Here are a number of relevant publications on top-down methods and applications.  Use the search box or browse all below.

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Tiambeng TN, Roberts DS, Brown KA, Zhu Y, Chen B, et al. 2020. Nanoproteomics enables proteoform-resolved analysis of low-abundance proteins in human serum. Nat Commun. 11(1):1–12
Wu Z, Roberts DS, Melby JA, Wenger K, Wetzel M, et al. 2020. MASH Explorer: A Universal Software Environment for Top-Down Proteomics. J. Proteome Res.
Choi IK, Abeysinghe E, Coulter E, Marru S, Pierce M, Liu X. 2020. TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation. Practice and Experience in Advanced Research Computing, pp. 461–464. Portland, OR, USA: Association for Computing Machinery
Lodge JM, Schauer KL, Brademan DR, Riley NM, Shishkova E, et al. 2020. Top-Down Characterization of an Intact Monoclonal Antibody using Activated Ion-Electron Transfer Dissociation. Anal. Chem.
Schaffer LV, Millikin RJ, Shortreed MR, Scalf M, Smith LM. 2020. Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. J. Proteome Res.
Serrao S, Firinu D, Olianas A, Deidda M, Contini C, et al. 2020. Top-down proteomics of human saliva discloses significant variations of the protein profile in patients with mastocytosis. J. Proteome Res.
Ives A, Su T, Durbin KR, Early BP, dos Santos Seckler H, et al. 2020. Using 10,000 fragment ions to inform scoring in native top-down proteomics. J. Am. Soc. Mass Spectrom.
Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, et al. 2020. Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform. Anal. Chem.
DeHart CJ, Anderson LC, Adams LM, Fornelli L, Hendrickson CL, Kelleher NL. 2020. Abstract A26: Precise characterization and comparison of KRAS proteoforms by top-down mass spectrometry. Mol Cancer Res. 18(5 Supplement):A26–A26
Gault J, Liko I, Landreh M, Shutin D, Bolla JR, et al. 2020. Combining native and 'omics' mass spectrometry to identify endogenous ligands bound to membrane proteins. Nat Methods. 17(5):505–8
McIlwain SJ, Wu Z, Wetzel M, Belongia D, Jin Y, et al. 2020. Enhancing Top-Down Proteomics Data Analysis by Combining Deconvolution Results through a Machine Learning Strategy. J. Am. Soc. Mass Spectrom.
Polasky DA, Dixit SM, Keating MF, Gadkari VV, Andrews PC, Ruotolo BT. 2020. Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data. J. Am. Chem. Soc.
Jeong K, Kim J, Gaikwad M, Hidayah SN, Heikaus L, et al. 2020. FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. cels. 10(2):213-218.e6
McGee JP, Melani RD, Goodwin M, McAlister G, Huguet R, et al. 2020. Voltage Rollercoaster Filtering of Low-Mass Contaminants During Native Protein Analysis. J. Am. Soc. Mass Spectrom.
Coradin M, Mendoza MR, Sidoli S, Alpert AJ, Lu C, Garcia BA. 2020. Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Methods
Chen D, Lubeckyj RA, Yang Z, McCool EN, Shen X, et al. 2020. Predicting Electrophoretic Mobility of Proteoforms for Large-Scale Top-Down Proteomics. Anal. Chem.
Kafader JO, Durbin KR, Melani RD, Des Soye BJ, Schachner LF, et al. 2020. Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry. J. Proteome Res.
He L, Rockwood AL, Agarwal AM, Anderson LC, Weisbrod CR, et al. 2020. Top-down proteomics—a near-future technique for clinical diagnosis? Ann Transl Med. 8(4):
Gallagher K, Palasser Michael, Hughes S, Mackay CL, Kilgour DPA, Clarke DJ. 2020. Isotope Depletion Mass Spectrometry (ID-MS) for accurate mass determination and improved top-down sequence coverage of intact proteins. J. Am. Soc. Mass Spectrom.
Giorgetti J, Beck A, Leize-Wagner E, François Y-N. 2020. Combination of intact, middle-up and bottom-up levels to characterize 7 therapeutic monoclonal antibodies by capillary electrophoresis – mass spectrometry. Journal of Pharmaceutical and Biomedical Analysis. 113107
DelGuidice CE, Ismaiel OA, Mylott Jr WR, Halquist MS. 2020. Quantitative Bioanalysis of Intact Large Molecules using Mass Spectrometry. J Appl Bioanal. 6(1):52–64
Vimer S, Ben-Nissan G, Sharon M. 2020. Direct characterization of overproduced proteins by native mass spectrometry. Nat Protoc. 1–30
Shliaha PV, Gorshkov V, Kovalchuk SI, Schwämmle V, Baird MA, et al. 2020. Middle-Down Proteomic Analyses with Ion Mobility Separations of Endogenous Isomeric Proteoforms. Anal. Chem.
Dubois C, Payen D, Simon S, Junot C, Fenaille F, et al. 2020. Top-down and bottom-up proteomics of circulating S100A8/S100A9 in plasma of septic shock patients. J. Proteome Res.
Cupp-Sutton KA, Wu S. 2020. High-throughput quantitative top-down proteomics. Mol. Omics
Patrie SM, Cline EN. 2020. Chapter 17 - Top-down mass spectrometry for protein molecular diagnostics, structure analysis, and biomarker discovery. In Proteomic and Metabolomic Approaches to Biomarker Discovery (Second Edition), eds. HJ Issaq, TD Veenstra, pp. 313–26. Boston: Academic Press
Zhong J, Sun Y, Xie M, Peng W, Zhang C, et al. 2020. Proteoform characterization based on top-down mass spectrometry. Brief Bioinform


Wu Z, Jin Y, Chen B, Gugger MK, Wilkinson-Johnson CL, et al. 2019. Comprehensive Characterization of the Recombinant Catalytic Subunit of cAMP-Dependent Protein Kinase by Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom.
Vincent D, Binos S, Rochfort S, Spangenberg G. 2019. Top-Down Proteomics of Medicinal Cannabis. Proteomes. 7(4):33
Wilkins John T, Seckler Henrique, Rink Jonathan S, Thaxton Colby, Compton Philip, et al. 2019. Associations Between Apolipoprotein A-I Proteoforms and Markers of Cardiometabolic Health. Circulation. 140(Suppl_1):A15086–A15086
Holt MV, Wang T, Young NL. 2019. High-Throughput Quantitative Top-Down Proteomics: Histone H4. J. Am. Soc. Mass Spectrom.
Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, et al. 2019. Proton transfer charge reduction enables high-throughput top-down analysis of large proteoforms. Anal. Chem.
Melby JA, Jin Y, Lin Z, Tucholski T, Wu Z, et al. 2019. Top-Down Proteomics Reveals Myofilament Proteoform Heterogeneity among Various Rat Skeletal Muscle Tissues. J. Proteome Res.
