Skip to Main Content U.S. Department of Energy
Proteomics Banner

Publications

Journal Publications by year


2017 Journal Publications

"A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements," Orton DJ, Tfaily MM, Moore RJ, LaMarche BL, Zheng X, Fillmore TL, Chu RK, Weitz KK, Monroe ME, Kelly RT, Smith RD, Baker ES. Anal Chem 90 (1): 737-744 (2017). doi: 10.1021/acs.analchem.7b02986
PMID: 29161511, PMCID: PMC5764703

"A Global Survey of ATPase Activity in Plasmodium falciparum Asexual Blood Stages and Gametocytes," Ortega C, Frando A, Webb-Robertson BJ, Anderson LN, Fleck N, Flannery EL, Fishbaugher M, Murphree TA, Hansen JR, Smith RD, Kappe SHI, Wright AT, Grundner C. Mol Cell Proteomics 17 (1): 111-120 (2017). doi: 10.1074/mcp.RA117.000088
PMID: 29079720, PMCID: PMC5750841

"A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations," Prabhakaran A, Hamid AM, Garimella SVB, Valenzuela BR, Ewing RG, Ibrahim YM, Smith RD. J Am Soc Mass Spectrom 29 (2): 342-351 (2017). doi: 10.1007/s13361-017-1841-6
PMID: 29235041, PMCID: PMC5815952

"A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination," Qiu J, Yu K, Fei X, Liu Y, Nakayasu ES, Piehowski PD, Shaw JB, Puvar K, Das C, Liu X, Luo ZQ. Cell Res 27 (7): 865-881 (2017). doi: 10.1038/cr.2017.66
PMID: 28497808, PMCID: PMC5518988

"Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S-Transferases," Stoddard EG, Killinger BJ, Nair RN, Sadler NC, Volk RF, Purvine SO, Shukla AK, Smith JN, Wright AT. J Am Chem Soc 139 (45): 16032-16035 (2017). doi: 10.1021/jacs.7b07378
PMID: 29068682

"Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies," Kyle JE, Casey CP, Stratton KG, Zink EM, Kim YM, Zheng X, Monroe ME, Weitz KK, Bloodsworth KJ, Orton DJ, Ibrahim YM, Moore RJ, Lee CG, Pedersen C, Orwoll E, Smith RD, Burnum-Johnson KE, Baker ES, Rapid Commun Mass Spectrom. 31 (5): 447-456 (2017).
PMID: 27958645

"Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)," Deng L, Garimella SVB, Hamid AM, Webb IK, Attah IK, Norheim RV, Prost SA, Zheng X, Sandoval JA, Baker ES, Ibrahim YM, Smith RD. Anal Chem 89 (12): 6432-6439 (2017). doi: 10.1021/acs.analchem.7b00189
PMID: 28497957, PMCID: PMC5627995

"Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses," Zheng X, Wojcik R, Zhang X, Ibrahim YM, Burnum-Johnson KE, Orton DJ, Monroe ME, Moore RJ, Smith RD, Baker ES. Annu Rev Anal Chem (Palo Alto Calif) 10 (1): 71-92 (2017). doi: 10.1146/annurev-anchem-061516-045212
PMID: 28301728, PMCID: PMC5627998

"De novo synthesis of alkyne substituted tryptophans as chemical probes for protein profiling studies," Nair RN, Rosnow JJ, Murphree TA, Bowden ME, Lindemann SR, Wright AT. Org Chem Front 4 (4): 495-499 (2017). doi: 10.1039/C6QO00819D
PMID: 28944064, PMCID: PMC5607013

"Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues," Nie S, Shi T, Fillmore TL, Schepmoes AA, Brewer H, Gao Y, Song E, Wang H, Rodland KD, Qian WJ, Smith RD, Liu T. Anal Chem 89 (17): 9139-9146 (2017). doi: 10.1021/acs.analchem.7b01878
PMID: 28724286, PMCID: PMC5627997

