@article{Soler2020,

title = {Proteome changes induced by a short, non-cytotoxic exposure to the mycoestrogen zearalenone in the pig intestine.},

author = {Laura Soler and Alexandre Stella and Juan Seva and Francisco Jose Pallarés and Tarek Lahjouji and Odile Burlet-Schiltz and Isabelle P Oswald},

year  = {2020},

date = {2020-01-01},

journal = {Journal of proteomics},

volume = {224},

pages = {103842},

address = {Netherlands},

abstract = {Intestinal epithelial homeostasis is regulated by a complex network of signaling pathways. Among them is estrogen signaling, important for the proliferation and differentiation of epithelial cells, immune signaling and metabolism. The mycotoxin zearalenone (ZEN) is an estrogen disruptor naturally found in food and feed. The exposure of the intestine to ZEN has toxic effects including alteration of the immune status and is possibly implicated in carcinogenesis, but the molecular mechanisms linked with these effects are not clear. Our objective was to explore the proteome changes induced by a short, non-cytotoxic exposure to ZEN in the intestine using pig jejunal explants. Our results indicated that ZEN promotes little proteome changes, but significantly related with an induction of ER$alpha$ signaling and a consequent disruption of highly interrelated signaling cascades, such as NF-$kappa$B, ERK1/2, CDX2 and HIF1$alpha$. The toxicity of ZEN leads also to an altered immune status characterized by the activation of the chemokine CXCR4/SDF-1 axis and an accumulation of MHC-I proteins. Our results connect the estrogen disrupting activity of ZEN with its intestinal toxic effect, associating the exposure to ZEN with cell-signaling disorders similar to those involved in the onset and progression of diseases such as cancer and chronic inflammatory disorders. SIGNIFICANCE: The proteomics results presented in our study indicate that the endocrine disruptor activity of ZEN is able to regulate a cascade of highly inter-connected signaling events essential for the small intestinal crypt-villus cycle and immune status. These molecular mechanisms are also implicated in the onset and progress of intestinal immune disorders and cancer indicating that exposure to ZEN could play an important role in intestinal pathogenesis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Blaize2020,

title = {CD5 signalosome coordinates antagonist TCR signals to control the generation of Treg cells induced by foreign antigens.},

author = {Gaëtan Blaize and Hélène Daniels-Treffandier and Meryem Aloulou and Nelly Rouquié and Cui Yang and Marlène Marcellin and Mylène Gador and Mehdi Benamar and Mariette Ducatez and Ki-Duk Song and Odile Burlet-Schiltz and Abdelhadi Saoudi and Paul E Love and Nicolas Fazilleau and Anne Peredo and Renaud Lesourne},

year  = {2020},

date = {2020-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {117},

number = {23},

pages = {12969--12979},

abstract = {CD5 is characterized as an inhibitory coreceptor with an important regulatory role during T cell development. The molecular mechanism by which CD5 operates has been puzzling and its function in mature T cells suggests promoting rather than repressing effects on immune responses. Here, we combined quantitative mass spectrometry and genetic studies to analyze the components and the activity of the CD5 signaling machinery in primary T cells. We found that T cell receptor (TCR) engagement induces the selective phosphorylation of CD5 tyrosine 429, which serves as a docking site for proteins with adaptor functions (c-Cbl, CIN85, CRKL), connecting CD5 to positive (PI3K) and negative (UBASH3A, SHIP1) regulators of TCR signaling. c-CBL acts as a coordinator in this complex enabling CD5 to synchronize positive and negative feedbacks on TCR signaling through the other components. Disruption of CD5 signalosome in mutant mice reveals that it modulates TCR signal outputs to selectively repress the transactivation of Foxp3 and limit the inopportune induction of peripherally induced regulatory T cells during immune responses against foreign antigen. Our findings bring insights into the paradigm of coreceptor signaling, suggesting that, in addition to providing dualistic enhancing or dampening inputs, coreceptors can engage concomitant stimulatory and inhibitory signaling events, which act together to promote specific functional outcomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bouyssie2020,

title = {Proline: an efficient and user-friendly software suite for large-scale proteomics.},

author = {David Bouyssié and Anne-Marie Hesse and Emmanuelle Mouton-Barbosa and Magali Rompais and Charlotte Macron and Christine Carapito and Anne Peredo and Yohann Couté and Véronique Dupierris and Alexandre Burel and Jean-Philippe Menetrey and Andrea Kalaitzakis and Julie Poisat and Aymen Romdhani and Odile Burlet-Schiltz and Sarah Cianférani and Jerome Garin and Christophe Bruley},

year  = {2020},

date = {2020-01-01},

journal = {Bioinformatics (Oxford, England)},

volume = {36},

number = {10},

pages = {3148--3155},

abstract = {MOTIVATION: The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study. RESULTS: Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline's ability to provide high quantification accuracy in a user-friendly interface for datasets of any size. AVAILABILITY AND IMPLEMENTATION: Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client-server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pechalrieu2020,

title = {Bisubstrate-Type Chemical Probes Identify GRP94 as a Potential Target of Cytosine-Containing Adenosine Analogs.},

author = {Dany Pechalrieu and Fanny Assemat and Ludovic Halby and Marlene Marcellin and Pengrong Yan and Karima Chaoui and Sahil Sharma and Gabriela Chiosis and Odile Burlet-Schiltz and Paola B Arimondo and Marie Lopez},