Melani RD, Srzentić K, Gerbasi VR, McGee JP, Huguet R, et al. 2019. Direct measurement of light and heavy antibody chains using ion mobility and middle-down mass spectrometry. mAbs. 0(0):1–7
Chen D, Geis-Asteggiante L, Gomes FP, Ostrand-Rosenberg S, Fenselau C. 2019. Top-down Proteomic Characterization of Truncated Proteoforms. J. Proteome Res.
Dai Y, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, et al. 2019. Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global PTM Discovery Database. J. Proteome Res.
O'Rourke MB, Town SEL, Dalla PV, Bicknell F, Koh Belic N, et al. 2019. What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows. Proteomes. 7(3):29
Shen X, Yang Z, McCool EN, Lubeckyj RA, Chen D, Sun L. 2019. Capillary zone electrophoresis-mass spectrometry for top-down proteomics. TrAC Trends in Analytical Chemistry. 115644
Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, et al. 2019. A five-level classification system for proteoform identifications. Nat Methods. 1–2
Basharat AR, Iman K, Khalid MF, Anwar Z, Hussain R, et al. 2019. SPECTRUM – A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data. Sci Rep. 9(1):1–14
Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, et al. 2019. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature Methods. 16(7):587
Dowling P, Zweyer M, Swandulla D, Ohlendieck K. 2019. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes. 7(2):25
Lermyte F, Tsybin YO, O'Connor PB, Loo JA. 2019. Top or Middle? Up or Down? Toward a Standard Lexicon for Protein Top-Down and Allied Mass Spectrometry Approaches. J. Am. Soc. Mass Spectrom.
Gregorich ZR, Patel JR, Cai W, Lin Z, Heurer R, et al. 2019. Deletion of Enigma Homologue from the Z-disc slows tension development kinetics in mouse myocardium. The Journal of General Physiology. 151(5):670–79
Pu Y, Chen Y, Nguyen T, Xu C-F, Zang L, et al. 2019. Application of a label-free and domain-specific free thiol method in monoclonal antibody characterization. Journal of Chromatography B. 1114–1115:93–99
Brown KA, Chen B, Guardado-Alvarez TM, Lin Z, Hwang L, et al. 2019. A photocleavable surfactant for top-down proteomics. Nature Methods. 1
LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, et al. 2019. Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics. Mol. Cell Proteomics. 18(4):796–805
Jin Y, Diffee GM, Colman RJ, Anderson RM, Ge Y. 2019. Top-down Mass Spectrometry of Sarcomeric Protein Post-translational Modifications from Non-human Primate Skeletal Muscle. J. Am. Soc. Mass Spectrom.
Lin Z, Wei L, Cai W, Zhu Y, Tucholski T, et al. 2019. Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome. Molecular & Cellular Proteomics. 18(3):594–605
Wang Z, Liu X, Muther J, James JA, Smith K, Wu S. 2019. Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments. Scientific Reports. 9(1):2345
Liang Y, Jin Y, Wu Z, Tucholski T, Brown KA, et al. 2019. Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-Down Proteomics. Anal. Chem. 91(3):1743–47
Lącki MK, Lermyte F, Miasojedow B, Startek MP, Sobott F, et al. 2019. masstodon: A tool for assigning peaks and modeling electron transfer reactions in top-down mass spectrometry. Anal. Chem.
Lesne J, Bousquet M-P, Marcoux J, Locard-Paulet M. 2019. Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS. Bioinform Biol Insights. 13:1177932219868223
Lakshmanan R, Loo JA. 2019. Top-down protein identification using a time-of-flight mass spectrometer and data independent acquisition. International Journal of Mass Spectrometry. 435:136–44
Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, et al. 2019. A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nature Protocols. 14(1):119
Sekera ER, Wood TD. 2019. Sequencing Proteins from Bottom to Top: Combining Techniques for Full Sequence Analysis of Glucokinase. In Advancements of Mass Spectrometry in Biomedical Research, eds. AG Woods, CC Darie, pp. 111–19. Cham: Springer International Publishing
Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, et al. 2019. Identification and Quantification of Proteoforms by Mass Spectrometry. PROTEOMICS. 19(10):1800361
Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, et al. 2019. Back Cover: Identification and Quantification of Proteoforms by Mass Spectrometry. PROTEOMICS. 19(10):1970085
Vialaret J, Lehmann S, Hirtz C. 2019. Intact Protein Analysis by LC-MS for Characterizing Biomarkers in Cerebrospinal Fluid. In Proteomics for Biomarker Discovery: Methods and Protocols, eds. V Brun, Y Couté, pp. 163–72. New York, NY: Springer New York
Coelho Graça D, Hartmer R, Jabs W, Scherl A, Clerici L, et al. 2019. Detection of Proteoforms Using Top-Down Mass Spectrometry and Diagnostic Ions. In Proteomics for Biomarker Discovery: Methods and Protocols, eds. V Brun, Y Couté, pp. 173–83. New York, NY: Springer New York
Boomathi Pandeswari P, Sabareesh V. 2019. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Advances. 9(1):313–44


Huilin L. 2018. Native top-down proteomics comes into light. Sci. China Life Sci.
Srzentic K, Nagornov KO, Fornelli L, Lobas AA, Ayoub D, et al. 2018. Multiplexed Middle-Down Mass Spectrometry Reveals Light and Heavy Chain Connectivity in a Monoclonal Antibody. Anal. Chem.
Yang R, Zhu D. 2018. A graph-based filtering method for top-down mass spectral identification. BMC Genomics. 19(7):666
Manconi B, Liori B, Cabras T, Vincenzoni F, Iavarone F, et al. 2018. Top-down proteomic profiling of human saliva in multiple sclerosis patients. Journal of Proteomics. 187:212–22
Wongkongkathep P, Han JY, Choi TS, Yin S, Kim HI, Loo JA. 2018. Native Top-Down Mass Spectrometry and Ion Mobility MS for Characterizing the Cobalt and Manganese Metal Binding of α-Synuclein Protein. J. Am. Soc. Mass Spectrom. 29(9):1870–80
Ghezellou P, Garikapati V, Kazemi SM, Strupat K, Ghassempour A, Spengler B. 2018. A perspective view of top-down proteomics in snake venom research. Rapid Communications in Mass Spectrometry. 0(ja):
Padiglia A, Orrù R, Boroumand M, Olianas A, Manconi B, et al. 2018. Extensive Characterization of the Human Salivary Basic Proline-Rich Proteins Family by Top-Down Mass Spectrometry. J. Proteome Res.
Cai W, Hite ZL, Lyu B, Wu Z, Lin Z, et al. 2018. Temperature-sensitive sarcomeric protein post-translational modifications revealed by top-down proteomics. Journal of Molecular and Cellular Cardiology
Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, et al. 2018. The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins. Anal. Chem.
