wilhelm Haas, Cyril H. Benes and Johnathan R. Whetstine Cancer Discovery, 2015 31 Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis (Proteomics) Simone Sidoli, Zuo-Fei Yuan, Shu Lin, Kelly Karch, Xiaoshi Wang, Natarajan Bhanu, Anna M. Arnaudo, Laura-Mae Britton, Xing-Jun Cao, Michelle Gonzales-Cope, Yumiao Han, Shichong Liu, Rosalynn C. Molden, SamuelWein, Leila Afjehi-Sadat and Benjamin A. Garcia Proteomics 2015 32 Hyaluronan synthase assembles chitin oligomers with -GlcNAc(α1)UDP at the reducing end (Glycomics) Paul H. Weigel, Christopher M. West, Peng Zhao, Lance Wells, Bruce A. Baggenstoss and Jennifer L. Washburn Glycobiology (2015) 33 Multiplexed quantification for data-independent acquisition (Proteomics) Catherine E. Minogue, Alexander S. Hebert, Jarred W. Rensvold, Michael S. Westphall, David J. Pagliarini, and Joshua J. Coon Anal. Chem., Just Accepted Manuscript 34 Dissociation behavior of a bifunctional tempoactive ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry (Proteomics) Christian Ihling, Francesco Falvo, Isabel Kratochvil, Andrea Sinz and Mathias Schäfer J. Mass Spectrom. 2015, 50, 396–406 35 Regulation and Function of Phosphorylation on VP8, the Major Tegument Protein of 2 Bovine Herpesvirus-1 (Proteomics) Kuan Zhang , Sharmin Afroz , Robert Brownlie, Marlene Snider , Sylvia van Drunen Littel-van den Hurk Journal of Virology 2015 36 Extending the Cross-Linking/Mass Spectrometry Strategy: Facile Incorporation of Photo-Activatable Amino Acids into the Model Protein Calmodulin in Escherichia coli Cells (Proteomics) Christine Piotrowski, Christian H. Ihling, and Andrea Sinz

Methods, 2015 In Press, Accepted Manuscript 37 Bottom-up and middle-down proteomics have comparable accuracies in defining histone PTM relative abundance and stoichiometry (Proteomics) Simone Sidoli, Shu Lin, Kelly Rose Karch, and Benjamin Aaron Garcia Anal. Chem., Just Accepted Manuscript 38 Phosphorylation of Synaptic GTPase-activating Protein (synGAP) by Ca2+/Calmodulin-dependent Protein Kinase II (CaMKII) and Cyclin-dependent Kinase 5 (CDK5) Alters the Ratio of Its GAP Activity toward Ras and Rap GTPases (Proteomics) Ward G. Walkup IV, Lorraine Washburn , Michael J. Sweredoski , Holly J. Carlisle, Robert L. Graham, Sonja Hess, and Mary B. Kennedy THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 290, NO. 8, pp. 4908-4927 39 “You produce while I clean up”, a strategy revealed by exoproteomics during Synechococcus-Roseobacter interactions (Proteomics) Joseph A. Christie-Oleza, David J. Scanlan, Jean Armengaud PROTEOMICS 2015 Accepted manuscript 40 Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation (Proteomics) Katherine A. Overmyer, Charles R. Evans, Nathan R. Qi, Catherine E. Minogue, Joshua J. Carson, Christopher J. Chermside-Scabbo, Lauren G. Koch, Steven L. Britton, David J. Pagliarini, Joshua J. Coon, Charles F. Burant Cell Metabolism 21, 2015, 468-478 41 Structure of Full-Length p53 Tumor Suppressor Probed by Chemical Cross-Linking and Mass Spectrometry Christian Arlt, Christian H. Ihling, and Andrea Sinz (Proteomics) Proteomics 2015 42 Venomics, lethality and Neutralization of Naja kaouthia (monocled cobra) venoms from three different geographical regions of Southeast Asia Kae Yi Tan , Choo Hock Tan, Shin Yee Fung, Nget Hong Tan (Proteomics) Journal of Proteomics 2015 43 Analysis of the Candida albicans phosphoproteome (Proteomics) Willger SD , Liu Z , Olarte RA , Adamo ME , Stajich JE , Myers LC , Kettenbach AN , Hogan DA Eukaryot Cell 2015 44 Cotranslational Stabilization of Sec62/63 within the ER Sec61 Translocon Is Controlled by Distinct Substrate-Driven Translocation Events (Proteomics) Brian J. Conti, Prasanna K. Devaraneni, Zhongying Yang, Larry L. David and William R.

Skach Molecular Cell 58, 1–15, 2015 45 Benchmarking multiple fragmentation methods on an Orbitrap Fusion for top-down phospho-proteoform characterization (Proteomics) Andrea M. Brunner, Philip Lossl, Fan Liu, Romain Huguet, Christopher Mullen, Masami Yamashita, Vlad Zabrouskov, Alexander Makarov, A. F. Maarten Altelaar, and Albert J.R. Heck Anal. Chem., 2015 46 Enrichment of Low-Abundant Protein Targets by Immunoprecipitation Upstream of Mass Spectrometry (Proteomics) Barbara Kaboord , Suzanne Smith , Bhavin Patel , and Scott Meier Methods Mol Biol. 2015;1295:135-151 47 Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm (Proteomics) Ethan S. Lippmann, Clay E. Williams, David A. Ruhl, Maria C. Estevez-Silva, Edwin R. Chapman, Joshua J. Coon and Randolph S. Ashton Stem Cell reports 2015, 4, 1-13 48 SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching (Proteomics) Kristin E. Dittenhafer-Reed, Alicia L. Richards, Jing Fan, Michael J. Smallegan, Alireza Fotuhi Siahpirani, Zachary A. Kemmerer, Tomas A. Prolla, Sushmita Roy, Joshua J. Coon and John M. Denu Cell Metabolism 21, 637–646, 2015 49 One-hour proteome analysis in yeast (Proteomics) Alicia L Richards, Alexander S Hebert, Arne Ulbrich, Derek J Bailey, Emma E Coughlin, Michael S Westphall and Joshua J Coon Nature Protocols 2015, 10, 701-714 50 The Plasmodium falciparum exportome contains non-canonical PEXEL/HT proteins (Proteomics) Jana Schulze, Marcel Kwiatkowski, Janus Borner, Hartmut Schlüter, Iris Bruchhaus, Thorsten Burmester, Tobias Spielmann, Christian Pick Mol Microbiol. 2015 Apr 8. doi: 10.1111/mmi.13024. [Epub ahead of print] 51 Identification of regulatory and cargo proteins of endosomal and secretory pathways in Arabidopsis thaliana by proteomic dissection (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 52 Deforestation fosters bacterial diversity and the cyanobacterial community

