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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2022

DiStefano N, Lloyd-Jones C, Seckler H, Compton P, Sniderman A, et al. 2022. Adaptation of Native GELFrEE for HDL Particle Size Subtype Separation and Differential Apolipoprotein Proteoform Quantification. The FASEB Journal. 36(S1):
Fornelli L, Toby TK. 2022. Characterization of large intact protein ions by mass spectrometry: What directions should we follow? Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1870(4):140758
Lin Y, Agarwal AM, Marshall AG, Anderson LC. 2022. Characterization of Structural Hemoglobin Variants by Top-Down Mass Spectrometry and R Programming Tools for Rapid Identification. J. Am. Soc. Mass Spectrom. 33(1):123–30
Brodbelt JS. 2022. Deciphering combinatorial post-translational modifications by top-down mass spectrometry. Current Opinion in Chemical Biology. 70:102180
Babović M, Shliaha PV, Gibb S, Jensen ON. 2022. Effective Amino Acid Sequencing of Intact Filgrastim by Multimodal Mass Spectrometry with Topdownr. J. Am. Soc. Mass Spectrom.
Shaw JB, Cooper-Shepherd DA, Hewitt D, Wildgoose JL, Beckman JS, et al. 2022. Enhanced Top-Down Protein Characterization with Electron Capture Dissociation and Cyclic Ion Mobility Spectrometry. Anal. Chem.
Jeong K, Babović M, Gorshkov V, Kim J, Jensen ON, Kohlbacher O. 2022. FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts. Nat Commun. 13(1):4407
Rojas Ramírez C, Murtada R, Gao J, Ruotolo BT. 2022. Free Radical-Based Sequencing for Native Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom.
Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, et al. 2022. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. Science Advances. 8(32):eabp9929
Almuslehi MSM, Sen MK, Shortland PJ, Mahns DA, Coorssen JR. 2022. Histological and Top-Down Proteomic Analyses of the Visual Pathway in the Cuprizone Demyelination Model. J Mol Neurosci
Wang Q, Sun L, Lundquist PK. 2022. Large-scale top-down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes. PROTEOMICS. n/a(n/a):2100377
Hale OJ, Cooper HJ. 2022. Native Ambient Mass Spectrometry of an Intact Membrane Protein Assembly and Soluble Protein Assemblies Directly from Lens Tissue. Angewandte Chemie International Edition. 61(31):e202201458
Liu R, Xia S, Li H. 2022. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. Mass Spectrometry Reviews. n/a(n/a):e21793
Rossetti DV, Inserra I, Nesticò A, Vincenzoni F, Iavarone F, et al. 2022. Pediatric Brain Tumors: Signatures from the Intact Proteome. International Journal of Molecular Sciences. 23(6):3196
Zhan Z, Wang L. 2022. Proteoform identification based on top-down tandem mass spectra with peak error corrections. Briefings in Bioinformatics. bbab599
Yang M, Hu H, Su P, Thomas PM, Camarillo JM, et al. 2022. Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. Angewandte Chemie International Edition. n/a(n/a):
Fornelli L, Ayoub D, Srzentic K, Nagornov K, Kozhinov A, et al. 2022. Structural Analysis of Monoclonal Antibodies with Top-down and Middledown Electron Transfer Dissociation Mass Spectrometry: The First Decade. CHIMIA. 76(1–2):114–114
Meier-Credo J, Preiss L, Wüllenweber I, Resemann A, Nordmann C, et al. 2022. Top-Down Identification and Sequence Analysis of Small Membrane Proteins Using MALDI-MS/MS. J. Am. Soc. Mass Spectrom.
McCool EN, Lubeckyj RA, Chen D, Sun L. 2022. Top-Down Proteomics by Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Large-Scale Characterization of Proteoforms in Complex Samples. In Capillary Electrophoresis-Mass Spectrometry : Methods and Protocols, eds. C Neusüß, K Jooß, pp. 107–24. New York, NY: Springer US
Rangel DL, Melani RD, Carvalho EL, Boldo JT, Gomes dos Santos T, et al. 2022. Venom characterization of the Brazilian Pampa snake Bothrops pubescens by top-down and bottom-up proteomics. Toxicon. 220:106937