year  = {2020},

date = {2020-01-01},

journal = {ACS chemical biology},

volume = {15},

number = {4},

pages = {952--961},

abstract = {We synthesized affinity-based chemical probes of cytosine-adenosine bisubstrate analogs and identified several potential targets by proteomic analysis. The validation of the proteomic analysis identified the chemical probe as a specific inhibitor of glucose-regulated protein 94 (GRP94), a potential drug target for several types of cancers. Therefore, as a result of the use of bisubstrate-type chemical probes and a chemical-biology methodology, this work opens the way to the development of a new family of GRP94 inhibitors that could potentially be of therapeutic interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Imbert2020,

title = {Resistance of melanoma to immune checkpoint inhibitors is overcome by targeting the sphingosine kinase-1.},

author = {Caroline Imbert and Anne Montfort and Marine Fraisse and Elie Marcheteau and Julia Gilhodes and Elodie Martin and Florie Bertrand and Marlène Marcellin and Odile Burlet-Schiltz and Anne Gonzalez Peredo and Virginie Garcia and Stéphane Carpentier and Sophie Tartare-Deckert and Pierre Brousset and Philippe Rochaix and Florent Puisset and Thomas Filleron and Nicolas Meyer and Laurence Lamant and Thierry Levade and Bruno Ségui and Nathalie Andrieu-Abadie and Céline Colacios},

year  = {2020},

date = {2020-01-01},

journal = {Nature communications},

volume = {11},

number = {1},

pages = {437},

abstract = {Immune checkpoint inhibitors (ICIs) have dramatically modified the prognosis of several advanced cancers, however many patients still do not respond to treatment. Optimal results might be obtained by targeting cancer cell metabolism to modulate the immunosuppressive tumor microenvironment. Here, we identify sphingosine kinase-1 (SK1) as a key regulator of anti-tumor immunity. Increased expression of SK1 in tumor cells is significantly associated with shorter survival in metastatic melanoma patients treated with anti-PD-1. Targeting SK1 markedly enhances the responses to ICI in murine models of melanoma, breast and colon cancer. Mechanistically, SK1 silencing decreases the expression of various immunosuppressive factors in the tumor microenvironment to limit regulatory T cell (Treg) infiltration. Accordingly, a SK1-dependent immunosuppressive signature is also observed in human melanoma biopsies. Altogether, this study identifies SK1 as a checkpoint lipid kinase that could be targeted to enhance immunotherapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Clement2020,

title = {Adipocyte extracellular vesicles carry enzymes and fatty acids that stimulate mitochondrial metabolism and remodeling in tumor cells.},

author = {Emily Clement and Ikrame Lazar and Camille Attané and Lorry Carrié and Stéphanie Dauvillier and Manuelle Ducoux-Petit and David Esteve and Thomas Menneteau and Mohamed Moutahir and Sophie Le Gonidec and Stéphane Dalle and Philippe Valet and Odile Burlet-Schiltz and Catherine Muller and Laurence Nieto},

year  = {2020},

date = {2020-01-01},

journal = {The EMBO journal},

volume = {39},

number = {3},

pages = {e102525},

abstract = {Extracellular vesicles are emerging key actors in adipocyte communication. Notably, small extracellular vesicles shed by adipocytes stimulate fatty acid oxidation and migration in melanoma cells and these effects are enhanced in obesity. However, the vesicular actors and cellular processes involved remain largely unknown. Here, we elucidate the mechanisms linking adipocyte extracellular vesicles to metabolic remodeling and cell migration. We show that adipocyte vesicles stimulate melanoma fatty acid oxidation by providing both enzymes and substrates. In obesity, the heightened effect of extracellular vesicles depends on increased transport of fatty acids, not fatty acid oxidation-related enzymes. These fatty acids, stored within lipid droplets in cancer cells, drive fatty acid oxidation upon being released by lipophagy. This increase in mitochondrial activity redistributes mitochondria to membrane protrusions of migrating cells, which is necessary to increase cell migration in the presence of adipocyte vesicles. Our results provide key insights into the role of extracellular vesicles in the metabolic cooperation that takes place between adipocytes and tumors with particular relevance to obesity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pirro2020,

title = {Characterization of Macrophage Galactose-type Lectin (MGL) ligands in colorectal cancer cell lines.},

author = {Martina Pirro and Yoann Rombouts and Alexandre Stella and Olivier Neyrolles and Odile Burlet-Schiltz and Sandra J Vliet and Arnoud H Ru and Yassene Mohammed and Manfred Wuhrer and Peter A Veelen and Paul J Hensbergen},

