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Items: 1 to 50 of 66

1.

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter.

Shen Y, Zhao R, Tolić N, Tfaily MM, Robinson EW, Boiteau R, Paša-Tolić L, Hess NJ.

Faraday Discuss. 2019 Jun 3. doi: 10.1039/c9fd00011a. [Epub ahead of print]

PMID:
31155623
2.

Author Correction: Informed-Proteomics: open-source software package for top-down proteomics.

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.

Nat Methods. 2018 Jul;15(7):554. doi: 10.1038/s41592-018-0040-0.

PMID:
29899368
3.

Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms.

Rivas-Ubach A, Liu Y, Bianchi TS, Tolić N, Jansson C, Paša-Tolić L.

Anal Chem. 2018 May 15;90(10):6152-6160. doi: 10.1021/acs.analchem.8b00529. Epub 2018 Apr 27.

PMID:
29671593
4.

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming.

Chen H, Yang Z, Chu RK, Tolic N, Liang L, Graham DE, Wullschleger SD, Gu B.

Environ Sci Technol. 2018 Apr 17;52(8):4555-4564. doi: 10.1021/acs.est.7b05469. Epub 2018 Apr 5.

5.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

Tolić N, Liu Y, Liyu A, Shen Y, Tfaily MM, Kujawinski EB, Longnecker K, Kuo LJ, Robinson EW, Paša-Tolić L, Hess NJ.

Anal Chem. 2017 Dec 5;89(23):12659-12665. doi: 10.1021/acs.analchem.7b03318. Epub 2017 Nov 21.

PMID:
29120613
6.

De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods.

Vyatkina K, Dekker LJM, Wu S, VanDuijn MM, Liu X, Tolić N, Luider TM, Paša-Tolić L.

Proteomics. 2017 Dec;17(23-24). doi: 10.1002/pmic.201600321.

PMID:
29110399
7.

Informed-Proteomics: open-source software package for top-down proteomics.

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.

Nat Methods. 2017 Sep;14(9):909-914. doi: 10.1038/nmeth.4388. Epub 2017 Aug 7. Erratum in: Nat Methods. 2018 Jul;15(7):554.

8.

Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry.

Tfaily MM, Chu RK, Toyoda J, Tolić N, Robinson EW, Paša-Tolić L, Hess NJ.

Anal Chim Acta. 2017 Jun 15;972:54-61. doi: 10.1016/j.aca.2017.03.031. Epub 2017 Mar 31.

PMID:
28495096
9.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

Kou Q, Wu S, Tolic N, Paša-Tolic L, Liu Y, Liu X.

Bioinformatics. 2017 May 1;33(9):1309-1316. doi: 10.1093/bioinformatics/btw806.

10.

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics.

Shen Y, Tolić N, Piehowski PD, Shukla AK, Kim S, Zhao R, Qu Y, Robinson E, Smith RD, Paša-Tolić L.

J Chromatogr A. 2017 May 19;1498:99-110. doi: 10.1016/j.chroma.2017.01.008. Epub 2017 Jan 5.

PMID:
28077236
11.

Molecular Characterization of Organosulfur Compounds in Biodiesel and Diesel Fuel Secondary Organic Aerosol.

Blair SL, MacMillan AC, Drozd GT, Goldstein AH, Chu RK, Paša-Tolić L, Shaw JB, Tolić N, Lin P, Laskin J, Laskin A, Nizkorodov SA.

Environ Sci Technol. 2017 Jan 3;51(1):119-127. doi: 10.1021/acs.est.6b03304. Epub 2016 Dec 22.

12.

21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox.

Shaw JB, Lin TY, Leach FE 3rd, Tolmachev AV, Tolić N, Robinson EW, Koppenaal DW, Paša-Tolić L.

J Am Soc Mass Spectrom. 2016 Dec;27(12):1929-1936. Epub 2016 Oct 12.

PMID:
27734325
13.

Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore.

Kou Q, Zhu B, Wu S, Ansong C, Tolić N, Paša-Tolić L, Liu X.

