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Items: 42

1.

Elucidating Proteoform Dynamics Underlying the Senescence Associated Secretory Phenotype.

Doubleday PF, Fornelli L, Kelleher NL.

J Proteome Res. 2020 Feb 7;19(2):938-948. doi: 10.1021/acs.jproteome.9b00739. Epub 2020 Jan 28.

PMID:
31940439
2.

Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics.

Fornelli L, Srzentić K, Toby TK, Doubleday PF, Huguet R, Mullen C, Melani RD, Dos Santos Seckler H, DeHart CJ, Weisbrod CR, Durbin KR, Greer JB, Early BP, Fellers RT, Zabrouskov V, Thomas PM, Compton PD, Kelleher NL.

Mol Cell Proteomics. 2020 Feb;19(2):405-420. doi: 10.1074/mcp.TIR119.001638. Epub 2019 Dec 30.

PMID:
31888965
3.

Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms.

Huguet R, Mullen C, Srzentić K, Greer JB, Fellers RT, Zabrouskov V, Syka JEP, Kelleher NL, Fornelli L.

Anal Chem. 2019 Dec 17;91(24):15732-15739. doi: 10.1021/acs.analchem.9b03925. Epub 2019 Nov 22.

PMID:
31714757
4.

Direct measurement of light and heavy antibody chains using ion mobility and middle-down mass spectrometry.

Melani RD, Srzentić K, Gerbasi VR, McGee JP, Huguet R, Fornelli L, Kelleher NL.

MAbs. 2019 Nov-Dec;11(8):1351-1357. doi: 10.1080/19420862.2019.1668226. Epub 2019 Oct 13.

5.

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.

Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Paša-Tolić L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN.

Nat Methods. 2019 Jul;16(7):587-594. doi: 10.1038/s41592-019-0457-0. Epub 2019 Jun 27. Review.

6.

Defining the NSD2 interactome: PARP1 PARylation reduces NSD2 histone methyltransferase activity and impedes chromatin binding.

Huang X, LeDuc RD, Fornelli L, Schunter AJ, Bennett RL, Kelleher NL, Licht JD.

J Biol Chem. 2019 Aug 16;294(33):12459-12471. doi: 10.1074/jbc.RA118.006159. Epub 2019 Jun 27.

PMID:
31248990
7.

Structural Analysis of Monoclonal Antibodies by Ultrahigh Resolution MALDI In-Source Decay FT-ICR Mass Spectrometry.

van der Burgt YEM, Kilgour DPA, Tsybin YO, Srzentić K, Fornelli L, Beck A, Wuhrer M, Nicolardi S.

Anal Chem. 2019 Feb 5;91(3):2079-2085. doi: 10.1021/acs.analchem.8b04515. Epub 2019 Jan 8.

8.

A comprehensive pipeline for translational top-down proteomics from a single blood draw.

Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL.

Nat Protoc. 2019 Jan;14(1):119-152. doi: 10.1038/s41596-018-0085-7.

9.

Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody.

Srzentić K, Nagornov KO, Fornelli L, Lobas AA, Ayoub D, Kozhinov AN, Gasilova N, Menin L, Beck A, Gorshkov MV, Aizikov K, Tsybin YO.

Anal Chem. 2018 Nov 6;90(21):12527-12535. doi: 10.1021/acs.analchem.8b02398. Epub 2018 Oct 12.

PMID:
30252447
10.

Accurate Sequence Analysis of a Monoclonal Antibody by Top-Down and Middle-Down Orbitrap Mass Spectrometry Applying Multiple Ion Activation Techniques.

Fornelli L, Srzentić K, Huguet R, Mullen C, Sharma S, Zabrouskov V, Fellers RT, Durbin KR, Compton PD, Kelleher NL.

Anal Chem. 2018 Jul 17;90(14):8421-8429. doi: 10.1021/acs.analchem.8b00984. Epub 2018 Jun 28.

11.

Chemical-Mediated Digestion: An Alternative Realm for Middle-down Proteomics?

Srzentić K, Zhurov KO, Lobas AA, Nikitin G, Fornelli L, Gorshkov MV, Tsybin YO.

J Proteome Res. 2018 Jun 1;17(6):2005-2016. doi: 10.1021/acs.jproteome.7b00834. Epub 2018 May 18.

PMID:
29722266
12.

A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity.

Seckler HDS, Fornelli L, Mutharasan RK, Thaxton CS, Fellers R, Daviglus M, Sniderman A, Rader D, Kelleher NL, Lloyd-Jones DM, Compton PD, Wilkins JT.

J Proteome Res. 2018 Jun 1;17(6):2156-2164. doi: 10.1021/acs.jproteome.8b00100. Epub 2018 Apr 27.

13.

Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk.

Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4140-4145. doi: 10.1073/pnas.1716122115. Epub 2018 Apr 2.

14.