"Derivation of the statistical distribution of the mass peak centroids of mass spectrometers employing analog-to digital converters and electron multipliers," Ipsen A, Anal Chem. 89 (4): 2232-2241 (2017).
PMID: 28194947

"Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions," Garimella SVB, Webb IK, Prabhakaran A, Attah IK, Ibrahim YM, Smith RD. J Am Soc Mass Spectrom 28 (7): 1442-1449 (2017). doi: 10.1007/s13361-017-1680-5
PMID: 28560562, PMCID: PMC5551421

"Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry," Zheng X, Deng L, Baker ES, Ibrahim YM, Petyuk VA, Smith RD. Chem Commun (Camb) 53 (56): 7913-7916. doi: 10.1039/c7cc03321d
PMID: 28654112, PMCID: PMC5555368

"Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses," Zheng X, Zhang X, Schocker NS, Renslow RS, Orton DJ, Khamsi J, Ashmus RA, Almeida IC, Tang K, Costello CE, Smith RD, Michael K, Baker ES, Anal Bioanal Chem. 409 (2): 467-476 (2017).
PMID: 27604268, PMCID: PMC5434874, NIHMS ID: NIHMS860020

"Identification of hip BMD loss and fracture risk markers through population –based serum proteomics," Nielson CM, Wiedrick J, Shen J, Jacobs J, Baker ES, Baraff A, Piehowski P, Lee CG, Baratt A, Petyuk V, McWeeney S, Lim JY, Bauer DC, Lane NE, Cawthon PM, Smith RD, Lapidus J, Orwoll ES, J Bone Miner Res. 32 (7): 1559-1567 (2017).
PMID: 28316103, PMCID: PMC5489383, NIHMS ID: NIHMS860664

"Informed-Proteomics: open-source software package for top-down proteomics," Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S. Nat Methods 14 (9): 909-914 (2017). doi: 10.1038/nmeth.4388
PMID: 28783154, PMCID: PMC5578875

"Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?," Metz TO, Baker ES, Schymanski EL, Renslow RS, Thomas DG, Causon TJ, Webb IK, Hann S, Smith RD, Teeguarden JG. Bioanalysis 9 (1): 81-98 (2017). PMID: 27921453, PMCID: PMC5674211

"Ion elevators and escalators in multi-level structures for lossless ion manipulations (SLIM)," Ibrahim YM, Hamid AM, Cox JT, Garimella SV, Smith RD, Anal Chem. 89: 1972-1977 (2017).
PMID: 28208272, PMCID: PMC5470846, NIHMS ID: NIHMS861879

"Lipid and glycolipid isomer analyses using ultra-high resolution ion mobility spectrometry separations," Wojcik R, Webb IK, Deng L, Garimella SV, Prost SA, Ibrahim YM, Baker ES, Smith RD, Int J Mol Sci. 18 (1): E183 (2017).
PMID: 28106768, PMCID: PMC5297815

"MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling," Burnum-Johnson KE, Kyle JE, Eisfeld AJ, Casey CP, Stratton KG, Gonzalez JF, Habyarimana F, Negretti NM, Sims AC, Chauhan S, Thackray LB, Halfmann PJ, Walters KB, Kim YM, Zink EM, Nicora CD, Weitz KK, Webb-Robertson BM, Nakayasu ES, Ahmer B, Konkel ME, Motin V, Baric RS, Diamond MS, Kawaoka Y, Waters KM, Smith RD, Metz TO, Analyst 142 (3): 442-448 (2017).
PMID: 28091625, PMCID: PMC5283721

"Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis," Eisfeld AJ, Halfmann PJ, Wendler JP, Kyle JE, Burnum-Johnson KE, Peralta Z, Maemura T, Walters KB, Watanabe T, Fukuyama S, Yamashita M, Jacobs JM, Kim YM, Casey CP, Stratton KG, Webb-Robertson BM, Gritsenko MA, Monroe ME, Weitz KK, Shukla AK, Tian M, Neumann G, Reed JL, van Bakel H, Metz TO, Smith RD, Waters KM, N'jai A, Sahr F, Kawaoka Y. Cell Host Microbe 22 (6): 817-829.e8 (2017). doi: 10.1016/j.chom.2017.10.011
PMID: 29154144, PMCID: PMC5730472

"Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation," Madar IH, Ko SI, Kim H, Mun DG, Kim S, Smith RD, Lee SW. Anal Chem 89 (2): 1244-1253 (2017). doi: 10.1021/acs.analchem.6b03874
PMID: 27966901, PMCID: PMC5627999

"Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins," Shi T, Quek SI, Gao Y, Nicora CD, Nie S, Fillmore TL, Liu T, Rodland KD, Smith RD, Leach RJ, Thompson IM, Vitello EA, Ellis WJ, Liu AY, Qian WJ. Oncotarget 8 (60): 101887-101898 (2017). doi: 10.18632/oncotarget.21710
PMID: 29254211, PMCID: PMC5731921

"New frontiers for mass spectrometry based upon structures for lossless ion manipulations," Ibrahim YM, Hamid AM, Deng L, Garimella SV, Webb IK, Baker ES, Smith RD, Analyst, 142 (7): 1010-1021 (2017).
PMID: 28262893, PMCID: PMC5431593, NIHMS ID: NIHMS857612

"Position-dependent termination and widespread obligatory frameshifting in Euplotes translation," Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S, Devaraj RR, Xie F, Petyuk VA, Smith RD, Klobutcher LA, Atkins JF, Miceli C, Hatfield DL, Baranov PV, Gladyshev VN. Nat Struct Mol Biol 24 (1): 61-68 (2016). doi: 10.1038/nsmb.3330
PMID: 27870834, PMCID: PMC5295771

"Pyroptosis by caspase11/4-gasdermin-D pathway in alcoholic hepatitis in mice and patients," Khanova E, Wu R, Wang W, Yan R, Chen Y, French SW, Llorente C, Pan SQ, Yang Q, Li Y, Lazaro R, Ansong C, Smith RD, Bataller R, Morgan T, Schnabl B, Tsukamoto H. Hepatology 2017 Nov 6 (2017). doi: 10.1002/hep.29645
PMID: 29108122

"Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines," Duan J, Gaffrey MJ, Qian WJ. Mol Biosyst 13 (5): 816-829. doi: 10.1039/c6mb00861e
PMID: 28357434, PMCID: PMC5493446

"Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease," Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T. J Pathol 243 (1): 78-88 (2017). doi: 10.1002/path.4929
PMID: 28657654, PMCID: PMC5647145

"Redeploying β-lactam antibiotics as a novel antivirulence strategy for the treatment for the treatment of methicillin-resistant staphylococcus aureus infections," Waters EM, Rudkin JK, Coughlan S, Clair GC, Adkins JN, Gore S, Xia G, Black NS, Downing T, O'Neill E, Kadioglu A, O'Gara JP, J Infect Dis. 215 (1): 80-87 (2017).
PMID: 28077586, PMCID: PMC5225249

"Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations," Deng L, Webb IK, Garimella SVB, Hamid AM, Zheng X, Norheim RV, Prost SA, Anderson GA, Sandoval JA, Baker ES, Ibrahim YM, Smith RD. Anal Chem 89 (8): 4628-4634 (2017). doi: 10.1021/acs.analchem.7b00185
PMID: 28332832, PMCID: PMC5627996

"Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry," Zheng X, Renslow RS, Makola MM, Webb IK, Deng L, Thomas DG, Govind N, Ibrahim YM, Kabanda MM, Dubery IA, Heyman HM, Smith RD, Madala NE, Baker ES. J Phys Chem Lett 8 (7): 1381-1388 (2017). doi: 10.1021/acs.jpclett.6b03015
PMID: 28267339, PMCID: PMC5627994

Acknowledgments

All publications that result from utilization of the Resource must acknowledge NIGMS grant support. Please include the following acknowledgment statement:

Portions of this research were supported by the NIH National Institute of General Medical Sciences (GM103493), and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory). Pacific Northwest National Laboratory is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RLO-1830.

Proteomics

Opportunities