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1

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

Leuenberger, Pascal, Ganscha, Stefan, Kahraman, Abdullah, Cappelletti, Valentina, Boersema, Paul J., von Mering, Christian, Claassen, Manfred, Picotti, Paola

Journal:

Year:

2017

Language:

english

File:

PDF, 2.53 MB

english, 2017

2

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

Boersema, Paul J, Raijmakers, Reinout, Lemeer, Simone, Mohammed, Shabaz, Heck, Albert J R

Journal:

Nature Protocols

Year:

2009

Language:

english

File:

PDF, 618 KB

english, 2009

3

The mitochondrial lysine acetylome of Arabidopsis

König, Ann-Christine, Hartl, Markus, Boersema, Paul J., Mann, Matthias, Finkemeier, Iris

Journal:

Year:

2014

Language:

english

File:

PDF, 1.09 MB

english, 2014

4

Global analysis of protein structural changes in complex proteomes

Feng, Yuehan, De Franceschi, Giorgia, Kahraman, Abdullah, Soste, Martin, Melnik, Andre, Boersema, Paul J, de Laureto, Patrizia Polverino, Nikolaev, Yaroslav, Oliveira, Ana Paula, Picotti, Paola

Journal:

Nature Biotechnology

Year:

2014

Language:

english

File:

PDF, 2.72 MB

english, 2014

5

Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides

Bergmann, Timothy J, Fregno, Ilaria, Fumagalli, Fiorenza, Rinaldi, Andrea, Bertoni, Francesco, Boersema, Paul J, Picotti, Paola, Molinari, Maurizio

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 1.27 MB

english, 2018

6

ChemInform Abstract: Phosphopeptide Fragmentation and Analysis by Mass Spectrometry

Paul J. Boersema, Shabaz Mohammed, Albert J. R. Heck

Journal:

Year:

2010

File:

PDF, 15 KB

2010

7

Phosphopeptide fragmentation and analysis by mass spectrometry

Paul J. Boersema, Shabaz Mohammed, Albert J. R. Heck

Journal:

Journal of Mass Spectrometry

Year:

2009

Language:

english

File:

PDF, 358 KB

english, 2009

8

2-D DIGE as a quantitative tool for investigating the HUPO Brain Proteome Project mouse series

Melanie Föcking, Paul J. Boersema, Niaobh O'Donoghue, Gert Lubec, Stephen R. Pennington, David R. Cotter, Michael J. Dunn

Journal:

Year:

2006

Language:

english

File:

PDF, 377 KB

english, 2006

9

Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates

Paul J. Boersema, Thin Thin Aye, Toon A. B. van Veen, Albert J. R. Heck, Shabaz Mohammed

Journal:

Year:

2008

Language:

english

File:

PDF, 457 KB

english, 2008

10

Hydrophilic interaction liquid chromatography (HILIC) in proteomics

Paul J. Boersema, Shabaz Mohammed, Albert J. R. Heck

Journal:

Analytical and Bioanalytical Chemistry

Year:

2008

Language:

english

File:

PDF, 250 KB

english, 2008

11

Evaluation and Optimization of ZIC-HILIC-RP as an Alternative MudPIT Strategy

Boersema, Paul J., Divecha, Nullin, Heck, Albert J. R., Mohammed, Shabaz

Journal:

Journal of Proteome Research

Year:

2007

Language:

english

File:

PDF, 275 KB

english, 2007

12

Wnt Signaling through Inhibition of β-Catenin Degradation in an Intact Axin1 Complex

Vivian S.W. Li, Ser Sue Ng, Paul J. Boersema, Teck Y. Low, Wouter R. Karthaus, Jan P. Gerlach, Shabaz Mohammed, Albert J.R. Heck, Madelon M. Maurice, Tokameh Mahmoudi, Hans Clevers

Journal:

Year:

2012

Language:

english

File:

PDF, 1.20 MB

english, 2012

13

Targeted Quantitative Phosphoproteomics Approach for the Detection of Phospho-tyrosine Signaling in Plants

Mithoe, Sharon C., Boersema, Paul J., Berke, Lidija, Snel, Berend, Heck, Albert J. R., Menke, Frank L. H.

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 910 KB

english, 2012

14

Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC and ZIC-cHILIC) Provide High Resolution Separation and Increase Sensitivity in Proteome Analysis

Di Palma, Serena, Boersema, Paul J., Heck, Albert J. R., Mohammed, Shabaz

Journal:

Analytical Chemistry

Year:

2011

Language:

english

File:

PDF, 1.92 MB

english, 2011

15

Effect of Chemical Modifications on Peptide Fragmentation Behavior upon Electron Transfer Induced Dissociation

Hennrich, Marco L., Boersema, Paul J., van den Toorn, Henk, Mischerikow, Nikolai, Heck, Albert J. R., Mohammed, Shabaz

Journal:

Analytical Chemistry

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

16

A sentinel protein assay for simultaneously quantifying cellular processes

Soste, Martin, Hrabakova, Rita, Wanka, Stefanie, Melnik, Andre, Boersema, Paul, Maiolica, Alessio, Wernas, Timon, Tognetti, Marco, von Mering, Christian, Picotti, Paola

Journal:

Year:

2014

Language:

english

File:

PDF, 548 KB

english, 2014

17

Colorectal Anastomotic Leakage Caused by Insufficient Suturing after Partial Colectomy: A New Experimental Model

Wu, Zhouqiao, Daams, Freek, Boersema, Geesien S.A., Vakalopoulos, Konstantinos A., Lam, King H., van der Horst, Paul H., Kleinrensink, Gert-Jan, Jeekel, Johannes, Lange, Johan F.