year  = {2020},

date = {2020-01-01},

journal = {Biochimica et biophysica acta. General subjects},

volume = {1864},

number = {4},

pages = {129513},

address = {Netherlands},

abstract = {BACKGROUND: The Ca(2+)-dependent C-type lectin receptor Macrophage Galactose-type Lectin (MGL) is highly expressed by tolerogenic dendritic cells (DC) and macrophages. MGL exhibits a high binding specificity for terminal alpha- and beta-linked GalNAc residues found in Tn, sTn and LacdiNAc antigens. These glycan epitopes are often overexpressed in colorectal cancer (CRC), and, as such, MGL can be used to discriminate tumor from the corresponding healthy tissues. Moreover, the high expression of MGL ligands is associated with poor disease-free survival in stage III of CRC tumors. Nonetheless, the glycoproteins expressed by tumor cells that are recognized by MGL have hitherto remained elusive. METHODS: Using a panel of three CRC cell lines (HCT116, HT29 and LS174T), recapitulating CRC diversity, we performed FACS staining and pull-down assays using a recombinant soluble form of MGL (and a mutant MGL as control) combined with mass spectrometry-based (glyco)proteomics. RESULTS: HCT116 and HT29, but not LS174T, are high MGL-binding CRC cell lines. On these cells, the major cell surface binding proteins are receptors (e.g. MET, PTK7, SORL1, PTPRF) and integrins (ITGB1, ITGA3). From these proteins, several N- and/or O-glycopeptides were identified, of which some carried either a LacdiNAc or Tn epitope. CONCLUSIONS: We have identified cell surface MGL-ligands on CRC cell lines. GENERAL SIGNIFICANCE: Advances in (glyco)proteomics have led to identification of candidate key mediators of immune-evasion and tumor growth in CRC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31287496,

title = {HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data},

author = {D Bouyssié and J Lesne and M Locard-Paulet and R Albigot and O Burlet-Schiltz and J Marcoux},

doi = {10.1093/bioinformatics/btz550},

year  = {2019},

date = {2019-12-15},

journal = {Bioinformatics},

volume = {35},

number = {24},

pages = {5331--5333},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31819159,

title = {Mitochondrial 4-ĦNE derived from MAO-A promotes mitoCa2+ overload in chronic postischemic cardiac remodeling},

author = {Y Santin and L Fazal and Y Sainte-Marie and P Sicard and D Maggiorani and F Tortosa and Y Y Y?cel and L Teyssedre and J Rouquette and M Marcellin and C Vindis and J C Shih and O Lairez and O Burlet-Schiltz and A Parini and F Lezoualc'h and J Mialet-Perez},

doi = {10.1038/s41418-019-0470-y},

year  = {2019},

date = {2019-12-09},

journal = {Cell Death Differ.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{652,

title = {An Investigation into the Stephens-Castro Synthesis of Dehydrotriaryl[12]annulenes: Factors Influencing the Cyclotrimerization},

author = {P N W Baxter and A Al Ouahabi and L Karmazin and A Varnek and J M Strub and S Cianferani},

doi = {10.1002/ejoc.201901053},

year  = {2019},

date = {2019-10-18},

journal = {European Journal of Organic Chemistry},

volume = {40},

pages = {6783-6795},

note = {2019-02},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31635354,

title = {Insights into the Allergenic Potential of the Edible Yellow Mealworm (Ŧenebrio molitor)},

author = {A Barre and C Pichereaux and E Velazquez and A Maudouit and M Simplicien and L Garnier and F Bienvenu and J Bienvenu and O Burlet-Schiltz and C Auriol and H Benoist and P Rougé},

doi = {10.3390/foods8100515},

year  = {2019},

date = {2019-10-18},

journal = {Foods},

volume = {8},

number = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31591574,

title = {Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics},

author = {G Voisinne and K Kersse and K Chaoui and L Lu and J Chaix and L Zhang and M Goncalves Menoita and L Girard and Y Ounoughene and H Wang and O Burlet-Schiltz and H Luche and F Fiore and M Malissen and A Gonzalez Peredo and Y Liang and R Roncagalli and B Malissen},

doi = {10.1038/s41590-019-0489-8},

year  = {2019},

date = {2019-10-07},

journal = {Nat. Immunol.},

volume = {20},

number = {11},

pages = {1530--1541},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{651,

title = {Zika virus enhances monocyte adhesion and transmigration favoring viral dissemination to neural cells},

author = {NV. Ayala-Nunez and G Follain and F Delalande and A Hirschler and E Partiot and GL. Hale and BC. Bollweg and J Roels and M Chazal and F Bakoa and M Carocci and S Bourdoulous and O Faklaris and SR. Zaki and A Eckly and B Uring-Lambert and F Doussau and S Cianferani and C Carapito and FMJ. Jacobs and N Jouvenet and JG. Goetz and R Gaudin},

doi = {10.1038/s41467-019-12408-x},

year  = {2019},

date = {2019-09-27},

journal = {Nat Commun. 2019 Sep 27;10(1):4430.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{649,

title = {A Case Study to Identify the Drug Conjugation Site of a Site-Specific Antibody-Drug-Conjugate Using Middle-Down Mass Spectrometry},

author = {Hessmann Erb Rabuka Huguet Josephs Beck Drake PM Cianférani S S D R J A S Hernandez-Alba O Houel S},

doi = {10.1007/s13361-019-02296-2},

year  = {2019},

date = {2019-09-19},

journal = {J Am Soc Mass Spectrom.},

volume = {30},

number = {11},

pages = {2419-2429.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{653,

title = {A Pilot Study on Continuous Infusion of 4% Albumin in Critically Ill Patients: Impact on Nosocomial Infection via a Reduction Mechanism for Oxidized Substrates},

author = {F Schneider and A -F Dureau and S Hellé and C Betscha and B Senger and G Cremel and F Boulmedais and J M Strub and A Corti and N Meyer and M Guillot and P Schaaf and M H Metz-Boutigue},

doi = {10.1097/CCE.0000000000000044},

year  = {2019},

date = {2019-09-19},

journal = {Critical Care Explorations},

volume = {1},

number = {9},

note = {non},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{650,

title = {Toxoplasma gondii ROP16 kinase silences the cyclin B1 gene promoter by hijacking host cell UHRF1-dependent epigenetic pathways},

