Acquisition of a mass spectrometer coupled to a liquid chromatography system for increasing the capacity to meet the needs of users and for making new technologies available in the Laboratory of Mass Spectrometry

• Grant number: 09/54067-3
• Support Opportunities: Multi-user Equipment Program
• Start date: August 01, 2010
• End date: July 31, 2012
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Adriana Franco Paes Leme
• Grantee: Adriana Franco Paes Leme
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil
• EMU web page: Página do Equipamento Multiusuário não informada
• Type of equipment: Tipo de Equipamento Multiusuário não informado
• Manufacturer: Fabricante não informado
• Model: Modelo não informado

Abstract

The approved multi-user equipment was installed in August 2011 at Mass Spectrometry Laboratory, located at Brazilian Biosciences National Laboratory (LNBio), ABTLuS-CNPEM. The multi-user equipment is ETD enabled Orbitrap Velos instrument (Thermo Fisher Scientific) connected to nanoflow liquid chromatography EASY-nLC II system (Proxeon Biosystem) through a Proxeon nanoelectrospray ion source. These instruments combine mass accuracy and high resolution of the Orbitrap mass analyzer, with the increased sensitivity of LTQ Velos. It can provide multiple fragmentation techniques: CID, HCD and ETD, which have extended the possibilities within tandem mass spectrometry, increasing the speed and confidence of identification of large-scale complex proteomes, binding partners and post-translational modifications, analysis of cross-linked complexes to map protein interaction, and likely quantitative proteomic approaches. The equipment is available to the Brazilian scientific community in the same manner as is the other multi-user equipment of the Mass Spectrometry Laboratory. The Laboratory started the operation in continuous mode, in terms of the submission of proposals and analyses in June 2009. One of the characteristics of the Laboratory is that users are provided with technical support in the operation of the mass spectrometers and the data analysis, as well as with training in the area of mass spectrometry/proteomics that is fundamental for the development of individual research. The implementation of the new cutting-edge technology ETD enabled Orbitrap Velos instrument at Mass Spectrometry Laboratory has included the Brazilian scientific community in the international panorama of competitiveness in the area of mass spectrometry/ proteomics. (AU)

Scientific publications

(30)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

KAWAHARA, REBECA; GRANATO, DANIELA CAMPOS; YOKOO, SAMI; DOMINGUES, ROMENIA RAMOS; TRINDADE, DANIEL MARAGNO; PAES LEME, ADRIANA FRANCO. Mass spectrometry-based proteomics revealed Glypican-1 as a novel ADAM17 substrate. JOURNAL OF PROTEOMICS, v. 151, n. SI, p. 53-65, JAN 16 2017. (11/22421-2, 09/54067-3, 10/19278-0)

CARNIELLI, CAROLINA M.; WINCK, FLAVIA V.; LEME, ADRIANA F. PAES. Functional annotation and biological interpretation of proteomics data. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v. 1854, n. 1, p. 46-54, JAN 2015. (09/54067-3, 10/19278-0)

KAWAHARA, REBECA; MEIRELLES, GABRIELA V.; HEBERLE, HENRY; DOMINGUES, ROMENIA R.; GRANATO, DANIELA C.; YOKOO, SAMI; CANEVAROLO, RAFAEL R.; WINCK, FLAVIAV.; RIBEIRO, ANA CAROLINA P.; BRANDAO, THAIS BIANCA; et al. Integrative analysis to select cancer candidate biomarkers to targeted validation. ONCOTARGET, v. 6, n. 41, p. 43635-43652, DEC 22 2015. (11/22421-2, 09/54067-3, 09/53839-2, 10/19278-0)

HANSEN, HINRICH P.; TRAD, AHMAD; DAMS, MARIA; ZIGRINO, PAOLA; MOSS, MARCIA; TATOR, MAXIMILIAN; SCHOEN, GISELA; GRENZI, PATRICIA C.; BACHURSKI, DANIEL; AQUINO, BRUNO; et al. CD30 on extracellular vesicles from malignant Hodgkin cells supports damaging of CD30 ligand-expressing bystander cells with Brentuximab-Vedotin, in vitro. ONCOTARGET, v. 7, n. 21, p. 30523-30535, MAY 24 2016. (09/54067-3)