2021

Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, et al. 2021. Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal. Chem.
Rommelfanger SR, Zhou M, Shaghasi H, Tzeng S-C, Evans BS, et al. 2021. An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications. J. Am. Soc. Mass Spectrom.
Lantz C, Zenaidee MA, Wei B, Hemminger Z, Ogorzalek Loo RR, Loo JA. 2021. ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry. J. Proteome Res. 20(4):1928–35
Schaffer LV, Anderson LC, Butcher DS, Shortreed MR, Miller RM, et al. 2021. Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. J. Proteome Res. 20(1):317–25
Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, et al. 2021. Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. Anal. Chem.
Borges Lima D, Dupré M, Mariano Santos MD, Carvalho PC, Chamot-Rooke J. 2021. DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search. J. Am. Soc. Mass Spectrom.
Barbu IM, Lamers R-JAN, Gerritsen HW, Blokland MH, Bremer MGEG, Alewijn M. 2021. Endogenous protein and peptide analysis with LC-MS/(MS): A feasibility study for authentication of raw-milk farmer's cheese. International Dairy Journal. 117:104990
Beckman JS, Voinov VG, Hare M, Sturgeon D, Vasil'ev Y, et al. 2021. Improved Protein and PTM Characterization with a Practical Electron-Based Fragmentation on Q-TOF Instruments. J. Am. Soc. Mass Spectrom.
Lu L, Scalf M, Shortreed MR, Smith LM. 2021. Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. J. Am. Soc. Mass Spectrom.
Melby JA, Roberts DS, Larson EJ, Brown KA, Bayne EF, et al. 2021. Novel Strategies to Address the Challenges in Top-Down Proteomics. J. Am. Soc. Mass Spectrom. 32(6):1278–94
Römer J, Stolz A, Kiessig S, Moritz B, Neusüß C. 2021. Online Top-down Mass Spectrometric Identification of CE(SDS)-separated Antibody Fragments by Two-dimensional Capillary Electrophoresis. Journal of Pharmaceutical and Biomedical Analysis. 114089
Luise A, De Cecco E, Ponzini E, Sollazzo M, Mauri P, et al. 2021. Profiling Dopamine-Induced Oxidized Proteoforms of β-synuclein by Top-Down Mass Spectrometry. Antioxidants. 10(6):893
Arauz-Garofalo G, Jodar M, Vilanova M, de la Iglesia Rodriguez A, Castillo J, et al. 2021. Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN. Proteomes. 9(2):21
Jeanne Dit Fouque K, Kaplan D, Voinov VG, Holck FHV, Jensen ON, Fernandez-Lima F. 2021. Proteoform Differentiation using Tandem Trapped Ion Mobility, Electron Capture Dissociation, and ToF Mass Spectrometry. Anal. Chem.
Brunner AM, Lössl P, Geurink PP, Ovaa H, Albanese P, et al. 2021. Quantifying Positional Isomers (QPI) by top-down mass spectrometry. Molecular & Cellular Proteomics. 100070
Yu D, Wang Z, Cupp-Sutton KA, Guo Y, Kou Q, et al. 2021. Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling. J. Am. Soc. Mass Spectrom.
Schachner LF, Tran DP, Lee A, McGee JP, Jooss K, et al. 2021. Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode. International Journal of Mass Spectrometry. 116591
Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, et al. 2021. Recent advances in top-down proteome sample processing ahead of MS analysis. Mass Spectrometry Reviews. n/a(n/a):
Kline JT, Mullen C, Durbin KR, Oates RN, Huguet R, et al. 2021. Sequential Ion–Ion Reactions for Enhanced Gas-Phase Sequencing of Large Intact Proteins in a Tribrid Orbitrap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 32(9):2334–45
Zhang Z, Hug C, Tao Y, Bitsch F, Yang Y. 2021. Solving Complex Biologics Truncation Problems by Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom.
Roberts DS, Mann MW, Melby JA, Larson EJ, Zhu Y, et al. 2021. Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry. bioRxiv. 2021.02.28.433291
Smith LM, Agar JN, Chamot-Rooke J, Danis PO, Ge Y, et al. 2021. The Human Proteoform Project: Defining the human proteome. Science Advances. 7(46):
Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. 2021. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses. 13(4):668
Lefebvre D, Fenaille F, Merda D, Blanco-Valle K, Feraudet-Tarisse C, et al. 2021. Top-Down Mass Spectrometry for Trace Level Quantification of Staphylococcal Enterotoxin A Variants. J. Proteome Res.
Lermyte F. 2021. Top-Down Mass Spectrometry of Intact Proteins and Complexes: From Rare to Routine. Chromatography Online. www.chromatographyonline.com
Nagy C, Andrási M, Hamidli N, Gyémánt G, Gáspár A. 2021. Top-down proteomic analysis of monoclonal antibodies by capillary zone electrophoresis - mass spectrometry. Journal of Chromatography Open. 100024
Choi IK, Jiang T, Kankara SR, Wu S, Liu X. 2021. TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization. J. Am. Soc. Mass Spectrom.
Wei B, Zenaidee MA, Lantz C, Ogorzalek Loo RR, Loo JA. 2021. Towards understanding the formation of internal fragments generated by collisionally activated dissociation for top-down mass spectrometry. Analytica Chimica Acta. 339400

