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Items: 45

1.

SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation.

Budnik B, Levy E, Harmange G, Slavov N.

Genome Biol. 2018 Oct 22;19(1):161. doi: 10.1186/s13059-018-1547-5.

2.

Quantifying homologous proteins and proteoforms.

Malioutov D, Chen T, Airoldi E, Jaffe JD, Budnik B, Slavov N.

Mol Cell Proteomics. 2018 Oct 3. pii: mcp.TIR118.000947. doi: 10.1074/mcp.TIR118.000947. [Epub ahead of print]

3.

Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation.

Serebryany E, Yu S, Trauger SA, Budnik B, Shakhnovich EI.

J Biol Chem. 2018 Sep 21. pii: jbc.RA118.004551. doi: 10.1074/jbc.RA118.004551. [Epub ahead of print]

4.

A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells.

Maoz BM, Herland A, FitzGerald EA, Grevesse T, Vidoudez C, Pacheco AR, Sheehy SP, Park TE, Dauth S, Mannix R, Budnik N, Shores K, Cho A, Nawroth JC, Segrè D, Budnik B, Ingber DE, Parker KK.

Nat Biotechnol. 2018 Oct;36(9):865-874. doi: 10.1038/nbt.4226. Epub 2018 Aug 20.

PMID:
30125269
5.

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

Krasemann S, Madore C, Cialic R, Baufeld C, Calcagno N, El Fatimy R, Beckers L, O'Loughlin E, Xu Y, Fanek Z, Greco DJ, Smith ST, Tweet G, Humulock Z, Zrzavy T, Conde-Sanroman P, Gacias M, Weng Z, Chen H, Tjon E, Mazaheri F, Hartmann K, Madi A, Ulrich JD, Glatzel M, Worthmann A, Heeren J, Budnik B, Lemere C, Ikezu T, Heppner FL, Litvak V, Holtzman DM, Lassmann H, Weiner HL, Ochando J, Haass C, Butovsky O.

Immunity. 2017 Sep 19;47(3):566-581.e9. doi: 10.1016/j.immuni.2017.08.008.

6.

Neurons derived from different brain regions are inherently different in vitro: a novel multiregional brain-on-a-chip.

Dauth S, Maoz BM, Sheehy SP, Hemphill MA, Murty T, Macedonia MK, Greer AM, Budnik B, Parker KK.

J Neurophysiol. 2017 Mar 1;117(3):1320-1341. doi: 10.1152/jn.00575.2016. Epub 2016 Dec 28.

7.

A human microprotein that interacts with the mRNA decapping complex.

D'Lima NG, Ma J, Winkler L, Chu Q, Loh KH, Corpuz EO, Budnik BA, Lykke-Andersen J, Saghatelian A, Slavoff SA.

Nat Chem Biol. 2017 Feb;13(2):174-180. doi: 10.1038/nchembio.2249. Epub 2016 Dec 5.

8.

Differential Stoichiometry among Core Ribosomal Proteins.

Slavov N, Semrau S, Airoldi E, Budnik B, van Oudenaarden A.

Cell Rep. 2015 Nov 3;13(5):865-73. doi: 10.1016/j.celrep.2015.09.056. Epub 2015 Oct 22.

9.

Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress.

Wallace EW, Kear-Scott JL, Pilipenko EV, Schwartz MH, Laskowski PR, Rojek AE, Katanski CD, Riback JA, Dion MF, Franks AM, Airoldi EM, Pan T, Budnik BA, Drummond DA.

Cell. 2015 Sep 10;162(6):1286-98. doi: 10.1016/j.cell.2015.08.041.

10.

Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship.

Bershtein S, Choi JM, Bhattacharyya S, Budnik B, Shakhnovich E.

Cell Rep. 2015 Apr 28;11(4):645-56. doi: 10.1016/j.celrep.2015.03.051. Epub 2015 Apr 16.

11.

Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis.

Slavov N, Budnik BA, Schwab D, Airoldi EM, van Oudenaarden A.

Cell Rep. 2014 May 8;7(3):705-14. doi: 10.1016/j.celrep.2014.03.057. Epub 2014 Apr 24.

12.

A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining.

Slavoff SA, Heo J, Budnik BA, Hanakahi LA, Saghatelian A.

J Biol Chem. 2014 Apr 18;289(16):10950-7. doi: 10.1074/jbc.C113.533968. Epub 2014 Mar 7.