Krupke A, Chen C-H, Feng H, Guo R, Li P, et al. 2018. Intact NIST Monoclonal Antibody Characterization - Proteoforms, Glycoforms - using CE-MS and CE-LIF. Cogent Chemistry. 1480455
Floris F, Chiron L, Lynch A, Barrow MP, Delsuc M-A, O'Connor PB. 2018. Top-down deep sequencing of Ubiquitin using two-dimensional mass spectrometry. Anal. Chem.
Gargano AFG, Roca LS, Fellers RT, Bocxe M, Domínguez Vega E, Somsen GW. 2018. Capillary HILIC-MS: a new tool for sensitive top-down proteomics. Anal. Chem.
dos Santos Seckler H, Fornelli L, Mutharasan RK, Thaxton CS, Fellers RT, et al. 2018. A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity. J. Proteome Res.
Jiang T, Hoover ME, Holt MV, Freitas MA, Marshall AG, Young NL. 2018. Middle-Down Characterization of the Cell Cycle Dependence of Histone H4 Post-Translational Modifications and Proteoforms. Proteomics. 0(0):1700442
Kachuk C, Doucette AA. 2018. The benefits (and misfortunes) of SDS in top-down proteomics. Journal of Proteomics. 175:75–86
Schmit P-O, Vialaret J, Wessels HJCT, van Gool AJ, Lehmann S, et al. 2018. Towards a routine application of Top-Down approaches for label-free discovery workflows. Journal of Proteomics. 175:12–26
Smith LM, Kelleher NL. 2018. Proteoforms as the next proteomics currency. Science. 359(6380):1106–7
Chen D, Gomes F, Abeykoon D, Lemma B, Wang Y, et al. 2018. Top-Down Analysis of Branched Proteins Using Mass Spectrometry. Anal. Chem.
LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, et al. 2018. ProForma: A Standard Proteoform Notation. J. Proteome Res. 17(3):1321–25
Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, et al. 2018. How many human proteoforms are there? Nature Chemical Biology. 14(3):206–14
Davis RG, Park H-M, Kim K, Greer JB, Fellers RT, et al. 2018. Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains. Anal. Chem.
Delcourt V, Franck J, Quanico J, Gimeno J-P, Wisztorski M, et al. 2018. Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions. Mol Cell Proteomics. 17(2):357–72
Breuker K. 2018. Mass spectrometry: Raw protein from the top down. Nature Chemistry. 10(2):114
Polasky DA, Lermyte F, Nshanian M, Sobott F, Andrews PC, et al. 2018. Fixed-charge Trimethyl Pyrilium Modification Enables Enhanced Top-down Mass Spectrometry Sequencing of Intact Protein Complexes. Anal. Chem.
Garabedian A, Baird MA, Porter J, Jeanne Dit Fouque K, Shliaha PV, et al. 2018. Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms. Anal. Chem.
Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, et al. 2018. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. J. Proteome Res. 17(1):568–78
Regnier FE, Kim J. 2018. Proteins and Proteoforms: New Separation Challenges. Anal. Chem. 90(1):361–73
Gomes F, Lemma B, Abeykoon D, Chen D, Wang Y, et al. 2018. Top-down Analysis of Novel Synthetic Branched Proteins. Journal of Mass Spectrometry. 0(ja):
Locard-Paulet M, Parra J, Albigot R, Mouton-Barbosa E, Bardi L, et al. 2018. VisioProt-MS: interactive 2D maps from intact protein mass spectrometry. Bioinformatics
Wu H, Xiao K, Tian Z. 2018. Top-down characterization of chicken core histones. Journal of Proteomics
Vialaret J, Schmit P-O, Lehmann S, Gabelle A, Wood J, et al. 2018. Identification of multiple proteoforms biomarkers on clinical samples by routine Top-Down approaches. Data in Brief
Why Should We Weigh Every Protein in the Human Body? 2018. News Medical.


Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, et al. 2017. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Anal. Chem.
Chang H-Y, Chen C-T, Ko C-L, Chen Y-J, Chen Y-J, et al. 2017. iTop-Q: an intelligent tool for top-down proteomics quantitation us-ing DYAMOND algorithm. Anal. Chem.
Chen B, Brown KA, Lin Z, Ge Y. 2017. Top-down Proteomics: Ready for Prime Time? Anal. Chem.
Skinner OS, Haverland NA, Fornelli L, Melani RD, Vale LHFD, et al. 2017. Top-down characterization of endogenous protein complexes with native proteomics. Nature Chemical Biology. nchembio.2515
Manconi B, Liori B, Cabras T, Vincenzoni F, Iavarone F, et al. 2017. Salivary Cystatins: Exploring New Post-Translational Modifications and Polymorphisms by Top-Down High-Resolution Mass Spectrometry. J. Proteome Res. 16(11):4196–4207
Cai W, Zhang J, Lange WJ de, Gregorich Z, Ralphe JC, et al. 2017. Top-down proteomics for assessing the maturation of stem cell-derived cardiomyocytes. Journal of Molecular and Cellular Cardiology. 112:165–66
Melani RD, Nogueira FCS, Domont GB. 2017. It is time for top-down venomics. Journal of Venomous Animals and Toxins including Tropical Diseases. 23:44
Lyon YA, Riggs D, Fornelli L, Compton PD, Julian RR. 2017. The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics. J. Am. Soc. Mass Spectrom. 1–8
Chen B, Guo X, Tucholski T, Lin Z, McIlwain S, Ge Y. 2017. The Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective. J. Am. Soc. Mass Spectrom. 28(9):1805–14
Kar UK, Simonian M, Whitelegge JP. 2017. Integral membrane proteins: bottom-up, top-down and structural proteomics. Expert Review of Proteomics. 14(8):715–23
Delcourt V, Franck J, Leblanc E, Narducci F, Robin Y-M, et al. 2017. Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine. 21:55–64
Gregorich ZR, Cai W, Lin Z, Chen AJ, Peng Y, et al. 2017. Distinct sequences and post-translational modifications in cardiac atrial and ventricular myosin light chains revealed by top-down mass spectrometry. Journal of Molecular and Cellular Cardiology. 107:13–21
