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Items: 1 to 50 of 99

1.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.

Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS.

J Proteome Res. 2019 Oct 10. doi: 10.1021/acs.jproteome.9b00542. [Epub ahead of print]

PMID:
31599596
2.

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N.

mSystems. 2019 Sep 24;4(5). pii: e00375-19. doi: 10.1128/mSystems.00375-19.

3.

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.

Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC.

Food Chem. 2020 Jan 1;302:125290. doi: 10.1016/j.foodchem.2019.125290. Epub 2019 Jul 30.

PMID:
31404873
4.

CoII Cryptates Convert CO2 into CO and CH4 under Visible Light.

Realista S, Almeida JC, Milheiro SA, Bandeira NAG, Alves LG, Madeira F, Calhorda MJ, Martinho PN.

Chemistry. 2019 Sep 6;25(50):11670-11679. doi: 10.1002/chem.201901806. Epub 2019 Aug 7.

PMID:
31237368
5.

ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets.

Pullman BS, Wertz J, Carver J, Bandeira N.

J Proteome Res. 2018 Dec 7;17(12):4227-4234. doi: 10.1021/acs.jproteome.8b00496. Epub 2018 Oct 15.

PMID:
30985146
6.

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome.

Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC.

Microbiome. 2019 Feb 13;7(1):23. doi: 10.1186/s40168-019-0636-3.

7.

Tuning and mechanistic insights of metal chalcogenide molecular catalysts for the hydrogen-evolution reaction.

McAllister J, Bandeira NAG, McGlynn JC, Ganin AY, Song YF, Bo C, Miras HN.

Nat Commun. 2019 Jan 22;10(1):370. doi: 10.1038/s41467-018-08208-4.

8.

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains.

Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, Gupta GD, Abdouni H, Lin ZY, Tucholska M, Knight JDR, Gonzalez-Badillo B, St-Denis N, Newman JA, Stucki M, Pelletier L, Bandeira N, Wilson MD, Filippakopoulos P, Gingras AC.

Mol Cell. 2019 Feb 7;73(3):621-638.e17. doi: 10.1016/j.molcel.2018.11.006. Epub 2018 Dec 13.

9.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11. Review.

10.

Assembling the Community-Scale Discoverable Human Proteome.

Wang M, Wang J, Carver J, Pullman BS, Cha SW, Bandeira N.

Cell Syst. 2018 Oct 24;7(4):412-421.e5. doi: 10.1016/j.cels.2018.08.004. Epub 2018 Aug 29.

11.

Are homoleptic complexes of ethylene with group 12 metals isolable in solution? A DFT study.

Fianchini M, Bandeira NAG.

J Mol Model. 2018 Jun 14;24(7):161. doi: 10.1007/s00894-018-3683-y.

PMID:
29904887
12.

Significance estimation for large scale metabolomics annotations by spectral matching.

Scheubert K, Hufsky F, Petras D, Wang M, Nothias LF, Dührkop K, Bandeira N, Dorrestein PC, Böcker S.

Nat Commun. 2017 Nov 14;8(1):1494. doi: 10.1038/s41467-017-01318-5.

13.

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.

Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4. doi: 10.1016/j.chom.2017.10.001. Epub 2017 Oct 19.

14.

Evaluation of the rotating disk sorptive extraction technique with polymeric sorbent for multiresidue determination of pesticides in water by ultra-high-performance liquid chromatography-tandem mass spectrometry.

Donato FF, Bandeira NMG, Dos Santos GC, Prestes OD, Adaime MB, Zanella R.

J Chromatogr A. 2017 Sep 22;1516:54-63. doi: 10.1016/j.chroma.2017.08.025. Epub 2017 Aug 12.

PMID:
28823784
15.

A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom.

Trevisan-Silva D, Bednaski AV, Fischer JSG, Veiga SS, Bandeira N, Guthals A, Marchini FK, Leprevost FV, Barbosa VC, Senff-Ribeiro A, Carvalho PC.

Sci Data. 2017 Jul 11;4:170090. doi: 10.1038/sdata.2017.90.

16.

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.

Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC.

Elife. 2017 May 11;6. pii: e24214. doi: 10.7554/eLife.24214.

17.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

18.

Synthesis, structure and bonding of actinide disulphide dications in the gas phase.

Lucena AF, Bandeira NAG, Pereira CCL, Gibson JK, Marçalo J.

Phys Chem Chem Phys. 2017 Apr 19;19(16):10685-10694. doi: 10.1039/c7cp01446e.

19.

Metal-Free Synthesis of N-Aryl Amides using Organocatalytic Ring-Opening Aminolysis of Lactones.