2020

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
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
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
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
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
Vimer S, Ben-Nissan G, Sharon M. 2020. Direct characterization of overproduced proteins by native mass spectrometry. Nat Protoc. 1–30
Gadkari VV, Ramírez CR, Vallejo DD, Kurulugama RT, Fjeldsted JC, Ruotolo BT. 2020. Enhanced Collision Induced Unfolding and Electron Capture Dissociation of Native-like Protein Ions. Anal. Chem.
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.
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
Cupp-Sutton KA, Wu S. 2020. High-throughput quantitative top-down proteomics. Mol. Omics
Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, et al. 2020. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem. Sci.
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.
Weisbrod CR, Anderson LC, Greer JB, DeHart CJ, Hendrickson CL. 2020. Increased Single Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading. 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.
Srzentić K, Fornelli L, Tsybin YO, Loo JA, Seckler H, et al. 2020. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom. 31(9):1783–1802
Zenaidee MA, Lantz C, Perkins T, Jung W, Loo RRO, Loo JA. 2020. Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom.
Zenaidee MA, Lantz C, Perkins T, Jung W, Loo RRO, Loo JA. 2020. Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom. 31(9):1896–1902
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.
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.
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.
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
Hale OJ, Cooper HJ. 2020. Native Mass Spectrometry Imaging and In Situ Top-Down Identification of Intact Proteins Directly from Tissue. J. Am. Soc. Mass Spectrom. 31(12):2531–37
Dupré M, Duchateau M, Malosse C, Lima DB, Calvaresi V, et al. 2020. Optimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination. J. Proteome Res.
Takemori A, Butcher DS, Harman VM, Brownridge P, Shima K, et al. 2020. PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry. J. Proteome Res. 19(9):3779–91
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.
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.
Lima DB, Dupré M, Duchateau M, Gianetto QG, Rey M, et al. 2020. ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment. Bioinformatics
Zhong J, Sun Y, Xie M, Peng W, Zhang C, et al. 2020. Proteoform characterization based on top-down mass spectrometry. Brief Bioinform
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
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.
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.
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.
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.
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):