Haverland NA, Skinner OS, Fellers RT, Tariq AA, Early BP, et al. 2017. Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom. 28(6):1203–15
Chen B, Hwang L, Ochowicz W, Lin Z, Guardado-Alvarez TM, et al. 2017. Coupling functionalized cobalt ferrite nanoparticle enrichment with online LC/MS/MS for top-down phosphoproteomics. Chem. Sci. 8(6):4306–11
Cai W, Tucholski T, Chen B, Alpert AJ, McIlwain S, et al. 2017. Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Anal. Chem. 89(10):5467–75
Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, et al. 2017. High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer. J. Proteome Res. 16(5):2072–79
Gil G, Mao P, Avula B, Ali Z, Chittiboyina AG, et al. 2017. Proteoform-Specific Protein Binding of Small Molecules in Complex Matrices. ACS Chem. Biol. 12(2):389–97
Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, et al. 2017. Top-down proteomics: Where we are, where we are going? Journal of Proteomics
Fornelli L, Durbin KR, Fellers RT, Early BP, Greer JB, et al. 2017. Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer. J. Proteome Res. 16(2):609–18
Anderson LC, DeHart CJ, Kaiser NK, Fellers RT, Smith DF, et al. 2017. Identification and Characterization of Human Proteoforms by Top-Down LC-21 Tesla FT-ICR Mass Spectrometry. J. Proteome Res. 16(2):1087–96
Xiao K, Yu F, Tian Z. 2017. Top-down protein identification using isotopic envelope fingerprinting. Journal of Proteomics. 152:41–47
Liu X, St. Ange K, Lin L, Zhang F, Chi L, Linhardt RJ. 2017. Top-down and bottom-up analysis of commercial enoxaparins. Journal of Chromatography A. 1480:32–40
Guthals A, Gan Y, Murray L, Chen Y, Stinson J, et al. 2017. De Novo MS/MS Sequencing of Native Human Antibodies. J. Proteome Res. 16(1):45–54
Lermyte F, Łącki MK, Valkenborg D, Gambin A, Sobott F. 2017. Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin. J. Am. Soc. Mass Spectrom. 28(1):69–76
Penque D, Marcus K, Torres VM. 2017. Editorial: Breakthroughs in top-down proteomics. Journal of Proteomics
DeHart CJ, Fellers RT, Fornelli L, Kelleher NL, Thomas PM. 2017. Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite. In Protein Bioinformatics, pp. 381–94. Humana Press, New York, NY
Nedelkov D. 2017. Mass spectrometry protein tests: ready for prime time (or not). Expert Review of Proteomics. 14(1):1–7


Campuzano IDG, Li H, Bagal D, Lippens JL, Svitel J, et al. 2016. Native MS Analysis of Bacteriorhodopsin and an Empty Nanodisc by Orthogonal Acceleration Time-of-Flight, Orbitrap and Ion Cyclotron Resonance. Anal. Chem. 88(24):12427–36
Lössl P, Waterbeemd M van de, Heck AJ. 2016. The diverse and expanding role of mass spectrometry in structural and molecular biology. The EMBO Journal. 35(24):2634–57
Wang X, Liu X, Li L, Zhang F, Hu M, et al. 2016. GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data. PLOS ONE. 11(12):e0167727
Pan J, Zhang S, Borchers CH. 2016. Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1864(12):1801–8
Shaw JB, Lin T-Y, Leach FE, Tolmachev AV, Tolić N, et al. 2016. 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox. J. Am. Soc. Mass Spectrom. 27(12):1929–36
Liu H, Zhang N, Cui M, Liu Z, Liu S. 2016. Mass spectrometry based strategy for studies of binding sites and structural changes of cisplatin binding to myoglobin. Rapid Commun. Mass Spectrom. 30(22):2433–41
Vehus T, Roberg-Larsen H, Waaler J, Aslaksen S, Krauss S, et al. 2016. Versatile, sensitive liquid chromatography mass spectrometry – Implementation of 10 μm OT columns suitable for small molecules, peptides and proteins. Scientific Reports. 6:srep37507
Geis-Asteggiante L, Ostrand-Rosenberg S, Fenselau C, Edwards NJ. 2016. Evaluation of Spectral Counting for Relative Quantitation of Proteoforms in Top-Down Proteomics. Anal. Chem. 88(22):10900–907
Quijada JV, Schmitt ND, Salisbury JP, Auclair JR, Agar JN. 2016. Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism. Anal. Chem. 88(22):11139–46
Yang Y, Liu F, Franc V, Halim LA, Schellekens H, Heck AJR. 2016. Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity. Nature Communications. 7:ncomms13397
Lomonte B, Rey-Suárez P, Fernández J, Sasa M, Pla D, et al. 2016. Venoms of Micrurus coral snakes: Evolutionary trends in compositional patterns emerging from proteomic analyses. Toxicon. 122:7–25
Vorontsov EA, Rensen E, Prangishvili D, Krupovic M, Chamot-Rooke J. 2016. Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics. Mol Cell Proteomics. 15(11):3388–3404
Anderson DMG, Van de Plas R, Rose KL, Hill S, Schey KL, et al. 2016. 3-D imaging mass spectrometry of protein distributions in mouse Neurofibromatosis 1 (NF1)-associated optic glioma. Journal of Proteomics. 149:77–84
Cammarata MB, Schardon CL, Mehaffey MR, Rosenberg J, Singleton J, et al. 2016. Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. J. Am. Chem. Soc. 138(40):13187–96
Wang EH, Nagarajan Y, Carroll F, Schug KA. 2016. Reversed-phase separation parameters for intact proteins using liquid chromatography with triple quadrupole mass spectrometry. J Sep Sci. 39(19):3716–27
Vyatkina K, Wu S, Dekker LJM, VanDuijn MM, Liu X, et al. 2016. Top-down analysis of protein samples by de novo sequencing techniques. Bioinformatics. 32(18):2753–59
Randall EC, Race AM, Cooper HJ, Bunch J. 2016. MALDI Imaging of Liquid Extraction Surface Analysis Sampled Tissue. Anal. Chem. 88(17):8433–40
Arba M, Iavarone F, Vincenzoni F, Manconi B, Vento G, et al. 2016. Proteomic characterization of the acid-insoluble fraction of whole saliva from preterm human newborns. Journal of Proteomics. 146:48–57