FLORES, ISADORA L.; KAWAHARA, REBECA; MIGUEL, MARCIA C. C.; GRANATO, DANIELA C.; DOMINGUES, ROMENIA R.; MACEDO, CAROLINA C. S.; CARNIELLI, CAROLINA M.; YOKOO, SAMI; RODRIGUES, PRISCILA C.; MONTEIRO, BARBARA V. B.; et al. EEF1D modulates proliferation and epithelial-mesenchymal transition in oral squamous cell carcinoma. Clinical Science, v. 130, n. 10, p. 785-799, MAY 1 2016. (11/22421-2, 09/53839-2, 09/54067-3, 13/01607-6, 10/19278-0)

SIMABUCO, FERNANDO MOREIRA; KAWAHARA, REBECA; YOKOO, SAMI; GRANATO, DANIELA C.; MIGUEL, LUCAS; AGOSTINI, MICHELLE; ARAGAO, ANNELIZE Z. B.; DOMINGUES, ROMENIA R.; FLORES, ISADORA L.; MACEDO, CAROLINA C. S.; et al. ADAM17 mediates OSCC development in an orthotopic murine model. Molecular Cancer, v. 13, FEB 5 2014. (09/54067-3, 10/19278-0, 10/15675-5)

SCOTA FERREIRA, AMANDA PETRINA; CASSAGO, ALEXANDRE; GONCALVES, KALIANDRA DE ALMEIDA; DIAS, MARILIA MEIRA; ADAMOSKI, DOUGLAS; RODRIGUES ASCENCAO, CAROLLINE FERNANDA; HONORATO, RODRIGO VARGAS; DE OLIVEIRA, JULIANA FERREIRA; FERREIRA, IGOR MONTEZE; FORNEZARI, CAMILA; et al. Active Glutaminase C Self-assembles into a Supratetrameric Oligomer That Can Be Disrupted by an Allosteric Inhibitor. Journal of Biological Chemistry, v. 288, n. 39, p. 28009-28020, SEP 27 2013. (12/14298-9, 10/05003-0, 09/10875-9, 10/05987-0, 09/54067-3, 11/06654-7)

KAWAHARA, REBECA; LIMA, RENATO NIYAMA; DOMINGUES, ROMENIA R.; PAULETTI, BIANCA ALVES; MEIRELLES, GABRIELA V.; ASSIS, MICHELLE; MIGLIORINI FIGUEIRA, ANA CAROLINA; PAES LEME, ADRIANA FRANCO. Deciphering the Role of the ADAM17-Dependent Secretome in Cell Signaling. JOURNAL OF PROTEOME RESEARCH, v. 13, n. 4, p. 2080-2093, APR 2014. (11/22421-2, 09/54067-3, 09/53839-2, 10/19278-0)

GRANATO, DANIELA C.; ZANETTI, MARIANA R.; KAWAHARA, REBECA; YOKOO, SAMI; DOMINGUES, ROMENIA R.; ARAGAO, ANNELIZE Z.; AGOSTINI, MICHELLE; CARAZZOLLE, MARCELO F.; VIDAL, RAMON O.; FLORES, ISADORA L.; et al. Integrated Proteomics Identified Up-Regulated Focal Adhesion-Mediated Proteins in Human Squamous Cell Carcinoma in an Orthotopic Murine Model. PLoS One, v. 9, n. 5, MAY 23 2014. (11/22421-2, 11/02267-9, 09/53839-2, 09/54067-3, 10/19278-0)

KORVALA, JOHANNA; MOSAKHANI, NEDA; ZANDONADI, FLAVIA S.; MEIRELLES, GABRIELA V.; PAES LEME, ADRIANA FRANCO; COLETTA, RICARDO D.; LEIVO, ILMO; SALO, TUULA. MicroRNA and protein profiles in invasive versus non-invasive oral tongue squamous cell carcinoma cells in vitro. Experimental Cell Research, v. 350, n. 1, p. 9-18, JAN 1 2017. (09/54067-3, 13/01607-6, 10/19278-0)

RIVERA, CESAR; ZANDONADI, FLAVIA SILVA; SANCHEZ-ROMERO, CELESTE; SOARES, CIRO DANTAS; GRANATO, DANIELA CAMPOS; ALEJANDRO GONZALEZ-ARRIAGADA, WILFREDO; PAES LEME, ADRIANA FRANCO. Agrin has a pathological role in the progression of oral cancer. BRITISH JOURNAL OF CANCER, v. 118, n. 12, p. 1628-1638, JUN 2018. (16/07846-0, 10/19278-0, 09/54067-3)