author = {M Sabou and C Doderer-Lang and C Leyer and A Konjic and S Kubina and S Lennon and O Rohr and S Viville and S Cianférani and E Candolfi and AW. Pfaff and J Brunet},

doi = {10.1007/s00018-019-03267-2},

year  = {2019},

date = {2019-09-06},

journal = {Cell Mol Life Sci. 2019 Sep 6.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{648,

title = {VHH characterization. Comparison of recombinant with chemically synthesized anti-HER2 VHH},

author = {L Hartmann and T Botzanowski and M Galibert and M Jullian and E Chabrol and G Zeder-Lutz and V Kugler and J Stojko and JM. Strub and G Ferry and L Frankiewicz and K Puget and R Wagner and S Cianférani and JA. Boutin},

doi = {10.1002/pro.3712},

year  = {2019},

date = {2019-08-29},

journal = {Protein Sci.},

volume = {28},

number = {10},

pages = {1865-1879},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{647,

title = {Limited oxidative stress favors resistance to skeletal muscle atrophy in hibernating brown bears (Ursus arctos)},

author = {B Chazarin and A Ziemianin and A L Evans and E Meugnier and E Loizon and I Chery and J M Arnemo and J E Swenson and G Gauquelin-Koch and C Simon and S Blanc and E Lefai and F Bertile},

doi = {10.3390/antiox8090334},

year  = {2019},

date = {2019-08-22},

journal = {Antioxidants},

volume = {8},

number = {9},

pages = {334},

note = {2011/34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{638,

title = {Physiologically relevant reconstitution of iron-sulfur cluster biosynthesis uncovers persulfide-processing functions of ferredoxin-2 and frataxin},

author = {S Gervason and D Larkem and AB. Mansour and T Botzanowski and CS. Müller and L Pecqueur and G Le Pavec and A Delaunay-Moisan and O Brun and J Agramunt and A Grandas and M Fontecave and V Schünemann and S Cianférani and C Sizun and MB. Tolédano and B D'Autréaux},

doi = {10.1038/s41467-019-11470-9},

year  = {2019},

date = {2019-08-08},

journal = {Nat Commun.},

volume = {10},

number = {1},

pages = {3566},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{646,

title = {Phosphomimetic substitution at Ser-33 of the chloroquine resistance transporter PfCRT reconstitutes drug responses in Plasmodium falciparum},

author = {CP. Sanchez and S Moliner Cubel and B Nyboer and M Jankowska-Döllken and C Schaeffer-Reiss and D Ayoub and G Planelles and M Lanzer},

doi = {10.1074/jbc.RA119.009464},

year  = {2019},

date = {2019-07-08},

journal = {J Biol Chem.},

pages = {pii: jbc.RA119.009464.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{644,

title = {Division of labour in the black garden ant (Lasius niger) leads to three distinct proteomes},

author = {M Quque and M Benhaim-Delarbre and JL. Deneubourg and C Sueur and F Criscuolo and F Bertile},

doi = {10.1016/j.jinsphys.2019.103907},

year  = {2019},

date = {2019-06-27},

journal = {J Insect Physiol.},

volume = {117},

pages = {103907},

note = {2015/29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{639,

title = {A Proteomic View of Cellular Responses to Anticancer Quinoline-Copper Complexes},

author = {B Dalzon and J Bons and H Diemer and V Collin-Faure and C Marie-Desvergne and M Dubosson and S Cianferani and C Carapito and T Rabilloud},

doi = {10.3390/proteomes7020026},

year  = {2019},

date = {2019-06-24},

journal = {Proteomes},

volume = {7},

number = {2},

pages = {pii: E26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{645,

title = {Metabolic reprogramming involving glycolysis in the hibernating brown bear skeletal muscle},

author = {B Chazarin and KB. Storey and A Ziemianin and S Chanon and M Plumel and I Chery and C Durand and AL. Evans and JM. Arnemo and A Zedrosser and JE. Swenson and G Gauquelin-Koch and C Simon and S Blanc and E Lefai and F Bertile},

doi = {10.1186/s12983-019-0312-2},

year  = {2019},

date = {2019-05-06},

journal = {Front Zool.},

volume = {16},

pages = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{631,

title = {Circadian Analysis of the Mouse Cerebellum Proteome},

author = {M Plumel and S Dumont and P Maes and C Sandu and M P Felder-Scmittbuhl and E Challet and F Bertile},

doi = {10.3390/ijms20081852},

year  = {2019},

date = {2019-04-15},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {8},

pages = {1852},

note = {2012/26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{630,

title = {Lipidomics Reveals Seasonal Shifts in a Large-Bodied Hibernator, the Brown Bear},

author = {S Giroud and I Chery and Bertile; F. and J Bertrand-Michel and G Tascher and G Gauquelin-Koch and J M Arnemo and J E Swenson and N V Singh and E Lefai and A L Evans and C Simon and S Blanc},

doi = {10.3389/fphys.2019.00389},

year  = {2019},

date = {2019-04-12},

journal = {Front Physiol.},

volume = {10},

pages = {389},

note = {2011/30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30967366,

title = {Proteomic evidence of specific IGKV1-8 association with cystic lung light chain deposition disease},

author = {M Camus and S Hirschi and G Prevot and M P Chenard and H Mal and M Stern and M Reynaud-Gaubert and J Gilhodes and O Burlet-Schiltz and P Brousset and M Colombat},

doi = {10.1182/blood.2019898577},

year  = {2019},

date = {2019-04-09},

journal = {Blood},

volume = {133},

number = {26},

pages = {2741--2744},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31200944,