Martelli C, D'Angelo L, Barba M, Baranzini M, Inserra I, et al. 2016. Top-down proteomic characterization of DAOY medulloblastoma tumor cell line. EuPA Open Proteomics. 12:13–21
Helmich F, van Dongen JLJ, Kuijper PHM, Scharnhorst V, Brunsveld L, Broeren MAC. 2016. Rapid phenotype hemoglobin screening by high-resolution mass spectrometry on intact proteins. Clinica Chimica Acta. 460:220–26
Halim MA, Girod M, MacAleese L, Lemoine J, Antoine R, Dugourd P. 2016. Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization. J. Am. Soc. Mass Spectrom. 27(9):1435–42
Floris F, Agthoven M van, Chiron L, Soulby AJ, Wootton CA, et al. 2016. 2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach. J. Am. Soc. Mass Spectrom. 27(9):1531–38
Martelli C, Marzano V, Iavarone F, Huang L, Vincenzoni F, et al. 2016. Characterization of the Protein Components of Matrix Stones Sheds Light on S100-A8 and S100-A9 Relevance in the Inflammatory Pathogenesis of These Rare Renal Calculi. The Journal of Urology. 196(3):911–18
Tamara S, Dyachenko A, Fort KL, Makarov AA, Scheltema RA, Heck AJR. 2016. Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies. J. Am. Chem. Soc. 138(34):10860–68
Tran NH, Rahman MZ, He L, Xin L, Shan B, Li M. 2016. Complete De Novo Assembly of Monoclonal Antibody Sequences. Scientific Reports. 6:srep31730
Kachuk C, Faulkner M, Liu F, Doucette AA. 2016. Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis. J. Proteome Res. 15(8):2634–42
Kou Q, Zhu B, Wu S, Ansong C, Tolić N, et al. 2016. Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore. J. Proteome Res. 15(8):2422–32
Cai W, Tucholski TM, Gregorich ZR, Ge Y. 2016. Top-down Proteomics: Technology Advancements and Applications to Heart Diseases. Expert Review of Proteomics. 13(8):717–30
Aaberg MT, Aaberg TM. 2016. Pembrolizumab Administration Associated With Posterior Uveitis. Retinal Cases & Brief Reports. Publish Ahead of Print:
Zheng Y, Huang X, Kelleher NL. 2016. Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry. Current Opinion in Chemical Biology. 33:142–50
Pedro L, Quinn RJ. 2016. Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules. 21(8):984
Fang H, Xiao K, Li Y, Yu F, Liu Y, et al. 2016. Intact Protein Quantitation Using Pseudoisobaric Dimethyl Labeling. Anal. Chem. 88(14):7198–7205
Mikhailov VA, Liko I, Mize TH, Bush MF, Benesch JLP, Robinson CV. 2016. Infrared Laser Activation of Soluble and Membrane Protein Assemblies in the Gas Phase. Anal. Chem. 88(14):7060–67
Lohnes K, Quebbemann NR, Liu K, Kobzeff F, Loo JA, Ogorzalek Loo RR. 2016. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics. Methods. 104:163–69
Beveridge R, Migas LG, Payne KAP, Scrutton NS, Leys D, Barran PE. 2016. Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding. Nature Communications. 7:ncomms12163
Griffiths RL, Creese AJ, Race AM, Bunch J, Cooper HJ. 2016. LESA FAIMS Mass Spectrometry for the Spatial Profiling of Proteins from Tissue. Anal. Chem. 88(13):6758–66
Jafari M, Mirzaie M, Khodabandeh M, Rezadoost H, Ghassempour A, Aboul-Enein HY. 2016. Polarity-based fractionation in proteomics: hydrophilic interaction vs reversed-phase liquid chromatography. Biomed. Chromatogr. 30(7):1036–41
Savaryn JP, Toby TK, Catherman AD, Fellers RT, LeDuc RD, et al. 2016. Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection. Proteomics. 16(14):2048–58


Fu X, Xiao H, Liang S, Bao JJ, Li T, Zhang Y. 2015. A method developed to fractionate intact proteins based on capillary electrophoresis. Analyst. 141(1):305–10
Tvardovskiy A, Wrzesinski K, Sidoli S, Fey SJ, Rogowska-Wrzesinska A, Jensen ON. 2015. Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns. Mol Cell Proteomics. 14(12):3142–53
Wongkongkathep P, Li H, Zhang X, Ogorzalek Loo RR, Julian RR, Loo JA. 2015. Enhancing protein disulfide bond cleavage by UV excitation and electron capture dissociation for top-down mass spectrometry. International Journal of Mass Spectrometry. 390:137–45
Lorenzatto KR, Kim K, Ntai I, Paludo GP, Camargo de Lima J, et al. 2015. Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage. J. Proteome Res. 14(11):4805–14
Lermyte F, Verschueren T, Brown JM, Williams JP, Valkenborg D, Sobott F. 2015. Characterization of top-down ETD in a travelling-wave ion guide. Methods. 89:22–29
Petrotchenko EV, Borchers CH. 2015. HDX Match Software for the Data Analysis of Top-Down ECD-FTMS Hydrogen/Deuterium Exchange Experiments. J. Am. Soc. Mass Spectrom. 26(11):1895–98
Cabras T, Sanna M, Manconi B, Fanni D, Demelia L, et al. 2015. Proteomic investigation of whole saliva in Wilson's disease. Journal of Proteomics. 128:154–63
Gregorich ZR, Peng Y, Lane NM, Wolff JJ, Wang S, et al. 2015. Comprehensive assessment of chamber-specific and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. Journal of Molecular and Cellular Cardiology. 87:102–12
Gault J, Ferber M, Machata S, Imhaus A-F, Malosse C, et al. 2015. Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation. PLOS Pathogens. 11(9):e1005162
Kim K, Compton PD, Toby TK, Thomas PM, Wilkins JT, et al. 2015. Reducing protein oxidation in low-flow electrospray enables deeper investigation of proteoforms by top down proteomics. EuPA Open Proteomics. 8:40–47
Chen Y-C, Ayaz-Guner S, Peng Y, Lane NM, Locher MR, et al. 2015. Effective Top-Down LC/MS+ Method for Assessing Actin Isoforms as a Potential Cardiac Disease Marker. Anal. Chem. 87(16):8399–8406
Konijnenberg A, Bannwarth L, Yilmaz D, Koçer A, Venien-Bryan C, Sobott F. 2015. Top-down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment. Protein Science. 24(8):1292–1300