responsible for carbon fixation processes under semiarid climate: a metaproteomics study (Proteomics) Felipe Bastida, Carlos García, Martin von Bergen, José L. Moreno, Hans H. Richnow, Nico Jehmlich Applied Soil Ecology 93 (2015) 65–67 53 Enzymatic characterization of recombinant nitrate reductase expressed 5 and purified from Neurospora crassa (Proteomics) Phillip Ringel, Corinna Probst, Thorben Dammeyer, Sabine Buchmeier, Lothar Jänsch, Josef Wissing, Philip Tinnefeld, Ralf R. Mendel, Brigitte M. Jockusch, Tobias Kruse Fungal Genetics and Biology xxx (2015) xxx–xxx 54 Low pH Solid Phase Amino-Labelling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis (Proteomics) Gitte Böhm, Petra Prefot, Stephan Jung, Stefan Selzer, Vikram Mitra, David Britton, Karsten Kuhn, Ian Pike, and Andrew Hugin Thompson J. Proteome Res., Just Accepted Manuscript 55 N-lactoyl-amino acids are ubiquitous metabolites that originate from CNDP2-mediated reverse proteolysis of lactate and amino acids (Proteomics) (metabolimcs done Orbi XL) Robert S. Jansen , Ruben Addie , Remco Merk , Alexander Fish , Sunny Mahakena , Onno B. Bleijerveld, Maarten Altelaar, Lodewijk IJlste , Ronald J. Wanderse, P. Borst , and Koen van de Wetering PNAS Early Edition 56 Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications (Proteomics) Rosalynn C Molden, Natarajan V Bhanu, Gary LeRoy, Anna M Arnaudo and Benjamin A Garcia Molden et al. Epigenetics & Chromatin (2015) 8:15 57 SuperQuant: a Data Processing Approach to Increase Quantitative Proteome Coverage (Proteomics) Vladimir Gorshkov, Thiago Verano-Braga, and Frank Kjeldsen Anal. Chem., Just Accepted Manuscript 58 Subunit Interactions within the Carbon−Phosphorus Lyase Complex from Escherichia coli (Proteomics) Zhongjie Ren, Soumya Ranganathan, Nathanael F. Zinnel, William K. Russell, David H. Russell and Frank M. Raushel Biochemistry, Article ASAP

59 Identification of peptidic substrates for the human kinase Myt1 using peptide microarrays (Proteomics) Alexander Rohe, Charlott Platzer, Antonia Masch, Sandra Greiner, Claudia Henze, Christian Ihling, Frank Erdmann, Mike Schutkowski, Wolfgang Sippl, Matthias Schmidt Bioorganic & Medicinal Chemistry 2015 60 Redox Control of Protein Arginine Methyltransferase 1 (PRMT1) Activity (Proteomics) Yalemi Morales, Damon V. Nitzel, Owen M. Price, Shanying Gui, Jun Li, Jun Qu, Joan M. Hevel Journal of Biological Chemistry 2015 61 Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome (Proteomics) Kaylen Lott, Shreya Mukhopadhyay, Jun Li, Jie Wang, Jin Yao, Yijun Sun, Jun Qu and Laurie K. Read Nucl. Acids Res. (2015) 62 Rapid, optimized interactomic screening (Proteomics) Zhanna Hakhverdyan, Michal Domanski, Loren E Hough, Asha A Oroskar, Anil R Oroskar, Sarah Keegan, David J Dilworth, Kelly R Molloy, Vadim Sherman, John D Aitchison, David Fenyö, Brian T Chait, Torben Heick Jensen, Michael P Rout and John LaCava Nature Methods 2015 12, 553-560 63 Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii (Proteomics) Mahmoud Gargouri, Jeong-Jin Park, F. Omar Holguin, Min-Jeong Kim, Hongxia Wang, Rahul R. Deshpande, Yair Shachar-Hill, Leslie M. Hicks and David R. Gang Journal of Experimental Botany doi:10.1093/jxb/erv217 64 An Improvement on MS-based Epigenetic Analysis of Large Histone-derived Peptides by Using the IVU Interface (Proteomics) Tetsuya Fukuda, Hiroshi Hike, Fumihiko Usui, Yasuhiko Bando, Toshihide Nishimura, Tatsuhiko Kodama, and Takeshi Kawamura Analytical Biochemistry 2015 65 Venomics of the beaked sea snake, Hydrophis schistosus: a minimalist toxin arsenal and its cross-neutralization by heterologous antivenoms (Proteomics) Choo Hock Tan, Kae Yi Tan, Sin Ee Lim, Nget Hong Tan Journal of Proteomics 2015 66 Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy (Proteomics) Alban Ordureau, Jin-Mi Heo, David M. Duda, Joao A. Paulo, Jennifer L. Olszewski, David

Yanishevski, Jesse Rinehart, Brenda A. Schulman and J. Wade Harper PNAS 205, 112, 6637–6642

67 Primary Sequence Confirmation of a Protein Therapeutic using Top Down MS/MS and MS3 (Proteomics) Michaella J. Levy, Ashley C. Gucinski, and Michael T. Boyne Anal. Chem., Just Accepted Manuscript 68 An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas (Proteomics) Piero Giansanti, Thin Thin Aye, Henk van den Toorn, Mao Peng, Bas van Breukelen, Albert J.R. Heck Cell Reports 11, 1–10, June 23, 2015 69 Low-pH Solid-Phase Amino Labeling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis (Proteomics) Gitte Bohm, Petra Prefot, Stephan Jung, Stefan Selzer, Vikram Mitra, David Britton, Karsten Kuhn, Ian Pike and Andrew H. Thompson J. Proteome Res., 2015, 14 (6), pp 2500–2510 70 SuperQuant: A Data Processing Approach to Increase Quantitative Proteome Coverage Vladimir Gorshkov, Thiago Verano-Braga and Frank Kjeldsen (Proteomics) Anal. Chem., 2015, 87 (12), pp 6319–6327 71 Subunit Interactions within the Carbon−Phosphorus Lyase Complex from Escherichia coli (Proteomics) Zhongjie Ren, Soumya Ranganathan, Nathanael F. Zinnel, William K. Russell, David H. Russell, and Frank M. Raushel Biochemistry, 2015, 54 (21), pp 3400–3411 72 Comprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae (Proteomics) J. Patrick Murphy , Ekaterina Stepanova , Robert A. Everley, Joao A. Paulo and Steven P. Gygi Mol Cell Proteomics mcp.M114.045849. First Published on June 15, 2015,doi:10.1074/mcp.M114.045849 73 Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph (Proteomics) Carolina Grob, Martin Taubert, Alexandra M. Howat , Oliver J. Burns , Joanna L. Dixon , Hans H. Richnow , Nico Jehmlich , Martin von Bergen, Yin Chen and J. Colin Murrell Environmental Microbiology 2015

74 Undetectable Histone O-GlcNAcylation in Mammalian Cells (Proteomics) Jessica Gagnon , Salima Daou , Natalia Zamorano , Nicholas V G Ianantuono , Ian HammondMartel , Nazar Mashtalir , Eric Bonneil , Hugo Wurtele , Pierre Thibault and El Bachir Affar Epigenetics 2015

75 Fast Comparative Structural Characterization of Intact Therapeutic Antibodies Using Hydrogen−Deuterium Exchange and Electron Transfer Dissociation (Proteomics) Jingxi Pan, Suping Zhang, Albert Chou, Darryl B. Hardie and Christoph H. Borchers Anal. Chem., 2015, 87 (12), pp 5884–5890 76 Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics (Proteomics) Katarzyna Kulej, Daphne C. Avgousti, Matthew D. Weitzman and Benjamin A. Garcia Methods xxx (2015) xxx–xxx 77 Middle-down electron capture dissociation and electron transfer dissociation for histone analysis (Proteomics) Annie Moradian, Catarina Franco, Michael J. Sweredoski and Sonja Hess Journal of Analytical Science and Technology (2015) 6:21 78 Filamin A phosphorylation by Akt promotes cell migration in response to arsenic (Proteomics) Lingzhi Li, Yongju Lu, Paul M. Stemmer and Fei Chen Oncotarget 2015, 6, 12009-12019