Top-down characterization of endogenous protein complexes with native proteomics.

Skinner OS, Haverland NA, Fornelli L, Melani RD, Do Vale LHF, Seckler HS, Doubleday PF, Schachner LF, Srzentić K, Kelleher NL, Compton PD.

Nat Chem Biol. 2018 Jan;14(1):36-41. doi: 10.1038/nchembio.2515. Epub 2017 Nov 13.

15.

The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics.

Lyon YA, Riggs D, Fornelli L, Compton PD, Julian RR.

J Am Soc Mass Spectrom. 2018 Jan;29(1):150-157. doi: 10.1007/s13361-017-1823-8. Epub 2017 Oct 16.

16.

Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry.

Haverland NA, Skinner OS, Fellers RT, Tariq AA, Early BP, LeDuc RD, Fornelli L, Compton PD, Kelleher NL.

J Am Soc Mass Spectrom. 2017 Jun;28(6):1203-1215. doi: 10.1007/s13361-017-1635-x. Epub 2017 Apr 3.

17.

Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer.

Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, Makarov A, Beck A, Tsybin YO.

J Proteomics. 2017 Apr 21;159:67-76. doi: 10.1016/j.jprot.2017.02.013. Epub 2017 Feb 27.

18.

Top-down proteomics: Where we are, where we are going?

Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, DeHart CJ, Kelleher NL.

J Proteomics. 2018 Mar 20;175:3-4. doi: 10.1016/j.jprot.2017.02.002. Epub 2017 Feb 7. No abstract available.

19.

Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer.

Fornelli L, Durbin KR, Fellers RT, Early BP, Greer JB, LeDuc RD, Compton PD, Kelleher NL.

J Proteome Res. 2017 Feb 3;16(2):609-618. doi: 10.1021/acs.jproteome.6b00698. Epub 2016 Dec 2.

20.

Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite.

DeHart CJ, Fellers RT, Fornelli L, Kelleher NL, Thomas PM.

Methods Mol Biol. 2017;1558:381-394. doi: 10.1007/978-1-4939-6783-4_18.

21.

Chromatographic efficiency and selectivity in top-down proteomics of histones.

Zhou Y, Zhang X, Fornelli L, Compton PD, Kelleher N, Wirth MJ.

J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Feb 15;1044-1045:47-53. doi: 10.1016/j.jchromb.2016.12.027. Epub 2016 Dec 23.

22.

Progress in Top-Down Proteomics and the Analysis of Proteoforms.

Toby TK, Fornelli L, Kelleher NL.

Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):499-519. doi: 10.1146/annurev-anchem-071015-041550. Review.

23.

Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics.

Melani RD, Skinner OS, Fornelli L, Domont GB, Compton PD, Kelleher NL.

Mol Cell Proteomics. 2016 Jul;15(7):2423-34. doi: 10.1074/mcp.M115.056523. Epub 2016 May 13.

24.

Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa.

Durbin KR, Fornelli L, Fellers RT, Doubleday PF, Narita M, Kelleher NL.

J Proteome Res. 2016 Mar 4;15(3):976-82. doi: 10.1021/acs.jproteome.5b00997. Epub 2016 Feb 11.

25.

An informatic framework for decoding protein complexes by top-down mass spectrometry.

Skinner OS, Havugimana PC, Haverland NA, Fornelli L, Early BP, Greer JB, Fellers RT, Durbin KR, Do Vale LH, Melani RD, Seckler HS, Nelp MT, Belov ME, Horning SR, Makarov AA, LeDuc RD, Bandarian V, Compton PD, Kelleher NL.

Nat Methods. 2016 Mar;13(3):237-40. doi: 10.1038/nmeth.3731. Epub 2016 Jan 18.

26.

Probing Asymmetric Charge Partitioning of Protein Oligomers during Tandem Mass Spectrometry.

Compton PD, Fornelli L, Kelleher NL, Skinner OS.

Int J Mass Spectrom. 2015 Nov 15;390:132-136.

27.

Ion coalescence in Fourier transform mass spectrometry: should we worry about this in shotgun proteomics?

Tarasova IA, Surin AK, Fornelli L, Pridatchenko ML, Suvorina MY, Gorshkov MV.

Eur J Mass Spectrom (Chichester). 2015;21(3):459-70. doi: 10.1255/ejms.1356.

PMID:
26307727
28.

Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression.

Zheng Y, Fornelli L, Compton PD, Sharma S, Canterbury J, Mullen C, Zabrouskov V, Fellers RT, Thomas PM, Licht JD, Senko MW, Kelleher NL.

Mol Cell Proteomics. 2016 Mar;15(3):776-90. doi: 10.1074/mcp.M115.053819. Epub 2015 Aug 13.

29.

Targeted analysis of recombinant NF kappa B (RelA/p65) by denaturing and native top down mass spectrometry.