Baker ES, Burnum-Johnson KE, Ibrahim YM, Orton DJ, Monroe ME, et al. 2015. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics. 15(16):2766–76
Cammarata MB, Thyer R, Rosenberg J, Ellington A, Brodbelt JS. 2015. Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry. J. Am. Chem. Soc. 137(28):9128–35
Badugu R, Szmacinski H, Ray K, Descrovi E, Ricciardi S, et al. 2015. Fluorescence Spectroscopy with Metal–Dielectric Waveguides. J. Phys. Chem. C. 119(28):16245–55
Cabras T, Iavarone F, Martelli C, Delfino D, Rossetti DV, et al. 2015. High-resolution mass spectrometry for thymosins detection and characterization. Expert Opinion on Biological Therapy. 15(sup1):191–201
Scherl A. 2015. Clinical protein mass spectrometry. Methods. 81:3–14
Petras D, Heiss P, Süssmuth RD, Calvete JJ. 2015. Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches. J. Proteome Res. 14(6):2539–56
Azkargorta M, Soria J, Ojeda C, Guzmán F, Acera A, et al. 2015. Human Basal Tear Peptidome Characterization by CID, HCD, and ETD Followed by in Silico and in Vitro Analyses for Antimicrobial Peptide Identification. J. Proteome Res. 14(6):2649–58
Gustafsson OJR, Arentz G, Hoffmann P. 2015. Proteomic developments in the analysis of formalin-fixed tissue. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1854(6):559–80
Cai Y, Zheng Q, Liu Y, Helmy R, Loo JA, Chen H. 2015. Integration of Electrochemistry with Ultra-Performance Liquid Chromatography/Mass Spectrometry. Eur J Mass Spectrom (Chichester). 21(3):341–51
Zhang J, Malmirchegini GR, Clubb RT, Loo JA. 2015. Native Top-down Mass Spectrometry for the Structural Characterization of Human Hemoglobin. Eur J Mass Spectrom (Chichester). 21(3):221–31
Lee YS, Hwang SG, Kim JK, Park TH, Kim YR, et al. 2015. Topological network analysis of differentially expressed genes in cancer cells with acquired gefitinib resistance. Cancer Genomics Proteomics. 12(3):153–66
Martelli C, Iavarone F, D'Angelo L, Arba M, Vincenzoni F, et al. 2015. Integrated proteomic platforms for the comparative characterization of medulloblastoma and pilocytic astrocytoma pediatric brain tumors: a preliminary study. Mol. BioSyst. 11(6):1668–83
Tilton SC, Matzke MM, Sowa MB, Stenoien DL, Weber TJ, et al. 2015. Data integration reveals key homeostatic mechanisms following low dose radiation exposure. Toxicology and Applied Pharmacology. 285(1):1–11
Law KP, Han T-L, Tong C, Baker PN. 2015. Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth. International Journal of Molecular Sciences. 16(5):10952–85
Kim KH, Compton PD, Tran JC, Kelleher NL. 2015. Online Matrix Removal Platform for Coupling Gel-Based Separations to Whole Protein Electrospray Ionization Mass Spectrometry. J. Proteome Res. 14(5):2199–2206
Brunner AM, Lössl P, Liu F, Huguet R, Mullen C, et al. 2015. Benchmarking Multiple Fragmentation Methods on an Orbitrap Fusion for Top-down Phospho-Proteoform Characterization. Anal. Chem. 87(8):4152–58
Arentz G, Weiland F, Oehler MK, Hoffmann P. 2015. State of the art of 2D DIGE. Prot. Clin. Appl. 9(3–4):277–88
Cegelski L. 2015. Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition. Journal of Magnetic Resonance. 253:91–97
Chen Y-C, Sumandea MP, Larsson L, Moss RL, Ge Y. 2015. Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. J. Muscle Res. Cell. Motil. 36(2):169–81
Birner-Gruenberger R, Breinbauer R. 2015. Weighing the Proteasome for Covalent Modifications. Chemistry & Biology. 22(3):315–16
Jouiaei M, Casewell NR, Yanagihara AA, Nouwens A, Cribb BW, et al. 2015. Firing the Sting: Chemically Induced Discharge of Cnidae Reveals Novel Proteins and Peptides from Box Jellyfish (Chironex fleckeri) Venom. Toxins. 7(3):936–50
Nicolardi S, Switzar L, Deelder AM, Palmblad M, van der Burgt YEM. 2015. Top-Down MALDI-In-Source Decay-FTICR Mass Spectrometry of Isotopically Resolved Proteins. Anal. Chem. 87(6):3429–37
Chang Y-H, Gregorich ZR, Chen AJ, Hwang L, Guner H, et al. 2015. New mass-spectrometry-compatible degradable surfactant for tissue proteomics. J. Proteome Res. 14(3):1587–99
Lyon YA, Julian RR. 2015. Photolytic determination of charge state for large proteins and fragments in an ion trap mass spectrometer. Rapid Commun. Mass Spectrom. 29(4):322–26
Geis-Asteggiante L, Dhabaria A, Edwards N, Ostrand-Rosenberg S, Fenselau C. 2015. Top–down analysis of low mass proteins in exosomes shed by murine myeloid-derived suppressor cells. International Journal of Mass Spectrometry. 378:264–69
Zhang J, Loo RRO, Loo JA. 2015. Increasing fragmentation of disulfide-bonded proteins for top–down mass spectrometry by supercharging. International Journal of Mass Spectrometry. 377:546–56
Labas V, Spina L, Belleannee C, Teixeira-Gomes A-P, Gargaros A, et al. 2015. Analysis of epididymal sperm maturation by MALDI profiling and top-down mass spectrometry. Journal of Proteomics. 113:226–43
Jesus JR de, Campos BK de, Galazzi RM, Martinez JLC, Arruda MAZ. 2015. Bipolar disorder: recent advances and future trends in bioanalytical developments for biomarker discovery. Anal Bioanal Chem. 407(3):661–67
Halim A, Carlsson MC, Madsen CB, Brand S, Møller SR, et al. 2015. Glycoproteomic Analysis of Seven Major Allergenic Proteins Reveals Novel Post-translational Modifications. Mol Cell Proteomics. 14(1):191–204
Bladergroen MR, van der Burgt YEM. 2015. Solid-Phase Extraction Strategies to Surmount Body Fluid Sample Complexity in High-Throughput Mass Spectrometry-Based Proteomics. Journal of Analytical Methods in Chemistry.


Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, et al. 2014. Proteomics of muscle chronological ageing in post-menopausal women. BMC Genomics. 15:1165
Ree AH, Meltzer S, Flatmark K, Dueland S, Kalanxhi E. 2014. Biomarkers of Treatment Toxicity in Combined-Modality Cancer Therapies with Radiation and Systemic Drugs: Study Design, Multiplex Methods, Molecular Networks. International Journal of Molecular Sciences. 15(12):22835–56
Doucette AA, Vieira DB, Orton DJ, Wall MJ. 2014. Resolubilization of Precipitated Intact Membrane Proteins with Cold Formic Acid for Analysis by Mass Spectrometry. J. Proteome Res. 13(12):6001–12
Ichibangase T, Imai K. 2014. Straightforward proteomic analysis reveals real dynamics of proteins in cells. Journal of Pharmaceutical and Biomedical Analysis. 101:31–39
Kelleher NL, Thomas PM, Ntai I, Compton PD, LeDuc RD. 2014. Deep and quantitative top-down proteomics in clinical and translational research. Expert Review of Proteomics. 11(6):649–51
Labas V, Spina L, Belleannee C, Teixeira-Gomes A-P, Gargaros A, et al. 2014. Data in support of peptidomic analysis of spermatozoa during epididymal maturation. Data in Brief. 1:79–84
Li H, Wongkongkathep P, Orden SLV, Loo RRO, Loo JA. 2014. Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment. J. Am. Soc. Mass Spectrom. 25(12):2060–68
Han X, Wang Y, Aslanian A, Bern M, Lavallée-Adam M, Yates JR. 2014. Sheathless Capillary Electrophoresis-Tandem Mass Spectrometry for Top-Down Characterization of Pyrococcus furiosus Proteins on a Proteome Scale. Anal. Chem. 86(22):11006–12
Inserra I, Iavarone F, Martelli C, D'Angelo L, Delfino D, et al. 2014. Proteomic Study of Pilocytic Astrocytoma Pediatric Brain Tumor Intracystic Fluid. J. Proteome Res. 13(11):4594–4606
Sarsby J, Martin NJ, Lalor PF, Bunch J, Cooper HJ. 2014. Top-Down and Bottom-Up Identification of Proteins by Liquid Extraction Surface Analysis Mass Spectrometry of Healthy and Diseased Human Liver Tissue. J. Am. Soc. Mass Spectrom. 25(11):1953–61
Srzentić K, Fornelli L, Laskay ÜA, Monod M, Beck A, et al. 2014. Advantages of Extended Bottom-Up Proteomics Using Sap9 for Analysis of Monoclonal Antibodies. Anal. Chem. 86(19):9945–53
Peng Y, Gregorich ZR, Valeja SG, Zhang H, Cai W, et al. 2014. Top-down Proteomics Reveals Concerted Reductions in Myofilament and Z-disc Protein Phosphorylation after Acute Myocardial Infarction. Mol Cell Proteomics. 13(10):2752–64
Xiu L, Valeja SG, Alpert AJ, Jin S, Ge Y. 2014. Effective Protein Separation by Coupling Hydrophobic Interaction and Reverse Phase Chromatography for Top-down Proteomics. Anal. Chem. 86(15):7899–7906
Peng Y, Ayaz-Guner S, Yu D, Ge Y. 2014. Top-down mass spectrometry of cardiac myofilament proteins in health and disease. Prot. Clin. Appl. 8(7–8):554–68
Martelli C, Iavarone F, Vincenzoni F, Rossetti DV, D'Angelo L, et al. 2014. Proteomic characterization of pediatric craniopharyngioma intracystic fluid by LC-MS top-down/bottom-up integrated approaches. ELECTROPHORESIS. 35(15):2172–83
Warnke S, Baldauf C, Bowers MT, Pagel K, von Helden G. 2014. Photodissociation of Conformer-Selected Ubiquitin Ions Reveals Site-Specific Cis/Trans Isomerization of Proline Peptide Bonds. J. Am. Chem. Soc. 136(29):10308–14
LeDuc RD, Fellers RT, Early BP, Greer JB, Thomas PM, Kelleher NL. 2014. The C-Score: A Bayesian Framework to Sharply Improve Proteoform Scoring in High-Throughput Top Down Proteomics. J. Proteome Res. 13(7):3231–40
Sarbu M, Ghiulai RM, Zamfir AD. 2014. Recent developments and applications of electron transfer dissociation mass spectrometry in proteomics. Amino Acids. 46(7):1625–34
Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. 2014. High-Throughput Proteomics. Annual Rev. Anal. Chem. 7(1):427–54
Oliveira BM, Coorssen JR, Martins-de-Souza D. 2014. 2DE: The Phoenix of Proteomics. Journal of Proteomics. 104:140–50
Gregorich ZR, Chang Y-H, Ge Y. 2014. Proteomics in heart failure: top-down or bottom-up? Pflugers Arch - Eur J Physiol. 466(6):1199–1209
Polunina TA, Varshavskaia IS, Grigor’eva GV, Krasnov IM. 2014. [Proteomic methods of protein separation and analysis]. Zh. Mikrobiol. Epidemiol. Immunobiol. (3):107–14
Iavarone F, Melis M, Platania G, Cabras T, Manconi B, et al. 2014. Characterization of salivary proteins of schizophrenic and bipolar disorder patients by top-down proteomics. Journal of Proteomics. 103:15–22
Hung C-W, Jung S, Grötzinger J, Gelhaus C, Leippe M, Tholey A. 2014. Determination of disulfide linkages in antimicrobial peptides of the macin family by combination of top-down and bottom-up proteomics. Journal of Proteomics. 103:216–26
Kuppannan K, Julka S, Karnoup A, Dielman D, Schafer B. 2014. 2DLC-UV/MS Assay for the Simultaneous Quantification of Intact Soybean Allergens Gly m 4 and Hydrophobic Protein from Soybean (HPS). J. Agric. Food Chem. 62(21):4884–92
Ntai I, Kim K, Fellers RT, Skinner OS, Smith AD, et al. 2014. Applying Label-Free Quantitation to Top Down Proteomics. Anal. Chem. 86(10):4961–68
Skinner OS, Catherman AD, Early BP, Thomas PM, Compton PD, Kelleher NL. 2014. Fragmentation of Integral Membrane Proteins in the Gas Phase. Anal. Chem. 86(9):4627–34
Ait-Belkacem R, Berenguer C, Villard C, Ouafik L, Figarella-Branger D, et al. 2014. MALDI imaging and in-source decay for top-down characterization of glioblastoma. Proteomics. 14(10):1290–1301
Kiss A, Smith DF, Reschke BR, Powell MJ, Heeren RMA. 2014. Top-down mass spectrometry imaging of intact proteins by laser ablation ESI FT-ICR MS. Proteomics. 14(10):1283–89
Li Y, Compton PD, Tran JC, Ntai I, Kelleher NL. 2014. Optimizing capillary electrophoresis for top-down proteomics of 30–80 kDa proteins. Proteomics. 14(10):1158–64
Auclair JR, Salisbury JP, Johnson JL, Petsko GA, Ringe D, et al. 2014. Artifacts to avoid while taking advantage of top-down mass spectrometry based detection of protein S-thiolation. Proteomics. 14(10):1152–57
Dekker L, Wu S, Vanduijn M, Tolić N, Stingl C, et al. 2014. An integrated top-down and bottom-up proteomic approach to characterize the antigen-binding fragment of antibodies. Proteomics. 14(10):1239–48
Dang X, Scotcher J, Wu S, Chu RK, Tolić N, et al. 2014. The first pilot project of the consortium for top-down proteomics: A status report. Proteomics. 14(10):1130–40