79 Reductive dehalogenation of oligocyclic phenolic bromoaromatics by Dehalococcoides mccartyi strain CBDB1 (Proteomics) Chao Yang, Anja Kublik, Cindy Weidauer, Bettina Seiwert, and Lorenz Adrian Environ. Sci. Technol., Just Accepted Manuscript 80 Two serine residues in Pseudomonas syringae effector HopZ1a are required for acetyltransferase activity and association with the host co-factor (Proteomics) Ka-Wai Ma, Shushu Jiang, Eva Hawara, DongHyuk Lee, Songqin Pan, Gitta Coaker, Jikui Song and Wenbo Ma New Phytologist 2015

81 A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation (Proteomics)

Anand Minajigi, John E. Froberg, Chunyao Wei, Hongjae Sunwoo, Barry Kesner, David Colognori, Derek Lessing, Bernhard Payer, Myriam Boukhali, Wilhelm Haas Jeannie T. Lee Science DOI: 10.1126/science.aab2276 82 A Calibration Routine for Efficient ETD in Large-Scale Proteomics (Proteomics) Christopher M. Rose, Matthew J. P. Rush, Nicholas M. Riley, Anna E. Merrill, Nicholas W. Kwiecien, Dustin D. Holden, Christopher Mullen, Michael S. Westphall and Joshua J.

Coon J. Am. Soc. Mass Spectrom. (2015) 83 Determination of Histidine pKa Values in the Propeptides of Furin and PC1/3 using Histidine Hydrogen-Deuterium Exchange Mass Spectrometry (Proteomics) Johannes Elferich, Danielle M Williamson, Larry L. David, and Ujwal P Shinde Anal. Chem., Just Accepted Manuscript (2015) 84 Purification of wheat grain fructans from wheat bran (Glycomics) Joran Verspreet, Emmie Dornez, Jan A. Delcour, Scott J. Harrison, Christophe M. Courtin Journal of Cereal Science, 2015 85 Lenalidomide induces ubiquitination and degradation of CK1a in del(5q) MDS (Proteomics) Jan Kronke, Emma C. Fink, Paul W. Hollenbach, Kyle J. MacBeth, Slater N. Hurst, Namrata D. Udeshi, Philip P. Chamberlain, D. R. Mani, Hon Wah Man, Anita K. Gandhi, Tanya Svinkina, Rebekka K. Schneider, Marie McConkey, Marcus Jaras, Elizabeth Griffiths, Meir Wetzler, Lars Bullinger, Brian E. Cathers, Steven A. Carr, Rajesh Chopra & Benjamin L. Ebert Nature 2015 86 Differences in solution dynamics between lens β-crystallin homodimers and heterodimers probed by hydrogen-deuterium exchange and deamidation (Proteomics) Kirsten J. Lampi, Matthew R. Murray, Matthew P. Peterson, Bryce S. Eng, Eileen Yue, Alice R. Clark, Elisar Barbar, Larry L. David Biochimica et Biophysica Acta Available online 3 July 2015 87 High Resolution Parallel Reaction Monitoring with Electron Transfer Dissociation for Middle-Down Proteomics (Proteomics) Michael J. Sweredoski, Annie Moradian, Matthias Raedle, Catarina Franco and Sonja Hess Anal. Chem. XXXX, XXX, XXX−XXX 88 A High-Efficiency Cellular Extraction System for Biological Proteomics (Proteomics) Avantika Dhabaria, Paolo Cifani, Casie Reed, Hanno Steen and Alex Kentsis J. Proteome Res. XXXX, XXX, XXX−XXX 89 Acidosis-Induced Changes in Proteome Patterns of the Prostate Cancer-Derived Tumor Cell Line AT-1 (Proteomics) Angelika Ihling, Christian H. Ihling, Andrea Sinz, and Michael Gekle J. Proteome Res., Just Accepted Manuscript 90 Engineered CHO cells for production of diverse, homogeneous glycoproteins (Glycomics)

Zhang Yang, Shengjun Wang, Adnan Halim, Morten Alder Schulz, Morten Frodin, Shamim H Rahman, Malene B Vester-Christensen, Carsten Behrens, Claus Kristensen, Sergey Y Vakhrushev, Eric Paul Bennett, Hans H Wandall & Henrik Clausen Nature Biotechnology (2015) doi:10.1038/nbt.3280 91 Cyanate as an energy source for nitrifiers (Proteomics) Marton Palatinszky, Craig Herbold, Nico Jehmlich, Mario Pogoda, Ping Han, Martin von Bergen, Ilias Lagkouvardos, Søren M. Karst, Alexander Galushko, Hanna Koch, David Berry, Holger Daims and Michael Wagner Nature (2015) doi:10.1038/nature14856 92 Transcriptional control of autophagy–lysosome function drives pancreatic cancer metabolism (Proteomics) Rushika M. Perera, Svetlana Stoykova, Brandon N. Nicolay, Kenneth N. Ross, Julien Fitamant, Myriam Boukhali, Justine Lengrand, Vikram Deshpande, Martin K. Selig, Cristina R. Ferrone, Jeff Settleman, Gregory Stephanopoulos, Nicholas J. Dyson, Roberto Zoncu, Sridhar Ramaswamy, Wilhelm Haas & Nabeel Bardeesy Nature (2015) doi:10.1038/nature14587 93 Coordinate regulation of residual bone marrow function by paracrine trafficking of AML exosomes (Proteomics) J Huan, NI Hornick, NA Goloviznina, AN Kamimae- Lanning, LL David , PA Wilmarth , T Mori , JR Chevillet , A Narla , CT Roberts Jr, MM Loriaux, BH Chang and P Kurre Leukemia (2015), 1–11 94 The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment (Proteomics) F. Bastida, N. Jehmlich, K. Lima, B.E.L. Morris, H.H. Richnow, T. Hernandez, M. von Bergen, C. Garcıa Journal of Proteomics 2015 95 Selenocysteine-independent suppression of UGA codons in the archaeon Methanococcus maripaludis (Proteomics) Deniz Seyhan, Nico Jehmlich, Martin von Bergen, Julia Fersch, Michael Rother Biochimica et Biophysica Acta 2015 96 Zeus, Aesculapius, Amalthea and the proteome of goat milk (Proteomics) Vincenzo Cunsolo, Elisa Fasoli, Rosaria Saletti, Vera Muccilli, Serafina Gallina, Pier Giorgio Righetti, Salvatore Foti Journal of Proteomics 128 (2015) 69–82 97 High resolution data-independent acquisition with electron transfer dissociation mass spectrometry: Multiplexed analysis of post-translationally modified proteins