title = {A transgenic mouse model reproduces human hereditary systemic amyloidosis},

author = {M Chabert and X Rousset and M Colombat and M Lacasa and H Kakanakou and M Bourderioux and P Brousset and O Burlet-Schiltz and J J Liepnieks and B Kluve-Beckerman and G Lambert and F P Châtelet and M D Benson and A D Kalopissis},

doi = {10.1016/j.kint.2019.03.013},

year  = {2019},

date = {2019-03-28},

journal = {Kidney Int.},

volume = {96},

number = {3},

pages = {628--641},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{640,

title = {A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level},

author = {J Bons and C Macron and C Aude-Garcia and SA. Vaca-Jacome and M Rompais and S Cianférani and C Carapito and T Rabilloud},

doi = {10.1074/mcp.RA118.001269},

year  = {2019},

date = {2019-03-15},

journal = {Mol Cell Proteomics},

volume = {18},

number = {6},

pages = {1085-1095},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{632,

title = {Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics},

author = {L Muller and L Fornecker and S Cianferani and C Carapito},

doi = {10.1007/978-1-4939-9164-8_8},

year  = {2019},

date = {2019-03-10},

journal = {Methods Mol Biol.},

volume = {1959},

pages = {123-127},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30862563,

title = {Analysis of durum wheat proteome changes under marine and fungal biostimulant treatments using large-scale quantitative proteomics: A useful dataset of durum wheat proteins},

author = {C Pichereaux and E A Laurent and A Gargaros and S Viudes and C Durieu and T Lamaze and P Grieu and O Burlet-Schiltz},

doi = {10.1016/j.jprot.2019.03.003},

year  = {2019},

date = {2019-03-09},

journal = {J Proteomics},

volume = {200},

pages = {28--39},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{629,

title = {In-Depth Proteome Analysis Highlights HepaRG Cells as a Versatile Cell System Surrogate for Primary Human Hepatocytes},

author = {G Tascher and A Burban and S Camus and M Plumel and S Chanon and R Le Guevel and V Shevchenko and A Van Dorsselaer and E Lefai and C Guguen-Guillouzo and F Bertile},

doi = {10.3390/cells8020192},

year  = {2019},

date = {2019-02-21},

journal = {Cells},

volume = {8},

number = {2},

pages = {192},

note = {2012/20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{633,

title = {Cutting-edge multi-level analytical and structural characterization of antibody-drug conjugates: present and future},

author = {A Beck and V D'Atri and A Ehkirch and S Fekete and O Hernandez-Alba and R Gahoual and E Leize-Wagner and Y François and D Guillarme and S Cianférani},

doi = {10.1080/14789450.2019.1578215},

year  = {2019},

date = {2019-02-18},

journal = {Expert Rev Proteomics.},

volume = {16},

number = {4},

pages = {337-362.},

note = {review},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30084957,

title = {VisioProt-MS: interactive 2D maps from intact protein mass spectrometry},

author = {M Locard-Paulet and J Parra and R Albigot and E Mouton-Barbosa and L Bardi and O Burlet-Schiltz and J Marcoux},

doi = {10.1093/bioinformatics/bty680},

year  = {2019},

date = {2019-02-15},

journal = {Bioinformatics},

volume = {35},

number = {4},

pages = {679--681},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{637,

title = {An essential role for α4A-tubulin in platelet biogenesis},

author = {C Strassel and MM. Magiera and A Dupuis and M Batzenschlager and A Hovasse and I Pleines and P Guéguen and A Eckly and S Moog and L Mallo and Q Kimmerlin and S Chappaz and JM. Strub and N Kathiresan and H Salle and A Van Dorsselaer and C Ferec and JY. Py and C Gachet and C Schaeffer-Reiss and BT. Kile and C Janke and F Lanza},

doi = {10.26508/lsa.201900309},

year  = {2019},

date = {2019-02-13},

journal = {Life Sci Alliance},

volume = {2},

number = {1},

pages = {pii: e201900309.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{635,

title = {Studying the Fate of Tumor Extracellular Vesicles at High Spatiotemporal Resolution Using the Zebrafish Embryo},

author = {V Hyenne and S Ghoroghi and M Collot and J Bons and G Follain and S Harlepp and B Mary and J Bauer and L Mercier and I Busnelli and O Lefebvre and N Fekonja and MJ. Garcia-Leon and P Machado and F Delalande and AA. López and SG. Silva and FJ. Verweij and G Niel and F Djouad and H Peinado and C Carapito and AS. Klymchenko and JG. Goetz},

doi = {10.1016/j.devcel.2019.01.014},

year  = {2019},

date = {2019-02-07},

journal = {Dev Cell.},

volume = {48},

number = {4},

pages = {554-572.e7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30700495,

title = {Mass Spectrometry-based Absolute Quantification of 20S Proteasome Status for Controlled Ex-vivo Expansion of Ħuman Adipose-derived Mesenchymal Stromal/Stem Cells},

author = {T Menneteau and B Fabre and L Garrigues and A Stella and D Zivkovic and F Roux-Dalvai and E Mouton-Barbosa and M Beau and M L Renoud and F Amalric and L Sensébé and A Gonzalez-de-Peredo and I Ader and O Burlet-Schiltz and M P Bousquet},