J Proteome Res. 2016 Aug 5;15(8):2422-32. doi: 10.1021/acs.jproteome.5b01098. Epub 2016 Jul 1.

14.

Top-down analysis of protein samples by de novo sequencing techniques.

Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Luider TM, Paša-Tolić L, Pevzner PA.

Bioinformatics. 2016 Sep 15;32(18):2753-9. doi: 10.1093/bioinformatics/btw307. Epub 2016 May 14.

15.

Unique Organic Matter and Microbial Properties in the Rhizosphere of a Wetland Soil.

Kaplan DI, Xu C, Huang S, Lin Y, Tolić N, Roscioli-Johnson KM, Santschi PH, Jaffé PR.

Environ Sci Technol. 2016 Apr 19;50(8):4169-77. doi: 10.1021/acs.est.5b05165. Epub 2016 Apr 11.

PMID:
27091553
16.

Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures.

Anderton CR, Chu RK, Tolić N, Creissen A, Paša-Tolić L.

J Am Soc Mass Spectrom. 2016 Mar;27(3):556-9. doi: 10.1007/s13361-015-1324-6. Epub 2016 Jan 4.

PMID:
26729451
17.

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.

Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Dvorkin M, Alexandrova S, Luider TM, Paša-Tolić L, Pevzner PA.

J Proteome Res. 2015 Nov 6;14(11):4450-62. doi: 10.1021/pr501244v. Epub 2015 Oct 13.

PMID:
26412692
18.

Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry.

Mann BF, Chen H, Herndon EM, Chu RK, Tolic N, Portier EF, Roy Chowdhury T, Robinson EW, Callister SJ, Wullschleger SD, Graham DE, Liang L, Gu B.

PLoS One. 2015 Jun 12;10(6):e0130557. doi: 10.1371/journal.pone.0130557. eCollection 2015.

19.

Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry.

Tfaily MM, Chu RK, Tolić N, Roscioli KM, Anderton CR, Paša-Tolić L, Robinson EW, Hess NJ.

Anal Chem. 2015;87(10):5206-15. doi: 10.1021/acs.analchem.5b00116. Epub 2015 Apr 30.

PMID:
25884232
20.

Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes.

Xu Z, Wu C, Xie F, Slysz GW, Tolic N, Monroe ME, Petyuk VA, Payne SH, Fujimoto GM, Moore RJ, Fillmore TL, Schepmoes AA, Levine DA, Townsend RR, Davies SR, Li S, Ellis M, Boja E, Rivers R, Rodriguez H, Rodland KD, Liu T, Smith RD.

J Proteome Res. 2015 Jan 2;14(1):422-33. doi: 10.1021/pr500840w. Epub 2014 Nov 10.

21.

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

Liu X, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolić L, Pevzner PA.

J Proteome Res. 2014 Jul 3;13(7):3241-8. doi: 10.1021/pr401300m. Epub 2014 Jun 18.

PMID:
24874765
22.

The first pilot project of the consortium for top-down proteomics: a status report.

Dang X, Scotcher J, Wu S, Chu RK, Tolić N, Ntai I, Thomas PM, Fellers RT, Early BP, Zheng Y, Durbin KR, Leduc RD, Wolff JJ, Thompson CJ, Pan J, Han J, Shaw JB, Salisbury JP, Easterling M, Borchers CH, Brodbelt JS, Agar JN, Paša-Tolić L, Kelleher NL, Young NL.

Proteomics. 2014 May;14(10):1130-40. doi: 10.1002/pmic.201300438. Epub 2014 Apr 14.

23.

An integrated top-down and bottom-up proteomic approach to characterize the antigen-binding fragment of antibodies.

Dekker L, Wu S, Vanduijn M, Tolić N, Stingl C, Zhao R, Luider T, Paša-Tolić L.

Proteomics. 2014 May;14(10):1239-48. doi: 10.1002/pmic.201300366. Epub 2014 Apr 13.

PMID:
24634104
24.

Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry.

Wu S, Brown JN, Tolić N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolić L.