(Proteomics) Michael J. Sweredoski, Tonya Pekar Second, Jenny Broeker, Annie Moradian, Sonja Hess International Journal of Mass Spectrometry xxx (2015) xxx–xxx 98 Recognition pattern of kiwi seed storage proteins in kiwifruit allergic children (Proteomics) Caroline Nilsson, Peter Brostedt , Johanna Hidman , Jenny van Odijk , Magnus P Borres, Sigrid Sjölander , Hillevi Englund Pediatr Allergy Immunol. 2015 Jul 16. doi: 10.1111/pai.12449. [Epub ahead of print] 99 Global analysis of protein expression and phosphorylation levels in nicotine-treated pancreatic stellate cells (Proteomics) Joao A. Paulo, Aleksandr Gaun, and Steven P. Gygi J. Proteome Res., Just Accepted Manuscript • Publication Date (Web): 11 Aug 2015 100 Development of Selective Covalent JAK3 Inhibitors (Proteomics) Li Tan, Koshi Akahane, Randall McNally, Kathleen M.S.E Reyskens, Scott B Ficarro, Suhu Liu, Grit S. HerterSprie, Shohei Koyama, Michael J. Pattison, Katherine M. Labella, Liv Johannessen, Esra A Akbay, Kwok-Kin Wong, David A. Frank, Jarrod A. Marto, A Thomas Look, Simon Arthur, Michael J. Eck, and Nathanael S Gray J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.5b00710 • Publication Date (Web): 10 Aug 2015 101 Phthalimide conjugation as a strategy for in vivo target protein degradation (Proteomics) Georg E. Winter, Dennis L. Buckley, Joshiawa Paulk, Justin M. Roberts, Amanda Souza, Sirano Dhe-Paganon, James E. Bradner Science 19 June 2015 102 CC-122, a pleiotropic pathway modifier, mimics an interferon response and has antitumor activity in DLBCL (Proteomics) Patrick R. Hagner, Hon-Wah Man, Celia Fontanillo, Maria Wang, Suzana Couto, Mike Breider, Chad Bjorklund, Courtney G. Havens, Gang Lu, Emily Rychak, Heather Raymon, Rama Krishna Narla, Leo Barnes, Gody Khambatta, Hsiling Chiu, Jolanta Kosek, Jian Kang, Michael D. Amantangelo, Michelle Waldman, Antonia Lopez-Girona, Ti Cai, Michael Pourdehnad, Matthew Trotter, Thomas O. Daniel, Peter H. Schafer, Anke Klippel, Anjan Thakurta, Rajesh Chopra, and Anita K. Gandhi Blood. 2015 Aug 6;126(6):779-89. doi: 10.1182/blood-2015-02-628669. Epub 2015 May 22. 103 Separating myoblast differentiation from muscle cell fusion using IGF-I and the 5 p38 MAP kinase inhibitor SB202190 (Proteomics) Samantha Gardner, Sean M. Gross, Larry L. David, John E. Klimek and Peter Rotwein Am J Physiol Cell Physiol. 2015 Aug 5:ajpcell.00184.2015. doi:

10.1152/ajpcell.00184.2015. [Epub ahead of print] 104 The human tau interactome: binding to the ribonucleoproteome, and impaired binding of the P301L mutant to chaperones and the proteasome (Proteomics) C. Geeth Gunawardana , Mohadeseh Mehrabian, Xinzhu Wang, Iris Mueller , Isabela B. Lubambo , James E. N. Jonkman , Hansen Wang , Gerold Schmitt-Ulms Molecular & Cellular Proteomics 2015 doi:10.1074/mcp.M115.050724mcp.M115.050724. 105 Extended O-GlcNAc on HLA Class-I-Bound Peptides (Glycoproteomics) Fabio Marino, Marshall Bern, Geert P. M. Mommen, Aneika C. Leney, Jacqueline A. M. van Gaans-van den Brink, Alexandre M. J. J. Bonvin, Christopher Becker, Cecile A. C. M. van Els, and Albert J. R. Heck J Am Chem Soc. 2015 Aug 19. [Epub ahead of print] 106 Proteomics of the organohaliderespiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates (Proteomics) Tobias Goris, Christian L. Schiffmann, Jennifer Gadkari, Torsten Schubert, Jana Seifert, Nico Jehmlich, Martin von Bergen and Gabriele Diekert Sci Rep. 2015 Sep 21;5:13794. doi: 10.1038/srep13794. 107 Secreted and O-GlcNAcylated MIF binds to the human EGF receptor and inhibits its activation (Glycoproteomics) Yanhua Zheng , Xinjian Li, Xu Qian1, Yugang Wang, Jong-Ho Lee, Yan Xia, David H. Hawke, Gang Zhang, Jianxin Lyu and Zhimin Lu Nature Cell Biology 17, 1348–1355 2015 108 A strategy for dissecting the architectures of native macromolecular assemblies (Proteomics) Yi Shi, Riccardo Pellarin, Peter C Fridy, Javier Fernandez-Martinez, Mary K Thompson, Yinyin Li, Qing Jun Wang, Andrej Sali, Michael P Rout & Brian T Chait Nature Methods (2015) doi:10.1038/nmeth.3617 109 Characterization of the cardiac succinylome and its role in ischemia–reperfusion injury (Proteomics) Jennifer A. Boylston, Junhui Sun, Yong Chen, Marjan Gucek, Michael N. Sack, Elizabeth Murphy Journal of Molecular and Cellular Cardiology 88 (2015) 73–81 110 Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef (Proteomics) Nicholas J. Matheson, Jonathan Sumner, Kim Wals, Radu Rapiteanu, Michael P. Weekes, Raphael Vigan, Julia Weinelt, Michael Schindler, Robin Antrobus, Ana S.H. Costa, Christian Frezza, Clary B. Clish, Stuart J.D. Neil, and Paul J. Lehner

Cell Host & Microbe 18, 1–15, October 14, 2015 101 Bacterial Rotary Export ATPases Are Allosterically Regulated by the Nucleotide Second Messenger Cyclic-di-GMP (Proteomics) Eleftheria Trampari, Clare E. M. Stevenson, Richard H. Little, Thomas Wilhelm, David M. Lawson and Jacob G. Malone THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 290, NO. 40, pp. 24470 –24483 2015 102 Recognition pattern of kiwi seed storage proteins in kiwifruit-allergic children Caroline Nilsson, Peter Brostedt, Johanna Hidman, Jenny van Odijk, Magnus P Borres, Sigrid Sjölander and Hillevi Englund (Proteomics) PEDIATRIC ALLERGY AND IMMUNOLOGY

103 Mechanism-Based Post-Translational Modification and Inactivation in Terpene Synthases (Proteomics) Roland D. Kersten, Jolene K. Diedrich, John R. Yates, III, and Joseph P. Noel ACS Chem. Biol., Articles ASAP (As Soon As Publishable) 104 Fragment Ion Patchwork Quantification for Measuring Site-Specific Acetylation Degrees (Proteomics) Rasha ElBashir, Jens T. Vanselow, Amelie Kraus, Christian J. Janzen, Nicolai Siegel and Andreas Schlosser Anal. Chem., 2015, 87 (19), pp 9939–9945 105 Generation of Multiple Reporter Ions from a Single Isobaric Reagent Increases Multiplexing Capacity for Quantitative Proteomics (Proteomics) Craig R. Braun, Gregory H. Bird, Martin Wuhr, Brian K. Erickson, Ramin Rad, Loren D. Walensky, Steven P. Gygi and Wilhelm Haas Anal. Chem., 2015, 87 (19), pp 9855–9863 106 Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach (Proteomics) Julian Engel, AndreRichters, Matthaus Getlik, Stefano Tomassi, Marina Keul, Martin Termathe, Jonas Lategahn, Christian Becker, Svenja Mayer-Wrangowski, Christian Grutter, Niklas Uhlenbrock, Jasmin Krull, Niklas Schaumann, Simone Eppmann, Patrick Kibies, Franziska Hoffgaard, Jochen Heil, Sascha Menninger, Sandra Ortiz-Cuaran, Johannes M. Heuckmann, Verena Tinnefeld, ReneP. Zahedi, Martin L. Sos, Carsten Schultz-Fademrecht, Roman K. Thomas, Stefan M. Kast and Daniel Rauh J. Med. Chem., 2015, 58 (17), pp 6844–6863 107 Identification of the S-layer glycoproteins and their covalently linked glycans in the halophilic archaeon Haloarcula hispanica (Proteomics) Hua Lu, Yang Lü, Jinwei Ren, Zhongfu Wang, Qian Wang, Yuanming Luo, Jing Han, Hua Xiang, Yuguo Du, and Cheng Jin