13.

Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue.

Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A.

J Proteome Res. 2014 Mar 7;13(3):1757-65. doi: 10.1021/pr401280w. Epub 2014 Feb 14.

14.

Quantifying condition-dependent intracellular protein levels enables high-precision fitness estimates.

Geiler-Samerotte KA, Hashimoto T, Dion MF, Budnik BA, Airoldi EM, Drummond DA.

PLoS One. 2013 Sep 25;8(9):e75320. doi: 10.1371/journal.pone.0075320. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/9f5465d9-e9fa-4a80-84ca-9c9a3f6e82c7.

15.

Regulation of Toll signaling and inflammation by β-arrestin and the SUMO protease Ulp1.

Anjum SG, Xu W, Nikkholgh N, Basu S, Nie Y, Thomas M, Satyamurti M, Budnik BA, Ip YT, Veraksa A.

Genetics. 2013 Dec;195(4):1307-17. doi: 10.1534/genetics.113.157859. Epub 2013 Sep 27.

16.

Tunable signal processing through modular control of transcription factor translocation.

Hao N, Budnik BA, Gunawardena J, O'Shea EK.

Science. 2013 Jan 25;339(6118):460-4. doi: 10.1126/science.1227299.

17.

Peptidomic discovery of short open reading frame-encoded peptides in human cells.

Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A.

Nat Chem Biol. 2013 Jan;9(1):59-64. doi: 10.1038/nchembio.1120. Epub 2012 Nov 18.

18.

Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast.

Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, Drummond DA.

Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):680-5. doi: 10.1073/pnas.1017570108. Epub 2010 Dec 27.

19.

Insulin-stimulated phosphorylation of the Rab GTPase-activating protein TBC1D1 regulates GLUT4 translocation.

Peck GR, Chavez JA, Roach WG, Budnik BA, Lane WS, Karlsson HK, Zierath JR, Lienhard GE.

J Biol Chem. 2009 Oct 30;284(44):30016-23. doi: 10.1074/jbc.M109.035568. Epub 2009 Sep 9.

20.

System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties.

Kaushansky A, Gordus A, Budnik BA, Lane WS, Rush J, MacBeath G.

Chem Biol. 2008 Aug 25;15(8):808-17. doi: 10.1016/j.chembiol.2008.07.006.

21.

Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation.

Lee RS, Monigatti F, Lutchman M, Patterson T, Budnik B, Steen JA, Freeman MR, Steen H.

Proteomics. 2008 Mar;8(5):1097-112. doi: 10.1002/pmic.200700701.

PMID:
18324733
22.

Global methods for protein glycosylation analysis by mass spectrometry.

Budnik BA, Lee RS, Steen JA.

Biochim Biophys Acta. 2006 Dec;1764(12):1870-80. Epub 2006 Oct 18. Review.

PMID:
17118724
23.

Long-lived electron capture dissociation product ions experience radical migration via hydrogen abstraction.

O'Connor PB, Lin C, Cournoyer JJ, Pittman JL, Belyayev M, Budnik BA.

J Am Soc Mass Spectrom. 2006 Apr;17(4):576-585. doi: 10.1016/j.jasms.2005.12.015. Epub 2006 Feb 28.

24.

A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics.

O'connor PB, Pittman JL, Thomson BA, Budnik BA, Cournoyer JC, Jebanathirajah J, Lin C, Moyer S, Zhao C.

Rapid Commun Mass Spectrom. 2006;20(2):259-66.

PMID:
16353130
25.

Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins.

Jebanathirajah JA, Pittman JL, Thomson BA, Budnik BA, Kaur P, Rape M, Kirschner M, Costello CE, O'Connor PB.

J Am Soc Mass Spectrom. 2005 Dec;16(12):1985-99. Epub 2005 Nov 2.

26.
27.

Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure.

Adams CM, Kjeldsen F, Zubarev RA, Budnik BA, Haselmann KF.

J Am Soc Mass Spectrom. 2004 Jul;15(7):1087-98.

28.

Isolation of a library of aromadendranes from Landolphia dulcis and its characterization using the VolSurf approach.

Staerk D, Skole B, Jørgensen FS, Budnik BA, Ekpe P, Jaroszewski JW.

J Nat Prod. 2004 May;67(5):799-805.