2019

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
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
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
Cai Wenxuan, Zhang Jianhua, de Lange Willem J., Gregorich Zachery R., Karp Hannah, et al. 2019. An Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell–Derived Cardiomyocytes. Circulation Research. 125(11):936–53
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
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
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
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
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
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
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
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.
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.
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
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
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
Holt MV, Wang T, Young NL. 2019. High-Throughput Quantitative Top-Down Proteomics: Histone H4. J. Am. Soc. Mass Spectrom.
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
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
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.
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
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.
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
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
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
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.
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
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
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.
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
Chen D, Geis-Asteggiante L, Gomes FP, Ostrand-Rosenberg S, Fenselau C. 2019. Top-down Proteomic Characterization of Truncated Proteoforms. J. Proteome Res.
Vincent D, Binos S, Rochfort S, Spangenberg G. 2019. Top-Down Proteomics of Medicinal Cannabis. Proteomes. 7(4):33
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.
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

2018

Yang R, Zhu D. 2018. A graph-based filtering method for top-down mass spectral identification. BMC Genomics. 19(7):666
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):
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.
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.
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.
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.
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
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
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
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.
Breuker K. 2018. Mass spectrometry: Raw protein from the top down. Nature Chemistry. 10(2):114
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
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.
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
Huilin L. 2018. Native top-down proteomics comes into light. Sci. China Life Sci.
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
Regnier FE, Kim J. 2018. Proteins and Proteoforms: New Separation Challenges. Anal. Chem. 90(1):361–73
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
Smith LM, Kelleher NL. 2018. Proteoforms as the next proteomics currency. Science. 359(6380):1106–7
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
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
Kachuk C, Doucette AA. 2018. The benefits (and misfortunes) of SDS in top-down proteomics. Journal of Proteomics. 175:75–86
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.
Chen D, Gomes F, Abeykoon D, Lemma B, Wang Y, et al. 2018. Top-Down Analysis of Branched Proteins Using Mass Spectrometry. Anal. Chem.
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):
Wu H, Xiao K, Tian Z. 2018. Top-down characterization of chicken core histones. Journal of Proteomics
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.
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
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.
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
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2017

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
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
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
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
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
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
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
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
Penque D, Marcus K, Torres VM. 2017. Editorial: Breakthroughs in top-down proteomics. Journal of Proteomics
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.
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
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
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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
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
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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
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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
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
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2016

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
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
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
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
Skinner OS, Havugimana PC, Haverland NA, Fornelli L, Early BP, et al. 2016. An informatic framework for decoding protein complexes by top-down mass spectrometry. Nat Meth. 13(3):237–40
Anderson LC, Karch KR, Ugrin SA, Coradin M, English AM, et al. 2016. Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments. Mol Cell Proteomics. 15(3):975–88
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
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
Hühner J, Neusüß C. 2016. CIEF-CZE-MS applying a mechanical valve. Anal Bioanal Chem. 408(15):4055–61
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
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
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
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
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
Jin Y, Peng Y, Lin Z, Chen Y-C, Wei L, et al. 2016. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. J Muscle Res Cell Motil. 37(1–2):41–52
Yu D, Peng Y, Ayaz-Guner S, Gregorich ZR, Ge Y. 2016. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry. J. Am. Soc. Mass Spectrom. 27(2):220–32
Tran BQ, Barton C, Feng J, Sandjong A, Yoon SH, et al. 2016. Comprehensive glycosylation profiling of IgG and IgG-fusion proteins by top-down MS with multiple fragmentation techniques. Journal of Proteomics. 134:93–101
Thurlow SE, Kilgour DP, Campopiano DJ, Mackay CL, Langridge-Smith PRR, et al. 2016. Determination of Protein Thiol Reduction Potential by Isotope Labeling and Intact Mass Measurement. Anal. Chem. 88(5):2727–33
Sunagar K, Morgenstern D, Reitzel AM, Moran Y. 2016. Ecological venomics: How genomics, transcriptomics and proteomics can shed new light on the ecology and evolution of venom. Journal of Proteomics. 135:62–72
Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM. 2016. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. J. Proteome Res. 15(4):1213–21
Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, et al. 2016. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. J. Am. Soc. Mass Spectrom. 27(3):520–31
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
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
Resemann A, Jabs W, Wiechmann A, Wagner E, Colas O, et al. 2016. Full validation of therapeutic antibody sequences by middle-up mass measurements and middle-down protein sequencing. mAbs. 8(2):318–30
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
Tran BQ, Barton C, Feng J, Sandjong A, Yoon SH, et al. 2016. Glycosylation characterization of therapeutic mAbs by top- and middle-down mass spectrometry. Data in Brief. 6:68–76
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
Hausberger A, Lamanna WC, Hartinger M, Seidl A, Toll H, Holzmann J. 2016. Identification of Low-Level Product-Related Variants in Filgrastim Products Presently Available in Highly Regulated Markets. BioDrugs. 30(3):233–42
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
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
Soler L, Labas V, Thélie A, Grasseau I, Teixeira-Gomes A-P, Blesbois E. 2016. Intact Cell MALDI-TOF MS on Sperm: A Molecular Test For Male Fertility Diagnosis. Mol Cell Proteomics. 15(6):1998–2010
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
Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, et al. 2016. Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts. Mol Cell Proteomics. 15(1):45–56
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
Inserra I, Martelli C, Cipollina M, Cicione C, Iavarone F, et al. 2016. Lipoaspirate fluid proteome: A preliminary investigation by LC-MS top-down/bottom-up integrated platform of a high potential biofluid in regenerative medicine. ELECTROPHORESIS. 37(7–8):1015–26