Proteomics. 2014 May;14(10):1211-22. doi: 10.1002/pmic.201300378. Epub 2014 Apr 13.

PMID:
24591407
25.

Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation.

Cao L, Tolić N, Qu Y, Meng D, Zhao R, Zhang Q, Moore RJ, Zink EM, Lipton MS, Paša-Tolić L, Wu S.

Anal Biochem. 2014 May 1;452:96-102. doi: 10.1016/j.ab.2014.01.003. Epub 2014 Jan 15.

26.

Identification of ultramodified proteins using top-down tandem mass spectra.

Liu X, Hengel S, Wu S, Tolić N, Pasa-Tolić L, Pevzner PA.

J Proteome Res. 2013 Dec 6;12(12):5830-8. doi: 10.1021/pr400849y. Epub 2013 Nov 15.

27.

Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein.

Abdul Halim MF, Pfeiffer F, Zou J, Frisch A, Haft D, Wu S, Tolić N, Brewer H, Payne SH, Paša-Tolić L, Pohlschroder M.

Mol Microbiol. 2013 Jun;88(6):1164-75. doi: 10.1111/mmi.12248. Epub 2013 May 28.

28.

Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans.

Wu S, Brown RN, Payne SH, Meng D, Zhao R, Tolić N, Cao L, Shukla A, Monroe ME, Moore RJ, Lipton MS, Paša-Tolić L.

Int J Proteomics. 2013;2013:279590. doi: 10.1155/2013/279590. Epub 2013 Mar 10.

29.

Enhanced top-down characterization of histone post-translational modifications.

Tian Z, Tolić N, Zhao R, Moore RJ, Hengel SM, Robinson EW, Stenoien DL, Wu S, Smith RD, Paša-Tolić L.

Genome Biol. 2012 Oct 3;13(10):R86. doi: 10.1186/gb-2012-13-10-r86.

31.

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.

Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN.

BMC Genomics. 2011 Aug 25;12:433. doi: 10.1186/1471-2164-12-433.

32.

Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods.

Shen Y, Tolić N, Xie F, Zhao R, Purvine SO, Schepmoes AA, Moore RJ, Anderson GA, Smith RD.

J Proteome Res. 2011 Sep 2;10(9):3929-43. doi: 10.1021/pr200052c. Epub 2011 Aug 15.

33.

An integrated top-down and bottom-up strategy for characterization of protein isoforms and modifications.

Wu S, Tolić N, Tian Z, Robinson EW, Paša-Tolić L.

Methods Mol Biol. 2011;694:291-304. doi: 10.1007/978-1-60761-977-2_18.

PMID:
21082441
34.

Blood peptidome-degradome profile of breast cancer.

Shen Y, Tolić N, Liu T, Zhao R, Petritis BO, Gritsenko MA, Camp DG, Moore RJ, Purvine SO, Esteva FJ, Smith RD.

PLoS One. 2010 Oct 18;5(10):e13133. doi: 10.1371/journal.pone.0013133.

35.

Two-dimensional liquid chromatography system for online top-down mass spectrometry.

Tian Z, Zhao R, Tolić N, Moore RJ, Stenoien DL, Robinson EW, Smith RD, Paša-Tolić L.

Proteomics. 2010 Oct;10(20):3610-20. doi: 10.1002/pmic.201000367.

36.

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.

Jung HJ, Purvine SO, Kim H, Petyuk VA, Hyung SW, Monroe ME, Mun DG, Kim KC, Park JM, Kim SJ, Tolic N, Slysz GW, Moore RJ, Zhao R, Adkins JN, Anderson GA, Lee H, Camp DG 2nd, Yu MH, Smith RD, Lee SW.

Anal Chem. 2010 Oct 15;82(20):8510-8. doi: 10.1021/ac101388b.

37.

Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics.

López-Ferrer D, Petritis K, Robinson EW, Hixson KK, Tian Z, Lee JH, Lee SW, Tolić N, Weitz KK, Belov ME, Smith RD, Pasa-Tolić L.

Mol Cell Proteomics. 2011 Feb;10(2):M110.001479. doi: 10.1074/mcp.M110.001479. Epub 2010 Jul 12.