doi = {10.1074/mcp.RA118.000958},

year  = {2019},

date = {2019-01-30},

journal = {Mol. Cell Proteomics},

volume = {18},

number = {4},

pages = {744--759},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{628,

title = {Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma},

author = {LM. Fornecker and L Muller and F Bertrand and N Paul and A Pichot and R Herbrecht and MP. Chenard and L Mauvieux and L Vallat and S Bahram and S Cianférani and R Carapito and C Carapito},

doi = {10.1038/s41598-018-37273-4},

year  = {2019},

date = {2019-01-29},

journal = {Sci Rep.},

volume = {9},

number = {1},

pages = {895},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30697967,

title = {Muscle wasting in patients with end-stage renal disease or early-stage lung cancer: common mechanisms at work},

author = {J Aniort and A Stella and C Philipponnet and A Poyet and C Polge and A Claustre and L Combaret and D B?chet and D Attaix and S Boisgard and M Filaire and E Rosset and O Burlet-Schiltz and A E Heng and D Taillandier},

doi = {0.1002/jcsm.12376},

year  = {2019},

date = {2019-01-29},

journal = {J Cachexia Sarcopenia Muscle},

volume = {10},

number = {2},

pages = {323--337},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{634,

title = {Synthesis and biological evaluation of 2.4 nm thiolate-protected gold nanoparticles conjugated to Cetuximab for targeting glioblastoma cancer cells via the EGFR},

author = {N Groysbeck and A Stoessel and M Donzeau and EC. Silva and M Lehmann and JM. Strub and S Cianferani and K Dembélé and G Zuber},

doi = {10.1088/1361-6528/aaff0a},

year  = {2019},

date = {2019-01-16},

journal = {Nanotechnology},

volume = {30},

number = {18},

pages = {184005.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{627,

title = {Recurrent activating mutations of PPARγ associated with luminal bladder tumors},

author = {N Rochel and C Krucker and L Coutos-Thévenot and J Osz and R Zhang and E Guyon and W Zita and S Vanthong and O Hernandez-Alba and M Bourguet and K Al Badawy and F Dufour and C Peluso-Iltis and S Heckler-Beji and A Dejaegere and A Kamoun and A Reyniès and Y Neuzillet and S Rebouissou and C Béraud and H Lang and T Massfelder and Y Allory and S Cianférani and R H Stote and F Radvanyi and I Bernard-Pierrot},

doi = {10.1038/s41467-018-08157-y},

year  = {2019},

date = {2019-01-16},

journal = {Nature Communications},

volume = {10},

number = {1},

pages = {253},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{636,

title = {Cytosolic Isocitrate Dehydrogenase from Arabidopsis thaliana Is Regulated by Glutathionylation},

author = {AK. Niazi and L Bariat and C Riondet and C Carapito and A Mhamdi and G Noctor and JP. Reichheld},

doi = {10.3390/antiox8010016},

year  = {2019},

date = {2019-01-08},

journal = {Antioxidants (Basel)},

volume = {8},

number = {1},

pages = {pii: E16.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{desroches-castan_bone_2019,

title = {Bone Morphogenetic Protein 9 Is a Paracrine Factor Controlling Liver Sinusoidal Endothelial Cell Fenestration and Protecting Against Hepatic Fibrosis},

author = {Agnès Desroches-Castan and Emmanuelle Tillet and Nicolas Ricard and Marie Ouarné and Christine Mallet and Lucid Belmudes and Yohann Couté and Olivier Boillot and Jean-Yves Scoazec and Sabine Bailly and Jean-Jacques Feige},

doi = {10.1002/hep.30655},

issn = {1527-3350},

year  = {2019},

date = {2019-01-01},

journal = {Hepatology (Baltimore, Md.)},

volume = {70},

number = {4},

pages = {1392--1408},

abstract = {Bone morphogenetic protein 9 (BMP9) is a circulating factor produced by hepatic stellate cells that plays a critical role in vascular quiescence through its endothelial receptor activin receptor-like kinase 1 (ALK1). Mutations in the gene encoding ALK1 cause hereditary hemorrhagic telangiectasia type 2, a rare genetic disease presenting hepatic vessel malformations. Variations of both the circulating levels and the hepatic mRNA levels of BMP9 have been recently associated with various forms of hepatic fibrosis. However, the molecular mechanism that links BMP9 with liver diseases is still unknown. Here, we report that Bmp9 gene deletion in 129/Ola mice triggers hepatic perisinusoidal fibrosis that was detectable from 15 weeks of age. An inflammatory response appeared within the same time frame as fibrosis, whereas sinusoidal vessel dilation developed later on. Proteomic and mRNA analyses of primary liver sinusoidal endothelial cells (LSECs) both revealed that the expression of the LSEC-specifying transcription factor GATA-binding protein 4 was strongly reduced in Bmp9 gene knockout (Bmp9-KO) mice as compared with wild-type mice. LSECs from Bmp9-KO mice also lost the expression of several terminal differentiation markers (Lyve1, Stab1, Stab2, Ehd3, Cd209b, eNos, Maf, Plvap). They gained CD34 expression and deposited a basal lamina, indicating that they were capillarized. Another main characteristic of differentiated LSECs is the presence of permeable fenestrae. LSECs from Bmp9-KO mice had a significantly reduced number of fenestrae. This was already observable in 2-week-old pups. Moreover, we could show that addition of BMP9 to primary cultures of LSECs prevented the loss of their fenestrae and maintained the expression levels of Gata4 and Plvap. Conclusion: Taken together, our observations show that BMP9 is a key paracrine regulator of liver homeostasis, controlling LSEC fenestration and protecting against perivascular hepatic fibrosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{azevedo_uap56_2019,