BUSSO-LOPES, ARIANE F.; NEVES, LEANDRO X.; CAMARA, GUILHERME A.; GRANATO, DANIELA C.; PRETTI, MARCO ANTONIO M.; HEBERLE, HENRY; PATRONI, FABIO M. S.; SA, JAMILE; YOKOO, SAMI; RIVERA, CESAR; et al. Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer. NATURE COMMUNICATIONS, v. 13, n. 1, p. 24-pg., 2022-11-07. (19/21815-9, 15/19191-6, 15/50612-8, 09/53998-3, 18/18496-6, 11/00417-3, 09/54067-3, 10/19278-0, 16/07846-0)

KAWAHARA, REBECA; GRANATO, DANIELA CAMPOS; YOKOO, SAMI; DOMINGUES, ROMENIA RAMOS; TRINDADE, DANIEL MARAGNO; PAES LEME, ADRIANA FRANCO. Mass spectrometry-based proteomics revealed Glypican-1 as a novel ADAM17 substrate. JOURNAL OF PROTEOMICS, v. 151, p. 13-pg., 2017-01-16. (09/54067-3, 11/22421-2, 10/19278-0)

TAVARES, RAPHAEL; WAJNBERG, GABRIEL; SCHERER, NICOLE DE MIRANDA; PAULETTI, BIANCA ALVES; CASSOLI, JULIANA S.; FERREIRA, CARLOS GIL; PAES LEME, ADRIANA FRANCO; DE ARAUJO-SOUZA, PATRICIA SAVIO; MARTINS-DE-SOUZA, DANIEL; PASSETTI, FABIO. Unveiling alterative splice diversity from human oligodendrocyte proteome data. JOURNAL OF PROTEOMICS, v. 151, p. 9-pg., 2017-01-16. (14/10068-4, 10/19278-0, 09/54067-3, 14/14881-1, 13/08711-3)

TAVARES, RAPHAEL; WAJNBERG, GABRIEL; SCHERER, NICOLE DE MIRANDA; PAULETTI, BIANCA ALVES; CASSOLI, JULIANA S.; FERREIRA, CARLOS GIL; PAES LEME, ADRIANA FRANCO; DE ARAUJO-SOUZA, PATRICIA SAVIO; MARTINS-DE-SOUZA, DANIEL; PASSETTI, FABIO. Unveiling alterative splice diversity from human oligodendrocyte proteome data. JOURNAL OF PROTEOMICS, v. 151, n. SI, p. 293-301, JAN 16 2017. (14/14881-1, 09/54067-3, 13/08711-3, 14/10068-4, 10/19278-0)

ARAGAO, ANNELIZE Z. B.; NOGUEIRA, MARIA LUIZA C.; GRANATO, DANIELA C.; SIMABUCO, FERNANDO M.; HONORATO, RODRIGO V.; HOFFMAN, ZAIRA; YOKOO, SAMI; LAURINDO, FRANCISCO R. M.; SQUINA, FABIO M.; ZERI, ANA CAROLINA M.; et al. Identification of Novel Interaction between ADAM17 (a Disintegrin and Metalloprotease 17) and Thioredoxin-1. Journal of Biological Chemistry, v. 287, n. 51, p. 43071-43082, DEC 14 2012. (11/02267-9, 09/54067-3, 10/19278-0, 10/15675-5, 09/18301-1)

WINCK, FLAVIA V.; BELLONI, MARILIA; PAULETTI, BIANCA A.; ZANELLA, JACKELINE DE LIMA; DOMINGUES, ROMENIA R.; SHERMAN, NICHOLAS E.; PAES LEME, ADRIANA F.. Phosphoproteome analysis reveals differences in phosphosite profiles between tumorigenic and non-tumorigenic epithelial cells. JOURNAL OF PROTEOMICS, v. 96, p. 67-81, JAN 16 2014. (09/54067-3, 10/19278-0)

CAJADO-CARVALHO, DANIELA; GALVAO, JULIANA; KUNIYOSHI, ALEXANDRE K.; CARNEIRO, PATRICIA DOS SANTOS; PAES LEME, ADRIANA FRANCO; PAULETTI, BIANCA ALVES; MARENGO, ELIANA BLINI; PORTARO, FERNANDA V.. Tityus serrulatus Scorpion Venom: In Vitro Tests and Their Correlation with In Vivo Lethal Dose Assay. TOXINS, v. 9, n. 12, DEC 2017. (15/15364-3, 13/15344-7, 13/15343-0, 09/54067-3)