Glycobiology, 2015, vol. 25, no. 11, 1150–1162 108 Automated N-glycan profiling of a mutant Trypanosoma rangeli sialidase expressed in Pichia pastoris, using tandem mass spectrometry and bioinformatics (Glycoproteomics) Haiying Li, Morten I. Rasmussen, Martin R. Larsen, Yao Guo, Carsten Jers, Giuseppe Palmisano, Jørn D. Mikkelsen and Finn Kirpekar Glycobiology (2015)doi: 10.1093/glycob/cwv063 109 Top-down and middle-down protein analysis reveals that intact and clipped human histones differ in post-translational modification patterns (Proteomics) Andrey Tvardovskiy, Krzysztof Wrzesinski, Simone Sidoli, Stephen J. Fey , Adelina Rogowska-Wrzesinska, Ole N. Jensen Mol Cell Proteomics mcp.M115.048975. First Published on September 30, 2015, doi:10.1074/mcp.M115.048975 110 The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy (Proteomics) Jin-Mi Heo, Alban Ordureau, Joao A. Paulo, Jesse Rinehart, and J. Wade Harper Molecular Cell 60, 7–20, October 1, 2015 111 The Prion Protein Controls Polysialylation of Neural Cell Adhesion Molecule 1 during Cellular Morphogenesis (Proteomics) Mohadeseh Mehrabian, Dylan Brethour, Hansen Wang, Zhengrui Xi, Ekaterina Rogaeva, Gerold Schmitt-Ulms PLOS ONE | DOI:10.1371/journal.pone.0133741 August 19, 2015

112 Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells (Proteomics) Scott F. Rusin,1 Kate A. Schlosser,2 Mark E. Adamo,2 Arminja N. Kettenbach1,2* Sci Signal. 2015 Oct 13;8(398):rs12. doi: 10.1126/scisignal.aab3138 113 Multiplexed, Proteome-wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains (Proteomics) Marta Isasa, Christopher M. Rose, Suzanne Elsasser, José Navarrete-Perea, Joao A. Paulo, Daniel J. Finley and Steven P. Gygi Journal of Proteome Research 2015 114 Glycosylation of Human Plasma Clusterin Yields a Novel Candidate Biomarker of Alzheimer’s Disease (Glycoproteomics) Hui-Chung Liang, Claire Russell, Vikram Mitra, Raymond Chung, Abdul Hye , Chantal Bazenet, Simon Lovestone, Ian Pike, and Malcolm Ward J. Proteome Res., Just Accepted Manuscript

115 Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling (Proteomics) Baby Rorielyn T. Dimayacyac-Esleta, Chia-Feng Tsai, Reta Birhanu Kitata, Pei-Yi Lin, Wai-Kok Choong, Tai-Du Lin, Yi-Ting Wang, Shao-Hsing Weng, Pan-Chyr Yang, Susan D. Arco, Ting-Yi Sung, and Yu-Ju Chen Anal. Chem. 2015, 87, 12016−12023 116 The paracaspase MALT1 cleaves HOIL1 reducing linear ubiquitination by LUBAC to dampen lymphocyte NF-kB signalling (Proteomics) Theo Klein, Shan-Yu Fung, Florian Renner, Michael A. Blank, Antoine Dufour, Sohyeong Kang, Madison Bolger-Munro, Joshua M. Scurll, John J. Priatel, Patrick Schweigler, Samu Melkko, Michael R. Gold, Rosa I. Viner, Catherine H. Regnier, Stuart E. Turvey and Christopher M. Overall Nature Communications 6, Article number: 8777 doi:10.1038/ncomms9777 117 Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0 (Proteomics) Paulo C Carvalho, Diogo B Lima, Felipe V Leprevost, Marlon D M Santos, Juliana S G Fischer, Priscila F Aquino, James J Moresco, John R Yates III and Valmir C Barbosa Nature Protocols 11, 102–117 (2016) 118 An innate antiviral pathway acting before interferons at epithelial surfaces (Glycoproteomics) Marie B Iversen, Line S Reinert, Martin K Thomsen, Ieva Bagdonaite, Ramya Nandakumar, Natalia Cheshenko, Thaneas Prabakaran, Sergey Y Vakhrushev, Malgosha Krzyzowska, Sine K Kratholm, Fernando Ruiz-Perez, Steen V Petersen, Stanislas Goriely, Bo Martin Bibby, Kristina Eriksson, Jürgen Ruland, Allan R Thomsen, Betsy C Herold, Hans H Wandall, Sebastian Frische, Christian K Holm and Søren R Paludan Nature Immunology (2015) doi:10.1038/ni.3319 119 Terminal galactosylation and sialylation switching on membrane glycoproteins upon TNF-alpha-induced insulin resistance in adipocytes (N-Glycoproteomics) (Glycoproteomics) Benjamin L. Parker, Morten Thaysen-Andersen, Daniel J. Fazakerley, Mira Holliday, Nicolle H. Packer, David E. James MCP Papers in Press. Published on November 4, 2015 as Manuscript M115.054221 120 An Optimization of LC-MS/MS Workflow for Deep Proteome Profiling on Orbitrap Fusion (Proteomics) Litong Nie, Mingrui Zhu, Shengnan Sun, Linhui Zhai, Zhixiang Wu, Lili Qiana and Minjia Tan Anal. Methods, 2016, Advance Article 121 Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by

Multisite Glycosylation (Glycoproteomics) Joseph Gault, Mathias Ferber, Silke Machata, Anne-Flore Imhaus, Christian Malosse, Arthur Charles-Orszag, Corinne Millien, Guillaume Bouvier, Benjamin Bardiaux, Gérard Péhau-Arnaudet, Kelly Klinge, Isabelle Podglajen, Marie Cécile Ploy, H. Steven Seifert, Michael Nilges, Julia Chamot-Rooke, Guillaume Duménil PLoS Pathog. 2015 Sep 14;11(9):e1005162. doi: 10.1371/journal.ppat.1005162. eCollection 2015 122 Proteomic Analysis Identifies Ribosome Reduction as an Effective Proteotoxic Stress Response (Proteomics) Angel Guerra-Moreno, Marta Isasa, Meera K. Bhanu, David P. Waterman, Vinay V. Eapen, Steven P. Gygi, and John Hanna J Biol Chem. 2015 Dec 11;290(50):29695-706 123 Protein species-specific characterization of conformational change induced by multisite phosphorylation (Proteomics) Jingxi Pan, Suping Zhang, Christoph H. Borchers Journal of Proteomics 2015 124 Data detailing the platelet acetyl-lysine proteome (Proteomics) Joseph E. Aslan, Larry L. David, Owen J.T. McCarty Data in Brief 5 (2015) 368–371 125 Metabolic Interplay between the Asian Citrus Psyllid and Its Profftella Symbiont: An Achilles’ Heel of the Citrus Greening Insect Vector (Proteomics) John S. Ramsey, Richard S. Johnson, Jason S. Hoki, Angela Kruse, Jaclyn Mahoney, Mark E. Hilf , Wayne B. Hunter, David G. Hall , Frank C. Schroeder, Michael J. MacCoss , Michelle Cilia PLOS ONE | DOI:10.1371/journal.pone.0140826 126 Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization (Proteomics)