title = {UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis},

author = {Jacinthe Azevedo and Claire Picart and Laurent Dureau and Dominique Pontier and Sylvie Jaquinod-Kieffer and Mohamed-Ali Hakimi and Thierry Lagrange},

doi = {10.1002/2211-5463.12627},

issn = {2211-5463},

year  = {2019},

date = {2019-01-01},

journal = {FEBS open bio},

volume = {9},

number = {5},

pages = {973--985},

abstract = {Repeated sequence expression and transposable element mobilization are tightly controlled by multilayer processes, which include DNA 5'-cytosine methylation. The RNA-directed DNA methylation (RdDM) pathway, which uses siRNAs to guide sequence-specific directed DNA methylation, emerged specifically in plants. RdDM ensures DNA methylation maintenance on asymmetric CHH sites and specifically initiates de novo methylation in all cytosine sequence contexts through the action of DRM DNA methyltransferases, of which DRM2 is the most prominent. The RdDM pathway has been well described, but how DRM2 is recruited onto DNA targets and associates with other RdDM factors remains unknown. To address these questions, we developed biochemical approaches to allow the identification of factors that may escape genetic screens, such as proteins encoded by multigenic families. Through both conventional and affinity purification of DRM2, we identified DEAD box RNA helicases U2AF56 Associated Protein 56 (UAP56a/b), which are widespread among eukaryotes, as new DRM2 partners. We have shown that, similar to DRM2 and other RdDM actors, UAP56 has chromatin-associated protein properties. We confirmed this association both in vitro and in vivo in reproductive tissues. In addition, our experiments also suggest that UAP56 may exhibit differential distribution in cells depending on plant organ. While originally identified for its role in splicing, our study suggests that UAP56 may also have other roles, and our findings allow us to initiate discussion about its potential role in the RdDM pathway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vandenbrouck_bioinformatics_2019,

title = {Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer},

author = {Yves Vandenbrouck and David Christiany and Florence Combes and Valentin Loux and Virginie Brun},

doi = {10.1002/pmic.201800489},

issn = {1615-9861},

year  = {2019},

date = {2019-01-01},

journal = {Proteomics},

volume = {19},

number = {21-22},

pages = {e1800489},

abstract = {Secretome proteomics for the discovery of cancer biomarkers holds great potential to improve early cancer diagnosis. A knowledge-based approach relying on mechanistic criteria related to the type of cancer should help to identify candidates from available "omics" information. With the aim of accelerating the discovery process for novel biomarkers, a set of tools is developed and made available via a Galaxy-based instance to assist end-users biologists. These implemented tools proceed by a step-by-step strategy to mine transcriptomics and proteomics databases for information relating to tissue specificity, allow the selection of proteins that are part of the secretome, and combine this information with proteomics datasets to rank the most promising candidate biomarkers for early cancer diagnosis. Using pancreatic cancer as a case study, this strategy produces a list of 24 candidate biomarkers suitable for experimental assessment by MS-based proteomics. Among these proteins, three (SYCN, REG1B, and PRSS2) were previously reported as circulating candidate biomarkers of pancreatic cancer. Here, further refinement of this list allows to prioritize 14 candidate biomarkers along with their associated proteotypic peptides for further investigation, using targeted MS-based proteomics. The bioinformatics tools and the workflow implementing this strategy for the selection of candidate biomarkers are freely accessible at http://www.proteore.org.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{guillot_peptimapper:_2019,

title = {Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes},

author = {Laetitia Guillot and Ludovic Delage and Alain Viari and Yves Vandenbrouck and Emmanuelle Com and Andrés Ritter and Régis Lavigne and Dominique Marie and Pierre Peterlongo and Philippe Potin and Charles Pineau},

doi = {10.1186/s12864-019-5431-9},

issn = {1471-2164},

year  = {2019},

date = {2019-01-01},

journal = {BMC genomics},

volume = {20},

number = {1},

pages = {56},

abstract = {BACKGROUND: Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. 

RESULTS: Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. 

CONCLUSIONS: Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu . Data are available via ProteomeXchange under identifier PXD010618.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{legendre_pandoravirus_2019,

title = {Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes},

author = {Matthieu Legendre and Jean-Marie Alempic and Nadège Philippe and Audrey Lartigue and Sandra Jeudy and Olivier Poirot and Ngan Thi Ta and Sébastien Nin and Yohann Couté and Chantal Abergel and Jean-Michel Claverie},

doi = {10.3389/fmicb.2019.00430},

issn = {1664-302X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Microbiology},

volume = {10},

pages = {430},

abstract = {With genomes of up to 2.7 Mb propagated in $mu$m-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including three others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, pandoravirus celtis, closely related (96% identical genome) to the previously described p. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs, with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in p. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{do_trim9_2019,

title = {TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration},

author = {Le Duy Do and Stephanie L Gupton and Kunikazu Tanji and Joubert Bastien and Sabine Brugière and Yohann Couté and Isabelle Quadrio and Veronique Rogemond and Nicole Fabien and Virginie Desestret and Jerome Honnorat},