38.

Identification of disulfide bonds in protein proteolytic degradation products using de novo-protein unique sequence tags approach.

Shen Y, Tolić N, Purvine SO, Smith RD.

J Proteome Res. 2010 Aug 6;9(8):4053-60. doi: 10.1021/pr1002559.

39.

Strategy for degradomic-peptidomic analysis of human blood plasma.

Shen Y, Liu T, Tolić N, Petritis BO, Zhao R, Moore RJ, Purvine SO, Camp DG, Smith RD.

J Proteome Res. 2010 May 7;9(5):2339-46. doi: 10.1021/pr901083m.

40.

Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry.

Chowdhury SM, Du X, Tolić N, Wu S, Moore RJ, Mayer MU, Smith RD, Adkins JN.

Anal Chem. 2009 Jul 1;81(13):5524-32. doi: 10.1021/ac900853k.

41.

Integrated workflow for characterizing intact phosphoproteins from complex mixtures.

Wu S, Yang F, Zhao R, Tolić N, Robinson EW, Camp DG 2nd, Smith RD, Pasa-Tolić L.

Anal Chem. 2009 Jun 1;81(11):4210-9. doi: 10.1021/ac802487q.

42.

Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides.

Yang F, Wu S, Stenoien DL, Zhao R, Monroe ME, Gritsenko MA, Purvine SO, Polpitiya AD, Tolić N, Zhang Q, Norbeck AD, Orton DJ, Moore RJ, Tang K, Anderson GA, Pasa-Tolić L, Camp DG 2nd, Smith RD.

Anal Chem. 2009 May 15;81(10):4137-43. doi: 10.1021/ac802605m.

43.

An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications.

Wu S, Lourette NM, Tolić N, Zhao R, Robinson EW, Tolmachev AV, Smith RD, Pasa-Tolić L.

J Proteome Res. 2009 Mar;8(3):1347-57. doi: 10.1021/pr800720d.

44.

Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry.

Zhang H, Tang X, Munske GR, Tolic N, Anderson GA, Bruce JE.

Mol Cell Proteomics. 2009 Mar;8(3):409-20. doi: 10.1074/mcp.M800232-MCP200. Epub 2008 Oct 20.

45.

De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins.

Shen Y, Tolić N, Hixson KK, Purvine SO, Anderson GA, Smith RD.

Anal Chem. 2008 Oct 15;80(20):7742-54. doi: 10.1021/ac801123p. Epub 2008 Sep 11.

46.

Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins.

Shen Y, Hixson KK, Tolić N, Camp DG, Purvine SO, Moore RJ, Smith RD.

Anal Chem. 2008 Aug 1;80(15):5819-28. doi: 10.1021/ac800077w. Epub 2008 Jun 26.

47.

In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers.

Zhang H, Tang X, Munske GR, Zakharova N, Yang L, Zheng C, Wolff MA, Tolic N, Anderson GA, Shi L, Marshall MJ, Fredrickson JK, Bruce JE.

J Proteome Res. 2008 Apr;7(4):1712-20. doi: 10.1021/pr7007658. Epub 2008 Feb 28.

48.

Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags.

Shen Y, Tolić N, Hixson KK, Purvine SO, Pasa-Tolić L, Qian WJ, Adkins JN, Moore RJ, Smith RD.

Anal Chem. 2008 Mar 15;80(6):1871-82. doi: 10.1021/ac702328x. Epub 2008 Feb 14.

49.

Informatics strategies for large-scale novel cross-linking analysis.

Anderson GA, Tolic N, Tang X, Zheng C, Bruce JE.

J Proteome Res. 2007 Sep;6(9):3412-21. Epub 2007 Aug 3.

50.

VIPER: an advanced software package to support high-throughput LC-MS peptide identification.

Monroe ME, Tolić N, Jaitly N, Shaw JL, Adkins JN, Smith RD.

Bioinformatics. 2007 Aug 1;23(15):2021-3. Epub 2007 Jun 1.

PMID:
17545182

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