Savaryn JP, Skinner OS, Fornelli L, Fellers RT, Compton PD, Terhune SS, Abecassis MM, Kelleher NL.

J Proteomics. 2016 Feb 16;134:76-84. doi: 10.1016/j.jprot.2015.04.025. Epub 2015 May 4.

30.

Advantages of extended bottom-up proteomics using Sap9 for analysis of monoclonal antibodies.

Srzentić K, Fornelli L, Laskay ÜA, Monod M, Beck A, Ayoub D, Tsybin YO.

Anal Chem. 2014 Oct 7;86(19):9945-53. doi: 10.1021/ac502766n. Epub 2014 Sep 24.

PMID:
25207962
31.

Middle-down analysis of monoclonal antibodies with electron transfer dissociation orbitrap fourier transform mass spectrometry.

Fornelli L, Ayoub D, Aizikov K, Beck A, Tsybin YO.

Anal Chem. 2014 Mar 18;86(6):3005-12. doi: 10.1021/ac4036857. Epub 2014 Mar 3.

PMID:
24588056
32.

Distinguishing analyte from noise components in mass spectra of complex samples: where to cut the noise?

Zhurov KO, Kozhinov AN, Fornelli L, Tsybin YO.

Anal Chem. 2014 Apr 1;86(7):3308-16. doi: 10.1021/ac403278t. Epub 2014 Mar 17.

PMID:
24579830
33.

Practical considerations for improving the productivity of mass spectrometry-based proteomics.

Laskay UA, Srzentić K, Fornelli L, Upir O, Kozhinov AN, Monod M, Tsybin YO.

Chimia (Aarau). 2013;67(4):244-9.

PMID:
23967698
34.

Top-down analysis of 30-80 kDa proteins by electron transfer dissociation time-of-flight mass spectrometry.

Fornelli L, Parra J, Hartmer R, Stoermer C, Lubeck M, Tsybin YO.

Anal Bioanal Chem. 2013 Oct;405(26):8505-14. doi: 10.1007/s00216-013-7267-5. Epub 2013 Aug 10.

PMID:
23934349
35.

Principles of electron capture and transfer dissociation mass spectrometry applied to peptide and protein structure analysis.

Zhurov KO, Fornelli L, Wodrich MD, Laskay ÜA, Tsybin YO.

Chem Soc Rev. 2013 Jun 21;42(12):5014-30. doi: 10.1039/c3cs35477f. Review.

PMID:
23450212
36.

Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS.

Fornelli L, Damoc E, Thomas PM, Kelleher NL, Aizikov K, Denisov E, Makarov A, Tsybin YO.

Mol Cell Proteomics. 2012 Dec;11(12):1758-67. doi: 10.1074/mcp.M112.019620. Epub 2012 Sep 10.

37.

Observation of ion coalescence in Orbitrap Fourier transform mass spectrometry.

Gorshkov MV, Fornelli L, Tsybin YO.

Rapid Commun Mass Spectrom. 2012 Aug 15;26(15):1711-7. doi: 10.1002/rcm.6289.

PMID:
22730091
38.

In-spray supercharging of peptides and proteins in electrospray ionization mass spectrometry.

Miladinović SM, Fornelli L, Lu Y, Piech KM, Girault HH, Tsybin YO.

Anal Chem. 2012 Jun 5;84(11):4647-51. doi: 10.1021/ac300845n. Epub 2012 May 11.

PMID:
22571167
39.

Glycan variability on a recombinant IgG antibody transiently produced in HEK-293E cells.

Nallet S, Fornelli L, Schmitt S, Parra J, Baldi L, Tsybin YO, Wurm FM.

N Biotechnol. 2012 May 15;29(4):471-6. doi: 10.1016/j.nbt.2012.02.003. Epub 2012 Mar 6.

PMID:
22401955
40.

High-resolution and tandem mass spectrometry--the indispensable tools of the XXI century.

Tsybin YO, Fornelli L, Kozhinov AN, Vorobyev A, Miladinovic SM.

Chimia (Aarau). 2011;65(9):641-5. Review.

PMID:
22026169
41.

Structural analysis of intact monoclonal antibodies by electron transfer dissociation mass spectrometry.

Tsybin YO, Fornelli L, Stoermer C, Luebeck M, Parra J, Nallet S, Wurm FM, Hartmer R.

Anal Chem. 2011 Dec 1;83(23):8919-27. doi: 10.1021/ac201293m. Epub 2011 Nov 4.

PMID:
22017162
42.

Deamidation and transamidation of substance P by tissue transglutaminase revealed by electron-capture dissociation fourier transform mass spectrometry.

Fornelli L, Schmid AW, Grasso L, Vogel H, Tsybin YO.

Chemistry. 2011 Jan 10;17(2):486-97. doi: 10.1002/chem.201002483. Epub 2010 Nov 30.

PMID:
21207565

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