Guo W, Gómez JE, Martínez-Rodríguez L, Bandeira NAG, Bo C, Kleij AW.

ChemSusChem. 2017 May 9;10(9):1969-1975. doi: 10.1002/cssc.201700415. Epub 2017 Apr 13.

PMID:
28378941
20.

Electronic Structure Studies on the Whole Keplerate Family: Predicting New Members.

Melgar D, Bandeira NAG, Bo C.

Chemistry. 2017 Apr 19;23(22):5338-5344. doi: 10.1002/chem.201605981. Epub 2017 Mar 29.

PMID:
28370479
21.

Thermodynamic Stability of Heterodimetallic [LnLn'] Complexes: Synthesis and DFT Studies.

Gónzalez-Fabra J, Bandeira NA, Velasco V, Barrios LA, Aguilà D, Teat SJ, Roubeau O, Bo C, Aromí G.

Chemistry. 2017 Apr 11;23(21):5117-5125. doi: 10.1002/chem.201700095. Epub 2017 Mar 27.

PMID:
28220975
22.

Assessment of the adjuvant activity of mesoporous silica nanoparticles in recombinant Mycoplasma hyopneumoniae antigen vaccines.

Virginio VG, Bandeira NC, Leal FM, Lancellotti M, Zaha A, Ferreira HB.

Heliyon. 2017 Jan 6;3(1):e00225. doi: 10.1016/j.heliyon.2016.e00225. eCollection 2017 Jan.

23.

Anions coordinating anions: analysis of the interaction between anionic Keplerate nanocapsules and their anionic ligands.

Melgar D, Bandeira NA, Bonet Avalos J, Bo C.

Phys Chem Chem Phys. 2017 Feb 15;19(7):5343-5350. doi: 10.1039/c6cp08511c.

PMID:
28155941
24.

Magneto-Structural Analysis of Iron(III) Keggin Polyoxometalates.

Bandeira NA, Sadeghi O, Woods TJ, Zhang YZ, Schnack J, Dunbar K, Nyman M, Bo C.

J Phys Chem A. 2017 Feb 16;121(6):1310-1318. doi: 10.1021/acs.jpca.6b10763. Epub 2017 Feb 7.

PMID:
28099014
25.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18.

26.

Lifestyle chemistries from phones for individual profiling.

Bouslimani A, Melnik AV, Xu Z, Amir A, da Silva RR, Wang M, Bandeira N, Alexandrov T, Knight R, Dorrestein PC.

Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7645-E7654. Epub 2016 Nov 14.

27.

SPLASH, a hashed identifier for mass spectra.

Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O.

Nat Biotechnol. 2016 Nov 8;34(11):1099-1101. doi: 10.1038/nbt.3689. No abstract available.

28.

Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks.

Na S, Payne SH, Bandeira N.

Mol Cell Proteomics. 2016 Nov;15(11):3501-3512. Epub 2016 Sep 8.

29.

De Novo MS/MS Sequencing of Native Human Antibodies.

Guthals A, Gan Y, Murray L, Chen Y, Stinson J, Nakamura G, Lill JR, Sandoval W, Bandeira N.

J Proteome Res. 2017 Jan 6;16(1):45-54. doi: 10.1021/acs.jproteome.6b00608. Epub 2016 Nov 2.

30.

Data Independent Acquisition analysis in ProHits 4.0.

Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC.

J Proteomics. 2016 Oct 21;149:64-68. doi: 10.1016/j.jprot.2016.04.042. Epub 2016 Apr 29.

31.

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC.

Anal Chem. 2016 Nov 15;88(22):10775-10784. Epub 2016 Oct 24.

32.

On the privacy risks of sharing clinical proteomics data.

Li S, Bandeira N, Wang X, Tang H.

AMIA Jt Summits Transl Sci Proc. 2016 Aug 31;2016:122-31. eCollection 2016.

33.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.

Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.

34.

Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow.

Kulkarni S, Koller A, Mani KM, Wen R, Alfieri A, Saha S, Wang J, Patel P, Bandeira N, Guha C, Chen EI.

Int J Radiat Oncol Biol Phys. 2016 Nov 1;96(3):566-77. doi: 10.1016/j.ijrobp.2016.06.008. Epub 2016 Jun 18.

35.

A Mn(iii) single ion magnet with tridentate Schiff-base ligands.

Realista S, Fitzpatrick AJ, Santos G, Ferreira LP, Barroso S, Pereira LC, Bandeira NA, Neugebauer P, Hrubý J, Morgan GG, van Slageren J, Calhorda MJ, Martinho PN.