KAWAHARA, REBECA; GRANATO, DANIELA C.; CARNIELLI, CAROLINA M.; CERVIGNE, NILVA K.; OLIVERIA, CARINE E.; MARTINEZ, CESAR A. R.; YOKOO, SAMI; FONSECA, FELIPE P.; LOPES, MARCIO; SANTOS-SILVA, ALAN R.; et al. Agrin and Perlecan Mediate Tumorigenic Processes in Oral Squamous Cell Carcinoma. PLoS One, v. 9, n. 12, DEC 15 2014. (11/22421-2, 09/54067-3, 10/19278-0)

WINCK, FLAVIA V.; PRADO RIBEIRO, ANA CAROLINA; DOMINGUES, ROMENIA RAMOS; LING, LIU YI; RIANO-PACHON, DIEGO MAURICIO; RIVERA, CESAR; BRANDAO, THAIS BIANCA; GOUVEA, ADRIELE FERREIRA; SANTOS-SILVA, ALAN ROGER; COLETTA, RICARDO D.; et al. Insights into immune responses in oral cancer through proteomic analysis of saliva and salivary extracellular vesicles. SCIENTIFIC REPORTS, v. 5, NOV 5 2015. (09/54067-3, 10/19278-0)

NEVES, LEANDRO XAVIER; GRANATO, DANIELA C.; BUSSO-LOPES, ARIANE FIDELIS; CARNIELLI, CAROLINA M.; DE SA PATRONI, FABIO M.; DE ROSSI, TATIANE; OLIVEIRA, ANA KARINA; RIBEIRO, ANA CAROLINA P.; BRANDAO, THAIS BIANCA; RODRIGUES, ANDRE NIMTZ; et al. Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis. MOLECULAR & CELLULAR PROTEOMICS, v. 20, 2021. (09/54067-3, 18/11958-4, 18/18496-6, 10/19278-0, 16/07846-0)

HANSEN, HINRICH P.; ENGELS, HANNA-MAREIKE; DAMS, MARIA; PAES LEME, ADRIANA F.; PAULETTI, BIANCA ALVES; SIMHADRI, VIJAYA LAKSHMI; DUERKOP, HORST; REINERS, KATRIN S.; BARNERT, SABINE; ENGERT, ANDREAS; et al. Protrusion-guided extracellular vesicles mediate CD30 trans-signalling in the microenvironment of Hodgkin's lymphoma. JOURNAL OF PATHOLOGY, v. 232, n. 4, p. 405-414, MAR 2014. (09/54067-3)

RUBIO, MARCELO VENTURA; ZUBIETA, MARIANE PALUDETTI; LOURENO FRANCO CAIRO, JOAO PAULO; CALZADO, FELIPE; PAES LEME, ADRIANA FRANCO; SQUINA, FABIO MARCIO; PRADE, ROLF ALEXANDER; DE LIMA DAMASIO, ANDRE RICARDO. Mapping N-linked glycosylation of carbohydrate-active enzymes in the secretome of Aspergillus nidulans grown on lignocellulose. BIOTECHNOLOGY FOR BIOFUELS, v. 9, AUG 8 2016. (14/15403-6, 14/06923-6, 11/20977-3, 13/24988-5, 12/20549-4, 14/23051-2, 09/54067-3)

ZANDONADI, FLAVIA S.; YOKOO, SAMI; GRANATO, DANIELA CAMPOS; RIVERA, CESAR; SOARES MACEDO, CAROLINA CARNEIRO; SOARES, CIRO DANTAS; CARNIELLI, CAROLINA MORETTO; DOMINGUES, ROMENIA RAMOS; PAULETTI, BIANCA A.; CONSONNI, SILVIO ROBERTO; et al. Follistatin-related protein 1 interacting partner of Syndecan-1 promotes an aggressive phenotype on Oral Squamous cell carcinoma (OSCC) models. JOURNAL OF PROTEOMICS, v. 254, p. 13-pg., 2022-03-15. (13/02257-9, 18/18496-6, 16/50005-7, 18/15535-0, 16/07846-0, 19/18751-9, 09/54067-3, 10/19278-0)