Daniel Vinella, Frédéric Fischer, Egor Vorontsov , Julien Gallaud, Christian Malosse , Valérie Michel , Christine Cavazza , Marie Robbe-Saule , Pierre Richaud , Julia Chamot-Rooke , Céline Brochier-Armanet , Hilde De Reuse PLOS Pathogens | DOI:10.1371/journal.ppat.1005312 127 Schistosoma mansoni α1,3-fucosyltransferase-F generates the Lewis X antigen (Glycomics) Megan L Mickum, Teerapat Rojsajjakul, Ying Yu and Richard D Cummings Glycobiology, 2015, 1–16 128 Functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization

(Proteomics) Marta A. Witek and Graeme L. Conn Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv1306 129 The use of matrix coating assisted by an electric field (MCAEF) to enhance mass spectrometric imaging of human prostate cancer biomarkers (Proteomics) Xiaodong Wang, Jun Han, Darryl B. Hardie, Juncong Yang and Christoph H. Borchers Journal of Mass Spectrometry Volume 51, Issue 1, pages 86–95, January 2016 130 Distinctive MS/MS Fragmentation Pathways of Glycopeptide-Generated Oxonium Ions Provide Evidence of the Glycan Structure (Glycoproteomics) Jin Yu, Manuel Schorlemer, Alejandro Gomez Toledo, Christian Pett, Dr. Carina Sihlbom, Prof. Göran Larson, Dr. Ulrika Westerlind, Dr. Jonas Nilsson Chemistry. 2015 Dec 11. doi: 10.1002/chem.201503659. [Epub ahead of print] 131 Myc coordinates transcription and translation to enhance transformation and suppress invasiveness (Proteomics) Ran Elkon, Fabricio Loayza-Puch, Gozde Korkmaz, Rui Lopes, Pieter C van Breugel, Onno B Bleijerveld, AF Maarten Altelaar, Elmar Wolf, Francesca Lorenzin, Martin Eilers and Reuven Agami EMBO reports Volume 16, Issue 12, pages 1723–1736, December 2015 132 Comparative proteomics of a tor inducible Aspergillus fumigatus mutant reveals involvement of the Tor kinase in iron regulation Clara Baldin, Vito Valiante, Thomas Krüger, Lukas Schafferer, Hubertus Haas, Olaf Kniemeyer and Axel A. Brakhage Proteomics 2015 Feb 27. doi: 10.1002/pmic.201400584. [Epub ahead of print] 133 Casein Kinase 1 α Phosphorylates the Wnt Regulator Jade-1 and Modulates Its Activity* Lori Borgal, Markus M. Rinschen, Claudia Dafinger, Sylvia Hoff, Matthaus J. Reinert, Tobias Lamkemeyer, Soeren S. Lienkamp, Thomas Benzing and Bernhard Schermer The Journal of Biological Chemistry Vol. 289, NO. 38, pp. 26344–26356 134 Dye Free Porcine Model of Experimental Branch Retinal Vein Occlusion – a Suitable Approach for Retinal Proteomics Lasse Jørgensen Cehofski, Anders Kruse, Benedict Kjæ rgaard, Allan Stensballe, Bent Honoré, and Henrik Vorum Journal of Ophthalmology, 2015 135 Catching the tip of the iceberg – evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota Simon Deusch and Jana Seifert Proteomics 2015 Mar 13. doi: 10.1002/pmic.201400556. [Epub ahead of print]

136 Evaluating kinase ATP uptake and tyrosine phosphorylation using multiplexed quantification of chemically labeled and post-translationally modified peptides Bin Fang, Melissa A. Hoffman, Abu-Sayeef Mirza, Katie M. Mishall, Jiannong Li, Scott M. Peterman, Keiran S.M. Smalley, Kenneth H. Shain, Paul M. Weinberger, Jie Wu, Uwe Rix, Eric B. Haur, John M. Koomen Methods 2015 137 A novel adipokinetic peptide from the corpus cardiacumof the primitive caeliferan pygmy grasshopper Tetrix subulata(Caelifera, Tetrigidae) Gerd Gäde, Petr Simek, Heather G. Marco Peptides 2015 138 Detection and quantification of proteins in clinical samples using high resolution mass spectrometry Sebastien Gallien, Bruno Domon Methods 2015 139 Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring Sebastien Gallien, Sang Yoon Kim and Bruno Domon Mol Cell Proteomics 2015 Mar 9. pii: mcp.O114.043968. 140 Metabolome and Proteome Profiling of Complex I Deficiency Induced by Rotenone Ina Gielisch and David Meierhofer J. Proteome Res. 2015, 14, 224−235 141 Proteomics of Microparticles with SILAC Quantification (PROMIS-Quan): A Novel Proteomic Method for Plasma Biomarker Quantification Michal Harel, Pazit Oren-Giladi, Orit Kaidar-Person, Yuval Shaked, and Tamar Geiger Molecular & Cellular Proteomics 14: 10.1074/mcp.M114.043364, 1127–1136, 2015 142 CaMKII Phosphorylation of NaV1.5: Novel in Vitro Sites Identified by Mass Spectrometry and Reduced S516 Phosphorylation in Human Heart Failure Anthony W. Herren, Darren M. Weber, Robert R. Rigor, Kenneth B. Margulies, Brett S. Phinney and Donald M. Bers J. Proteome Res. 2015 143 Toxicoproteomic analysis of pulmonary carbon nanotube exposure using LC-MS/MS Gina M. Hilto, Alexia J. Taylor, Christina D. McClure, Gregory N. Parsons, James C. Bonner, Michael S. Bereman Toxicology 329 (2015) 80–87