doi = {10.1007/s12311-018-0987-5},

issn = {1473-4230},

year  = {2019},

date = {2019-01-01},

journal = {Cerebellum (London, England)},

volume = {18},

number = {2},

pages = {245--254},

abstract = {To describe autoantibodies (Abs) against tripartite motif-containing (TRIM) protein 9 and 67 in two patients with paraneoplastic cerebellar degeneration (PCD) associated with lung adenocarcinoma. Abs were characterized using immunohistochemistry, Western blotting, cultures of murine cortical, and hippocampal neurons, immunoprecipitation, mass spectrometry, knockout mice for Trim9 and 67, and cell-based assay. Control samples included sera from 63 patients with small cell lung cancer without any paraneoplastic neurological syndrome, 36 patients with lung adenocarcinoma and PNS, CSF from 100 patients with autoimmune encephalitis, and CSF from 165 patients with neurodegenerative diseases. We found Abs targeting TRIM9 and TRIM67 at high concentration in the serum and the cerebrospinal fluid (CSF) of a 78-year-old woman and a 65-year-old man. Both developed subacute severe cerebellar ataxia. Brain magnetic resonance imaging found no abnormality and no cerebellar atrophy. Both had CSF inflammation with mild pleiocytosis and a few oligoclonal bands. We identified a pulmonary adenocarcinoma, confirming the paraneoplastic neurological syndrome in both patients. They received immunomodulatory and cancer treatments without improvement of cerebellar ataxia, even though both were in remission of their cancer (for more than 10 years in one patient). Anti-TRIM9 and anti-TRIM67 Abs were specific to these two patients. All control serum and CSF samples tested were negative for anti-TRIM9 and 67. Anti-TRIM9 and anti-TRIM67 Abs appeared to be specific biomarkers of PCD and should be added to the panel of antigens tested when this is suspected.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wieczorek_five_2019,

title = {Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses},

author = {Samuel Wieczorek and Quentin Giai Gianetto and Thomas Burger},

url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391919302131},

doi = {10.1016/j.jprot.2019.103441},

issn = {18743919},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Proteomics},

volume = {207},

pages = {103441},

abstract = {Results from mass spectrometry based quantitative proteomics analysis correspond to a subset of proteins which are considered differentially abundant relative to a control. Their selection is delicate and often requires some statistical expertise in addition to a refined knowledge of the experimental data. To facilitate the selection process, we have considered differential analysis as a five-step process, and here we present the practical aspects of the different steps. Prostar software is used throughout this article for illustration, but the general methodology is applicable with many other tools. By applying the approach detailed here, researchers who may be less familiar with statistical considerations can be more confident in the results they present.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wei_ribosomal_2019,

title = {Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance},

author = {Jiajie Wei and Rigel J Kishton and Matthew Angel and Crystal S Conn and Nicole Dalla-Venezia and Virginie Marcel and Anne Vincent and Frédéric Catez and Sabrina Ferré and Lilia Ayadi and Virginie Marchand and Devin Dersh and James S Gibbs and Ivaylo P Ivanov and Nathan Fridlyand and Yohann Couté and Jean-Jacques Diaz and Shu-Bing Qian and Louis M Staudt and Nicholas P Restifo and Jonathan W Yewdell},

doi = {10.1016/j.molcel.2018.12.020},

issn = {1097-4164},

year  = {2019},

date = {2019-01-01},

journal = {Molecular Cell},

abstract = {The MHC class I antigen presentation system enables T cell immunosurveillance of cancers and viruses. A substantial fraction of the immunopeptidome derives from rapidly degraded nascent polypeptides (DRiPs). By knocking down each of the 80 ribosomal proteins, we identified proteins that modulate peptide generation without altering source protein expression. We show that 60S ribosomal proteins L6 (RPL6) and RPL28, which are adjacent on the ribosome, play opposite roles in generating an influenza A virus-encoded peptide. Depleting RPL6 decreases ubiquitin-dependent peptide presentation, whereas depleting RPL28 increases ubiquitin-dependent and -independent peptide presentation. 40S ribosomal protein S28 (RPS28) knockdown increases total peptide supply in uninfected cells by increasing DRiP synthesis from non-canonical translation of "untranslated" regions and non-AUG start codons and sensitizes tumor cells for T cell targeting. Our findings raise the possibility of modulating immunosurveillance by pharmaceutical targeting ribosomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kraut_protein_2019,

title = {Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry},

author = {Alexandra Kraut and Mathilde Louwagie and Christophe Bruley and Christophe Masselon and Yohann Couté and Virginie Brun and Anne-Marie Hesse},

doi = {10.1007/978-1-4939-9164-8_9},

issn = {1940-6029},

year  = {2019},

date = {2019-01-01},

journal = {Methods in Molecular Biology (Clifton, N.J.)},

volume = {1959},

pages = {129--150},

abstract = {In discovery proteomics experiments, tandem mass spectrometry and data-dependent acquisition (DDA) are classically used to identify and quantify peptides and proteins through database searching. This strategy suffers from known limitations such as under-sampling and lack of reproducibility of precursor ion selection in complex proteomics samples, leading to somewhat inconsistent analytical results across large datasets. Data-independent acquisition (DIA) based on fragmentation of all the precursors detected in predetermined isolation windows can potentially overcome this limitation. DIA promises reproducible peptide and protein quantification with deeper proteome coverage and fewer missing values than DDA strategies. This approach is particularly attractive in the field of clinical biomarker discovery, where large numbers of samples must be analyzed. Here, we describe a DIA workflow for non-depleted serum analysis including a straightforward approach through which to construct a dedicated spectral library, and indications on how to optimize chromatographic and mass spectrometry analytical methods to produce high-quality DIA data and results.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}