FONSECA, FELIPE PAIVA; SOARES MACEDO, CAROLINA CARNEIRO; DOS SANTOS COSTA, SARA FERREIRA; PAES LEME, ADRIANA FRANCO; RODRIGUES, ROMENIA RAMOS; REBELO PONTES, HELDER ANTONIO; ALTEMANI, ALBINA; VAN HEERDEN, WILLIE F. P.; MARTINS, MANOELA DOMINGUES; DE ALMEIDA, OSLEI PAES; et al. Mass spectrometry-based proteome profile may be useful to differentiate adenoid cystic carcinoma from polymorphous adenocarcinoma of salivary glands. ORAL SURGERY ORAL MEDICINE ORAL PATHOLOGY ORAL RADIOLOGY, v. 128, n. 6, p. 639-650, DEC 2019. (09/54067-3, 15/16056-0)

E COSTA, RUTE A. P.; GRANATO, DANIELA C.; TRINO, LUCIANA D.; YOKOO, SAMI; CARNIELLI, CAROLINA M.; KAWAHARA, REBECA; DOMINGUES, ROMENIA R.; PAULETTI, BIANCA ALVES; NEVES, LEANDRO XAVIER; SANTANA, ALINE G.; et al. ADAM17 cytoplasmic domain modulates Thioredoxin-1 conformation and activity. REDOX BIOLOGY, v. 37, OCT 2020. (16/01528-7, 18/12194-8, 19/18751-9, 18/18496-6, 09/54067-3, 18/15535-0, 14/23888-0, 16/07846-0, 16/24664-3, 14/06485-9, 10/19278-0)

SCHAEFER, MIRIAM; GRANATO, DANIELA C.; KROSSA, SEBASTIAN; BARTELS, ANNE-KATHRIN; YOKOO, SAMI; DUSTERHOFT, STEFAN; KOUDELKA, TOMAS; SCHEIDIG, AXEL J.; THOLEY, ANDREAS; PAES LEME, ADRIANA F.; et al. GRP78 protects a disintegrin and metalloprotease 17 against protein-disulfide isomerase A6 catalyzed inactivation. FEBS Letters, v. 591, n. 21, p. 3567-3587, NOV 2017. (11/02267-9, 09/54067-3, 10/19278-0)

GRANATO, DANIELA C.; P. E COSTA, RUTE A.; KAWAHARA, REBECA; YOKOO, SAMI; ARAGAO, ANNELIZE Z.; DOMINGUES, ROMENIA R.; PAULETTI, BIANCA A.; HONORATO, RODRIGO V.; FATTORI, JULIANA; FIGUEIRA, ANA CAROLINA M.; et al. Thioredoxin-1 Negatively Modulates ADAM17 Activity Through Direct Binding and Indirect Reductive Activity. Antioxidants & Redox Signaling, v. 29, n. 8, FEB 2018. (16/01528-7, 09/54067-3, 14/06485-9, 14/23888-0, 11/02267-9, 10/19278-0)

CARNIELLI, CAROLINA MORETTO; SOARES MACEDO, CAROLINA CARNEIRO; DE ROSSI, TATIANE; GRANATO, DANIELA CAMPOS; RIVERA, CESAR; DOMINGUES, ROMENIA RAMOS; PAULETTI, BIANCA ALVES; YOKOO, SAMI; HEBERLE, HENRY; BUSSO-LOPES, ARIANE FIDELIS; et al. Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer. NATURE COMMUNICATIONS, v. 9, SEP 5 2018. (16/07846-0, 09/54067-3, 13/16483-0, 10/19278-0, 09/53998-3)

GRANATO, DANIELA C.; NEVES, LEANDRO X.; TRINO, LUCIANA D.; CARNIELLI, CAROLINA M.; LOPES, ARIANE F. B.; YOKOO, SAMI; PAULETTI, BIANCA A.; DOMINGUES, ROMENIA R.; SA, JAMILE O.; PERSINOTI, GABRIELLA; et al. Meta-omics analysis indicates the saliva microbiome and its proteins associated with the prognosis of oral cancer patients. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v. 1869, n. 8, AUG 2021. (18/18496-6, 18/02180-0, 16/07846-0, 19/18751-9, 19/21815-9, 09/54067-3, 18/11958-4, 15/50590-4, 18/12194-8, 18/15728-3, 14/06485-9, 18/15535-0, 10/19278-0)