144 Application of high-resolution mass spectrometry to measure low abundance isotope enrichment in individual muscle proteins Kelly M. Hines, G. Charles Ford, Katherine A. Klaus, Brian A. Irving, Beverly L. Ford, Kenneth L. Johnson, Ian R. Lanza, K. Sreekumaran Nair Anal Bioanal Chem. 2015 Apr 2. [Epub ahead of print] 145 Identification and mutational analyses of phosphorylation sites of the calcineurin-binding protein CbpA and the identification of domains required for calcineurin binding in Aspergillus fumigatus Praveen R. Juvvadi, Yan Ma, Amber D. Richards, Erik J. Soderblom, M. Arthur Moseley, Frédéric Lamoth and William J. Steinbach Front Microbiol. 2015 Mar 13;6:175. doi: 10.3389/fmicb.2015.00175. eCollection 2015 146 Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury Hasmik Keshishian, Michael W. Burgess, Michael A. Gillette, Philipp Mertins, Karl R. Clauser, D.R.Mani, Eric W. Kuhn, Laurie A. Farrell, Robert E. Gerszten and Steven A. Carr Mol Cell Proteomics. 2015 Feb 27. pii: mcp.M114.046813. [Epub ahead of print] 147 SPECHT—Single-stage phosphopeptide enrichment and stable-isotope chemical tagging: Quantitative phosphoproteomics of insulin action in muscle Arminja N. Kettenbach, Hiroyuki Sano, Susanna R. Keller, Gustav E. Lienhard, Scott A. Gerber Journal of Proteomics 114, 2015, 48-60 148 Phosphodiesterase 9A controls nitric-oxideindependent cGMP and hypertrophic heart disease Dong I. Lee, Guangshuo Zhu, Takashi Sasaki, Gun-Sik Cho, Nazha Hamdani, Ronald Holewinski, Su-Hyun Jo, Thomas Danner, Manling Zhang, Peter P. Rainer, Djahida Bedja, Jonathan A. Kirk, Mark J. Ranek, Wolfgang R. Dostmann, Chulan Kwon, Kenneth B. Margulies, Jennifer E. Van Eyk, Walter J. Paulus, Eiki Takimoto & David A. Kass Nature 519, 2015, 472-476 149 Pleiotrophin regulates the ductular reaction by controlling the migration of cells in liver progenitor niches Gregory A Michelotti, Anikia Tucker, Marzena Swiderska-Syn, Mariana Verdelho Machado, Steve S Choi, Leandi Kruger, Erik Soderblom, J Will Thompson, Meredith Mayer-Salman, Heather A Himburg, Cynthia A Moylan, Cynthia D Guy, Katherine S Garman, Richard T Premont, John P Chute, Anna Mae Diehl Gut 2015, 0, 1-10 150 Quantitative proteomics analysis of platelet-derived microparticles reveals distinct protein signatures when stimulated by different physiological agonists Marco Milioli, Maria Ibáñez-Vea, Simone Sidoli, Giuseppe Palmisano, Maria Careri,

Martin R. Larsen Journal of Proteomics 121, 2015, 56-66 151 Novel MtCEP1 peptides produced in vivo differentially regulate root development in Medicago truncatula Nadiatul A. Mohd-Radzman, Steve Binos, Thy T. Truong, Nijat Imin, Michael Mariani and Michael A. Djordjevic J. Exp. Bot. (2015)doi: 10.1093/jxb/erv008 152 Degradation of Tiam1 by Casein Kinase 1 and the SCFβTrCP Ubiquitin Ligase Controls the Duration of mTOR-S6K Signaling Roberto Magliozzi, Jihoon Kim, Teck Yew Low, Albert J. R. Heck and Daniele Guardavaccaro THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 289, NO. 40, pp. 27400–27409 153 Processing of Protein ADP-ribosylation by Nudix Hydrolases Luca Palazzo, Benjamin Thomas, Ann-Sofie Jemth, Thomas Colby, Orsolya Leidecker, Karla Feijs, Roko Zaja, Olga Loseva, Jordi Carreras Puigvert, Ivan Matic, Thomas Helleday and Ivan Ahel Biochem. J. (2015) Immediate Publication, doi:10.1042/BJ20141554 154 Importance of Host Cell Arginine Uptake in Francisella Phagosomal Escape and Ribosomal Protein Amounts Elodie Ramond, Gael Gesbert, Ida Chiara Guerrera, Cerina Chhuon, Marion Dupuis, Melanie Rigard, Thomas Henry, Monique Barel, and Alain Charbit Molecular & Cellular Proteomics 14: 10.1074/mcp.M114.044552, 870–881, 2015 155 Piwi Proteins and piRNAs in Mammalian Oocytes and Early Embryos Elke F. Roovers, David Rosenkranz, Mahdi Mahdipour, Chung-Ting Han, Nannan He, Susana M. Chuva de Sousa Lopes, Lucette A.J. van der Westerlaken, Hans Zischler, Falk Butter, Bernard A.J. Roelen, and Rene F. Ketting Cell Reports 10, 2069–2082, 2015 156 MS1-Based Label-Free Proteomics Using a Quadrupole Orbitrap Mass Spectrometer Tali Shalit, Dalia Elinger, Alon Savidor, Alexandra Gabashvili and Yishai Levin J. Proteome Res. 2015, 14, 1979−1986 157 Analysis of the Candida albicans phosphoproteome Willger SD, Liu Z, Olarte RA, Adamo ME, Stajich JE, Myers LC, Kettenbach AN, Hogan DA Eukaryotic Cell 2015 doi:10.1128/EC.00011-15 158 The SNO/SOH TMT strategy for combinatorial analysis of reversible cysteine oxidations

Katarzyna Wojdyla, James Williamson, Peter Roepstorff, Adelina Rogowska-Wrzesinska Journal of Proteomics 113, 2015, 415-434 159 Suberoylanilide Hydroxamic Acid Treatment Reveals Crosstalks among Proteome, Ubiquitylome and Acetylome in Non-Small Cell Lung Cancer A549 Cell Line Quan Wu, Zhongyi Cheng, Jun Zhu, Weiqing Xu, Xiaojun Peng, Chuangbin Chen, Wenting Li, Fengsong Wang, Lejie Cao, Xingling Yi, Zhiwei Wu, Jing Li & Pingsheng Fan SCIENTIFIC REPORTS | 5 : 9520 | DOI: 10.1038/srep09520 160 System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel SUMO target proteins and acceptor lysines relevant for genome stability Zhenyu Xiao, Jer-Gung Chang, Ivo A. Hendriks, Jón Otti Sigurðsson, Jesper V. Olsen and Alfred C.O. Vertegaal Mol Cell Proteomics 2015 Mar 9. pii: mcp.O114.044792. [Epub ahead of print] 161 Quantitative Chemoproteomics for Site-Specific Analysis of Protein Alkylation by 4

‑ Hydroxy-2-Nonenal in Cells Jing Yang, Keri A. Tallman, Ned A. Porter and Daniel C. Liebler Anal. Chem. 2015, 87, 2535−2541 162 Indirect protein quantification of drug-transforming enzymes using peptide group-specific immunoaffinity enrichment and mass spectrometry Frederik Weiß, Anke Schnabel, Hannes Planatscher, Bart H. J. van den Berg, Bettina Serschnitzki, Andreas K. Nuessler, Wolfgang E. Thasler, Thomas S. Weiss, Matthias Reuss, Dieter Stoll, Markus F. Templin, Thomas O. Joos, Katrin Marcus and Oliver Poetz SCIENTIFIC REPORTS | 5 : 8759 | DOI: 10.1038/srep08759 163 Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics Tanveer S. Batth, Chiara Francavilla, and Jesper V. Olsen J. Proteome Res., 2014, 13 (12), pp 6176–6186

164 Plasma exosomal α‑ synuclein is likely CNS‑ derived and increased in Parkinson’s disease Min Shi, Changqin Liu, Travis J. Cook, Kristin M. Bullock, Yanchun Zhao, Carmen Ginghina, Yanfei Li, Patrick Aro, Romel Dator, Chunmei He, Michael J. Hipp, Cyrus P. Zabetian,

Elaine R. Peskind, Shu‑ Ching Hu, Joseph F. Quinn, Douglas R. Galasko, William A. Banks and Jing Zhang Acta Neuropathol (2014) 128:639–650 165 The nature and extent of contributions by defective ribosome products to the HLA peptidome Dmitry Bourdetsky, Christian E. H. Schmelzer, and Arie Admon Proc Natl Acad Sci USA 2014 Apr 22;111(16):E1591-9