Dalton Trans. 2016 Aug 2;45(31):12301-7. doi: 10.1039/c6dt02538b.

PMID:
27440193
36.

SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis.

Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G.

J Proteome Res. 2016 Aug 5;15(8):2826-40. doi: 10.1021/acs.jproteome.6b00417. Epub 2016 Jul 27.

PMID:
27399812
37.

Di- versus Trinuclear Copper(II) Cryptate for the Uptake of Dicarboxylate Anions.

Esteves CV, Mateus P, André V, Bandeira NA, Calhorda MJ, Ferreira LP, Delgado R.

Inorg Chem. 2016 Jul 18;55(14):7051-60. doi: 10.1021/acs.inorgchem.6b00945. Epub 2016 Jun 29.

PMID:
27355987
38.

Polynuclear Gold [Au(I) ]4 , [Au(I) ]8 , and Bimetallic [Au(I) 4 Ag(I) ] Complexes: C-H Functionalization of Carbonyl Compounds and Homogeneous Carbonylation of Amines.

Smirnova ES, Muñoz Molina JM, Johnson A, Bandeira NA, Bo C, Echavarren AM.

Angew Chem Int Ed Engl. 2016 Jun 20;55(26):7487-91. doi: 10.1002/anie.201603200. Epub 2016 May 11.

39.

Accuracy of embedded fragment calculation for evaluating electron interactions in mixed valence magnetic systems: study of 2e-reduced lindqvist polyoxometalates.

Suaud N, López X, Ben Amor N, Bandeira NA, de Graaf C, Poblet JM.

J Chem Theory Comput. 2015 Feb 10;11(2):550-9. doi: 10.1021/ct5010005.

PMID:
26580912
40.

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition.

Wang J, Tucholska M, Knight JD, Lambert JP, Tate S, Larsen B, Gingras AC, Bandeira N.

Nat Methods. 2015 Dec;12(12):1106-8. doi: 10.1038/nmeth.3655. No abstract available.

41.

Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems.

Hook V, Bandeira N.

J Am Soc Mass Spectrom. 2015 Dec;26(12):1970-80. doi: 10.1007/s13361-015-1251-6. Epub 2015 Oct 19. Review.

42.

A Metal-Free Synthesis of N-Aryl Carbamates under Ambient Conditions.

Guo W, Gónzalez-Fabra J, Bandeira NA, Bo C, Kleij AW.

Angew Chem Int Ed Engl. 2015 Sep 28;54(40):11686-90. doi: 10.1002/anie.201504956. Epub 2015 Aug 12.

PMID:
26385130
43.

The mechanism of CO2 hydration: a porous metal oxide nanocapsule catalyst can mimic the biological carbonic anhydrase role.

Bandeira NA, Garai S, Müller A, Bo C.

Chem Commun (Camb). 2015 Nov 4;51(85):15596-9. doi: 10.1039/c5cc06423f.

PMID:
26359657
44.

Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species.

Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR.

Chem Biol. 2015 Apr 23;22(4):460-471. doi: 10.1016/j.chembiol.2015.03.010. Epub 2015 Apr 9.

45.

Molecular cartography of the human skin surface in 3D.

Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2120-9. doi: 10.1073/pnas.1424409112. Epub 2015 Mar 30.

46.

Highly Efficient Chirality Transfer from Diamines Encapsulated within a Self-Assembled Calixarene-Salen Host.

Martínez-Rodríguez L, Bandeira NA, Bo C, Kleij AW.

Chemistry. 2015 May 4;21(19):7144-50. doi: 10.1002/chem.201500333. Epub 2015 Mar 24.

PMID:
25807915
47.

The generating function approach for Peptide identification in spectral networks.

Guthals A, Boucher C, Bandeira N.

J Comput Biol. 2015 May;22(5):353-66. doi: 10.1089/cmb.2014.0165. Epub 2014 Nov 25.

48.

Phosphinothiolates as ligands for polyhydrido copper nanoclusters.

Huertos MA, Cano I, Bandeira NA, Benet-Buchholz J, Bo C, van Leeuwen PW.

Chemistry. 2014 Dec 1;20(49):16121-7. doi: 10.1002/chem.201404763. Epub 2014 Oct 5.

PMID:
25284300
49.

MixGF: spectral probabilities for mixture spectra from more than one peptide.

Wang J, Bourne PE, Bandeira N.

Mol Cell Proteomics. 2014 Dec;13(12):3688-97. doi: 10.1074/mcp.O113.037218. Epub 2014 Sep 15.

50.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

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