2015

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
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
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
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
Cegelski L. 2015. Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition. Journal of Magnetic Resonance. 253:91–97
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
Scherl A. 2015. Clinical protein mass spectrometry. Methods. 81:3–14
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
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
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
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
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
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
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
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
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
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, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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. www.hindawi.com
Arentz G, Weiland F, Oehler MK, Hoffmann P. 2015. State of the art of 2D DIGE. Prot. Clin. Appl. 9(3–4):277–88
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
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
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
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
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
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
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
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
Birner-Gruenberger R, Breinbauer R. 2015. Weighing the Proteasome for Covalent Modifications. Chemistry & Biology. 22(3):315–16

2014

Oliveira BM, Coorssen JR, Martins-de-Souza D. 2014. 2DE: The Phoenix of Proteomics. Journal of Proteomics. 104:140–50
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
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
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
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
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
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
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
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
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
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
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
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
Brunner AM, Nanni P, Mansuy IM. 2014. Epigenetic marking of sperm by post-translational modification of histones and protamines. Epigenetics & Chromatin. 7:2
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
Tsybin YO. 2014. From High- to Super-resolution Mass Spectrometry. CHIMIA International Journal for Chemistry. 68(3):168–74
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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
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
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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
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
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
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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
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
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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
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
Ichibangase T, Imai K. 2014. Straightforward proteomic analysis reveals real dynamics of proteins in cells. Journal of Pharmaceutical and Biomedical Analysis. 101:31–39
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
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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
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
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
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
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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

2013

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
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
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
Zhao DS, Gregorich ZR, Ge Y. 2013. High throughput screening of disulfide-containing proteins in a complex mixture. Proteomics. 13(22):3256–60
Shvartsburg AA, Smith RD. 2013. High-Resolution Differential Ion Mobility Spectrometry of a Protein. Anal. Chem. 85(1):10–13
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
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
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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
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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
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
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
Chen X, Ge Y. 2013. Ultrahigh pressure fast size exclusion chromatography for top-down proteomics. Proteomics. 13(17):2563–66

2012

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
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
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
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
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

2011

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
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
Yin S, Loo JA. 2011. Top-down mass spectrometry of supercharged native protein–ligand complexes. International Journal of Mass Spectrometry. 300(2):118–22