166 Global analysis of protein structural changes in complex proteomes Yuehan Feng, Giorgia De Franceschi, Abdullah Kahraman, Martin Soste, Andre Melnik, Paul J Boersema, Patrizia Polverino de Laureto, Yaroslav Nikolaev, Ana Paula Oliveira & Paola Picotti Nature Biotechnology 2014, 32, 1036-1044 167 Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer Christian D. Kelstrup, Rosa R. Jersie-Christensen, Tanveer S. Batth, Tabiwang N. Arrey, Andreas Kuehn, Markus Kellmann, and Jesper V. Olsen J. Proteome Res. 2014, 13, 6187−6195 168 Peptide and small molecule inhibitors of HECT-type ubiquitin ligases Thomas Mund, Michael J. Lewis, Sarah Maslen, and Hugh R. Pelham PNAS 2014, 111, 16736–16741 169 COMPARISON OF COMMERCIAL LC MS/MS COMPATIBLE DETERGENTS WITH SODIUM DEOXYCHOLATE FOR SHOTGUN PROTEOMICS Caleb J. Porter1 and Michael S. Bereman JOURNAL OF PROTEINS AND PROTEOMICS 5(4), December 2014, pp. 151-161 170 The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer Richard Alexander Scheltema, Jan-Peter Hauschild, Oliver Lange, Daniel Hornburg, Eduard Denisov, Eugen Damoc, Andreas Kuehn, Alexander Makarov and Matthias Mann

Molecular & Cellular Proteomics, 13, 3698-3708, 2014 171 The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer Richard Alexander Scheltema, Jan-Peter Hauschild, Oliver Lange, Daniel Hornburg, Eduard Denisov, Eugen Damoc, Andreas Kuehn, Alexander Makarov and Matthias Mann Molecular & Cellular Proteomics, 13, 3698-3708, 2014 172 Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer Christian D. Kelstrup, Rosa R. Jersie-Christensen, Tanveer S. Batth, Tabiwang N. Arrey, Andreas Kuehn, Markus Kellmann and Jesper V. Olsen J. Proteome Res., 2014, 13 (12), pp 6187-6195 173 Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring

Sebastien Gallien1 , Sang Yoon Kim1 , and Bruno Domon Mol Cell Proteomics mcp.O114.043968. First Published on March 9, 2015 174 Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation Kenneth R. Durbin, Owen S. Skinner, Ryan T. Fellers, Neil L. Kelleher J. Am. Soc. Mass Spectrom. (2015) 175 An On-line Matrix Removal Platform for Coupling Gel-Based Separations to Whole Protein Electrospray Ionization Mass Spectrometry Ki Hun Kim, Philip Daniel Compton, John Cuong Tran, and Neil L. Kelleher J. Proteome Res., Just Accepted Manuscript 176 A double-barrel LC-MS/MS system to quantify 96 interactomes per day Fabian Hosp , Richard A. Scheltema , H. Christian Eberl , Nils A. Kulak, Eva C. Keilhauer , Korbinian Mayr and Matthias Mann Mol Cell Proteomics mcp.O115.049460. First Published on April 17, 2015,doi:10.1074/mcp.O115.049460 177 Using data independent acquisition to model high-responding peptides for targeted proteomics experiments Brian C. Searle, Jarrett D. Egertson, James G. Bollinger, Andrew B. Stergachis, and Michael J. MacCoss Mol Cell Proteomics mcp.M115.051300. First Published on June 22, 2015,doi:10.1074/mcp.M115.051300 178 Definitive screening design optimization of mass spectrometry parameters for sensitive comparison of filter and SPE purified, INLIGHT plasma N-glycans Elizabeth Sara Hecht, James P McCord, and David C. Muddiman Anal. Chem., Just Accepted Manuscript 179 Single molecule Förster resonance energy transfer studies of the effect of EndoS deglycosylation on the structure of IgG Mark S. Piraino, Michael T. Kelliher, Jihad Aburas, Cathrine A. Southern Immunology Letters 167 (2015) 29–33

180 Advancing Urinary Protein Biomarker Discovery by Data independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer Jan Muntel, Yue Xuan, Sebastian T Berger, Lukas Reiter, Richard Bachur, Alex Kentsis, and Hanno Steen J. Proteome Res., Just Accepted Manuscript 181 A quality control of proteomic experiments based on multiple isotopologous internal standards

Adele Bourmaud, Sebastien Gallien, Bruno Domon EuPA Open Proteomics 8 (2015) 16–21 182 Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis Zhenbin Zhang, Liangliang Sun, Guijie Zhu, Olivia F. Cox, Paul W. Huber, and Norman J. Dovichi Anal. Chem., Article ASAP 182 Lipidomic analyses of CEACAM1 knockout mouse liver and adipose tissue Gabriel Gugiu; Deirdre La Placa; Zhifang Zhang; John E. Shively; City of Hope, Duarte, CA 184 Super-Omics: Liquid-Liquid Extraction for Proteomics, Lipidomics and Metabolomics from a Single Sample, Towards a Method for Biopsies Susanne Breitkopf; Min Yuan; Gerburg Wulf; John M Asara; Beth Israel Deaconess Medical Center; Harvard Medical School; Boston, MA 185 Integrated Software for Data Processing and Analysis in Direct Infusion Ultra-High Resolution / Accurate Mass Spectrometry Based ‘Top-Down’ Lipidomics Workflows Yasuto Yokoi; Yukihiro Fukamachi; David Peake; Reiko Kiyonami; Eileen Ryan; Gavin E Reid; MKI Co, Tokyo, JP; Thermo Fisher Scientific, San Jose, CA; University of Melbourne, Victoria, AU 186 Lipidomic profiling of biological samples using off-line two-dimensional high-performance liquid chromatography-high resolution mass spectrometry Monica Narvaez-Rivas, Qibin Zhang; University of North Carolina at Greensboro, Greensboro, NC 187 Ambient Ionization Methods and Liquid Chromatography – Mass Spectrometry Analysis of Human Melanoma Biopsies Louis Searcy; Candice Ulmer; Matthew Kazaleh; Michael Costanzo; Nikolaus Gravenstein; Richard A. Yost; University of Florida, Gainesville, FL 188 Super-Omics: Liquid-Liquid Extraction for Proteomics, Lipidomics and Metabolomics from a Single Sample, Towards a Method for Biopsies Susanne Breitkopf; Min Yuan; Gerburg Wulf, 2; John M Asara; Beth Israel Deaconess Medical Center; Harvard Medical School; Boston, MA 189 Profiling Lipids in Plants Using Infusion and Chromatography Based High Resolution Mass Spectrometry Methods with Automated Data Processing Yelena A. Adelfinskaya; Daniel J J Gachotte; Jeffrey R Gilbert; Jesse L Balcer; Laura L Wayne; Dow AgroSciences, Indianapolis, IN 190 Comparative High Resolution Metabolomics of Metastatic vs. Non-Metastatic

Tumors in a Murine Medulloblastoma Model Danning Huang; Martin R L Paine; Jingbo Liu; Sophia Banton; Shuzhao Li; Tobey MacDonald; Facundo M Fernández; Georgia Institute of Technology, Atlanta, GA; Emory University School of Medicine, Atlanta, GA 191 Facilitate Biomarker Discovery Using Integrated “Omics” Differential Analysis with High Resolution Accurate LC/MS Approach Reiko Kiyonami; Julian A Saba; Sergei I Snovida; David Peake; Devin Drew; Andreas Huhmer; Ken Miller; ThermoFisher Scientific, San Jose, CA