PMID:
15165140
29.

De novo sequencing of antimicrobial peptides isolated from the venom glands of the wolf spider Lycosa singoriensis.

Budnik BA, Olsen JV, Egorov TA, Anisimova VE, Galkina TG, Musolyamov AK, Grishin EV, Zubarev RA.

J Mass Spectrom. 2004 Feb;39(2):193-201.

PMID:
14991689
30.

A high pressure matrix-assisted laser desorption ion source for Fourier transform mass spectrometry designed to accommodate large targets with diverse surfaces.

O'Connor PB, Budnik BA, Ivleva VB, Kaur P, Moyer SC, Pittman JL, Costello CE.

J Am Soc Mass Spectrom. 2004 Jan;15(1):128-32.

PMID:
14698563
31.

Attomole peptide analysis by high-pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry.

Moyer SC, Budnik BA, Pittman JL, Costello CE, O'Connor PB.

Anal Chem. 2003 Dec 1;75(23):6449-54.

PMID:
14640713
32.

Applications of electron-ion dissociation reactions for analysis of polycationic chitooligosaccharides in Fourier transform mass spectrometry.

Budnik BA, Haselmann KF, Elkin YN, Gorbach VI, Zubarev RA.

Anal Chem. 2003 Nov 1;75(21):5994-6001.

PMID:
14588042
33.
34.
35.

Electron capture dissociation of weakly bound polypeptide polycationic complexes.

Haselmann KF, Jørgensen TJ, Budnik BA, Jensen F, Zubarev RA.

Rapid Commun Mass Spectrom. 2002;16(24):2260-5.

PMID:
12478569
36.

Ionization energies of multiply protonated polypeptides obtained by tandem ionization in Fourier transform mass spectrometers.

Budnik BA, Tsybin YO, Håkansson P, Zubarev RA.

J Mass Spectrom. 2002 Nov;37(11):1141-4.

PMID:
12447890
37.
38.
39.

Cyanohydrin glycosides of Passiflora: distribution pattern, a saturated cyclopentane derivative from P. guatemalensis, and formation of pseudocyanogenic alpha-hydroxyamides as isolation artefacts.

Jaroszewski JW, Olafsdottir ES, Wellendorph P, Christensen J, Franzyk H, Somanadhan B, Budnik BA, Jørgensen LB, Clausen V.

Phytochemistry. 2002 Mar;59(5):501-11.

PMID:
11853745
40.

Leishmanicidal, antiplasmodial, and cytotoxic activity of novel diterpenoid 1,2-quinones from Perovskia abrotanoides: new source of tanshinones.

Sairafianpour M, Christensen J, Staerk D, Budnik BA, Kharazmi A, Bagherzadeh K, Jaroszewski JW.

J Nat Prod. 2001 Nov;64(11):1398-403.

PMID:
11720520
41.

Improved low-energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

Tsybin YO, Håkansson P, Budnik BA, Haselmann KF, Kjeldsen F, Gorshkov M, Zubarev RA.

Rapid Commun Mass Spectrom. 2001;15(19):1849-54.

PMID:
11565103
42.

Advantages of external accumulation for electron capture dissociation in Fourier transform mass spectrometry.

Haselmann KF, Budnik BA, Olsen JV, Nielsen ML, Reis CA, Clausen H, Johnsen AH, Zubarev RA.

Anal Chem. 2001 Jul 1;73(13):2998-3005.

PMID:
11467546
43.

Comparison of electron capture dissociation and collisionally activated dissociation of polycations of peptide nucleic acids.

Olsen JV, Haselmann KF, Nielsen ML, Budnik BA, Nielsen PE, Zubarev RA.

Rapid Commun Mass Spectrom. 2001;15(12):969-74.

PMID:
11400205
44.

Electron capture dissociation of b (2+) peptide fragments reveals the presence of the acylium ion structure.

Haselmann KF, Budnik BA, Zubarev RA.

Rapid Commun Mass Spectrom. 2000;14(23):2242-6.

PMID:
11114035
45.

Benefits of 2.94 micron infrared matrix-assisted laser desorption/ionization for analysis of labile molecules by Fourier transform mass spectrometry.

Budnik BA, Jensen KB, Jørgensen TJ, Haase A, Zubarev RA.

Rapid Commun Mass Spectrom. 2000;14(7):578-84.

PMID:
10775091

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