Bourgoin-Voillard S, Leymarie N, Costello CE. 2014. Top-down tandem mass spectrometry on RNase A and B using a Qh/FT-ICR hybrid mass spectrometer. Proteomics. 14(10):1174–84
Gregorich ZR, Ge Y. 2014. Top-down proteomics in health and disease: Challenges and opportunities. Proteomics. 14(10):1195–1210
Ye H, Mandal R, Catherman A, Thomas PM, Kelleher NL, et al. 2014. Top-Down Proteomics with Mass Spectrometry Imaging: A Pilot Study towards Discovery of Biomarkers for Neurodevelopmental Disorders. PLOS ONE. 9(4):e92831
Tsybin YO. 2014. From High- to Super-resolution Mass Spectrometry. CHIMIA International Journal for Chemistry. 68(3):168–74
Guner H, Close PL, Cai W, Zhang H, Peng Y, et al. 2014. MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization. J. Am. Soc. Mass Spectrom. 25(3):464–70
Cannon JR, Cammarata MB, Robotham SA, Cotham VC, Shaw JB, et al. 2014. Ultraviolet Photodissociation for Characterization of Whole Proteins on a Chromatographic Time Scale. Anal. Chem. 86(4):2185–92
Durbin KR, Fellers RT, Ntai I, Kelleher NL, Compton PD. 2014. Autopilot: An Online Data Acquisition Control System for the Enhanced High-Throughput Characterization of Intact Proteins. Anal. Chem. 86(3):1485–92
Cabras T, Iavarone F, Manconi B, Olianas A, Sanna MT, et al. 2014. Top-down analytical platforms for the characterization of the human salivary proteome. Bioanalysis. 6(4):563–81
Zhang H, Cui W, Gross ML. 2014. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Letters. 588(2):308–17


Liu X, Hengel S, Wu S, Tolić N, Pasa-Tolić L, Pevzner PA. 2013. Identification of Ultramodified Proteins Using Top-Down Tandem Mass Spectra. J. Proteome Res. 12(12):5830–38
Zhang J, Roth MJ, Chang AN, Plymire DA, Corbett JR, et al. 2013. Top-Down Mass Spectrometry on Tissue Extracts and Biofluids with Isoelectric Focusing and Superficially Porous Silica Liquid Chromatography. Anal. Chem. 85(21):10377–84
Zhao DS, Gregorich ZR, Ge Y. 2013. High throughput screening of disulfide-containing proteins in a complex mixture. Proteomics. 13(22):3256–60
Maier SK, Hahne H, Gholami AM, Balluff B, Meding S, et al. 2013. Comprehensive identification of proteins from MALDI imaging. Mol. Cell Proteomics. 12(10):2901–10
Chen X, Ge Y. 2013. Ultrahigh pressure fast size exclusion chromatography for top-down proteomics. Proteomics. 13(17):2563–66
Shaw JB, Li W, Holden DD, Zhang Y, Griep-Raming J, et al. 2013. Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation. J. Am. Chem. Soc. 135(34):12646–51
Canon F, Milosavljević AR, van der Rest G, Réfrégiers M, Nahon L, et al. 2013. Photodissociation and Dissociative Photoionization Mass Spectrometry of Proteins and Noncovalent Protein–Ligand Complexes. Angew. Chem. Int. Ed. 52(32):8377–81
Peng Y, Yu D, Gregorich Z, Chen X, Beyer AM, et al. 2013. In-depth Proteomic Analysis of Human Tropomyosin by Top-down Mass Spectrometry. J Muscle Res Cell Motil. 34(0):
Das R, Mitra G, Mathew B, Ross C, Bhat V, Mandal AK. 2013. Automated Analysis of Hemoglobin Variants Using NanoLC–MS and Customized Databases. J. Proteome Res. 12(7):3215–22
Cabras T, Pisano E, Montaldo C, Giuca MR, Iavarone F, et al. 2013. Significant Modifications of the Salivary Proteome Potentially Associated with Complications of Down Syndrome Revealed by Top-down Proteomics. Mol Cell Proteomics. 12(7):1844–52
Rose CM, Russell JD, Ledvina AR, McAlister GC, Westphall MS, et al. 2013. Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species. J. Am. Soc. Mass Spectrom. 24(6):816–27
Nicolardi S, van der Burgt YEM, Dragan I, Hensbergen PJ, Deelder AM. 2013. Identification of New Apolipoprotein-CIII Glycoforms with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry of Human Sera. J. Proteome Res. 12(5):2260–68
Guy MJ, Chen Y-C, Clinton L, Zhang H, Zhang J, et al. 2013. The Impact of Antibody Selection on the Detection of Cardiac Troponin I. Clin Chim Acta. 420:82–88
Smith LM, Kelleher NL, Proteomics TC for TD. 2013. Proteoform: a single term describing protein complexity. Nat Meth. 10(3):186–87
Catherman AD, Li M, Tran JC, Durbin KR, Compton PD, et al. 2013. Top Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions. Anal. Chem. 85(3):1880–88
Peng Y, Chen X, Zhang H, Xu Q, Hacker TA, Ge Y. 2013. Top-down Targeted Proteomics for Deep Sequencing of Tropomyosin Isoforms. J. Proteome Res. 12(1):187–98
Shvartsburg AA, Smith RD. 2013. High-Resolution Differential Ion Mobility Spectrometry of a Protein. Anal. Chem. 85(1):10–13


Marty MT, Zhang H, Cui W, Blankenship RE, Gross ML, Sligar SG. 2012. Native Mass Spectrometry Characterization of Intact Nanodisc Lipoprotein Complexes. Anal. Chem. 84(21):8957–60
Edwards RL, Griffiths P, Bunch J, Cooper HJ. 2012. Top-Down Proteomics and Direct Surface Sampling of Neonatal Dried Blood Spots: Diagnosis of Unknown Hemoglobin Variants. J. Am. Soc. Mass Spectrom. 23(11):1921–30
Castagnola M, Cabras T, Iavarone F, Vincenzoni F, Vitali A, et al. 2012. Top-down platform for deciphering the human salivary proteome. The Journal of Maternal-Fetal & Neonatal Medicine. 25(sup5):27–43
Wigginton KR, Menin L, Sigstam T, Gannon G, Cascella M, et al. 2012. UV Radiation Induces Genome-Mediated, Site-Specific Cleavage in Viral Proteins. ChemBioChem. 13(6):837–45
Peng Y, Chen X, Sato T, Rankin SA, Tsuji RF, Ge Y. 2012. Purification and High-Resolution Top-Down Mass Spectrometric Characterization of Human Salivary α-Amylase. Anal. Chem. 84(7):3339–46
Nicolardi S, Andreoni A, Tabares LC, van der Burgt YEM, Canters GW, et al. 2012. Top-Down FTICR MS for the Identification of Fluorescent Labeling Efficiency and Specificity of the Cu-Protein Azurin. Anal. Chem. 84(5):2512–20


Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD, et al. 2011. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature. 480(7376):254–58
Tsybin YO, Fornelli L, Stoermer C, Luebeck M, Parra J, et al. 2011. Structural Analysis of Intact Monoclonal Antibodies by Electron Transfer Dissociation Mass Spectrometry. Anal. Chem. 83(23):8919–27
Tipton JD, Tran JC, Catherman AD, Ahlf DR, Durbin KR, Kelleher NL. 2011. Analysis of Intact Protein Isoforms by Mass Spectrometry. J. Biol. Chem. 286(29):25451–58
Yin S, Loo JA. 2011. Top-down mass spectrometry of supercharged native protein–ligand complexes. International Journal of Mass Spectrometry. 300(2):118–22