Journal:

Surgical Infections

Year:

2014

Language:

english

File:

PDF, 392 KB

english, 2014

18

Proteomics beyond large-scale protein expression analysis

Boersema, Paul J, Kahraman, Abdullah, Picotti, Paola

Journal:

Current Opinion in Biotechnology

Year:

2015

Language:

english

File:

PDF, 2.13 MB

english, 2015

19

The prevention of colorectal anastomotic leakage with tissue adhesives in a contaminated environment is associated with the presence of anti-inflammatory macrophages

Wu, Zhouqiao, Vakalopoulos, Konstantinos A., Boersema, Geesien S. A., Kroese, Leonard F., Lam, King H., van der Horst, Paul H., Mulder, Irene M., M. Bastiaansen-Jenniskens, Yvonne, Kleinrensink, Gert-

Journal:

International Journal of Colorectal Disease

Year:

2014

Language:

english

File:

PDF, 441 KB

english, 2014

20

MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway

Sue Ng, Ser, Mahmoudi, Tokameh, Li, Vivian S.W., Hatzis, Pantelis, Boersema, Paul J., Mohammed, Shabaz, Heck, Albert J., Clevers, Hans

Journal:

Biological Chemistry

Year:

2010

Language:

english

File:

PDF, 459 KB

english, 2010

21

Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry

Schopper, Simone, Kahraman, Abdullah, Leuenberger, Pascal, Feng, Yuehan, Piazza, Ilaria, Müller, Oliver, Boersema, Paul J, Picotti, Paola

Journal:

Nature Protocols

Year:

2017

Language:

english

File:

PDF, 2.25 MB

english, 2017

22

Mitotic Disassembly of Nuclear Pore Complexes Involves CDK1- and PLK1-Mediated Phosphorylation of Key Interconnecting Nucleoporins

Linder, Monika I., Köhler, Mario, Boersema, Paul, Weberruss, Marion, Wandke, Cornelia, Marino, Joseph, Ashiono, Caroline, Picotti, Paola, Antonin, Wolfram, Kutay, Ulrike

Journal:

Developmental Cell

Year:

2017

Language:

english

File:

PDF, 5.75 MB

english, 2017

23

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

Hartl, Markus, Füßl, Magdalena, Boersema, Paul J, Jost, Jan‐Oliver, Kramer, Katharina, Bakirbas, Ahmet, Sindlinger, Julia, Plöchinger, Magdalena, Leister, Dario, Uhrig, Glen, Moorhead, Greg BG, Cox, J

Journal:

Molecular Systems Biology

Year:

2017

Language:

english

File:

PDF, 3.23 MB

english, 2017

24

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

Liu, Yansheng, Borel, Christelle, Li, Li, Müller, Torsten, Williams, Evan G., Germain, Pierre-Luc, Buljan, Marija, Sajic, Tatjana, Boersema, Paul J., Shao, Wenguang, Faini, Marco, Testa, Giuseppe, Bey

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 1.85 MB

english, 2017

25

Tyrosine Phosphorylation Profiling in FGF-2 Stimulated Human Embryonic Stem Cells

Ding, Vanessa M. Y., Boersema, Paul J., Foong, Leong Yan, Preisinger, Christian, Koh, Geoffrey, Natarajan, Subaashini, Lee, Dong-Yup, Boekhorst, Jos, Snel, Berend, Lemeer, Simone, Heck, Albert J. R.,

Journal:

Year:

2011

Language:

english

File:

PDF, 1.15 MB

english, 2011

26

Evaluating Experimental Bias and Completeness in Comparative Phosphoproteomics Analysis

Boekhorst, Jos, Boersema, Paul J., Tops, Bastiaan B. J., van Breukelen, Bas, Heck, Albert J. R., Snel, Berend, Pant, Harish

Journal:

Year:

2011

Language:

english

File:

PDF, 259 KB

english, 2011

27

The Biology and Disease-driven Initiative on Protein Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date

Boersema, Paul J., Melnik, Andre, Hazenberg, Bouke P.C., Rezeli, Melinda, Marko-Varga, György, Kamiie, Junichi, Portelius, Erik, Blennow, Kaj, Zubarev, Roman A., Polymenidou, Magdalini, Picotti, Paola

Journal:

Journal of Proteome Research

Year:

2018

File:

PDF, 666 KB

2018

28

The Biology and Disease-driven Initiative on Protein Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date

Boersema, Paul J., Melnik, Andre, Hazenberg, Bouke P.C., Rezeli, Melinda, Marko-Varga, György, Kamiie, Junichi, Portelius, Erik, Blennow, Kaj, Zubarev, Roman A., Polymenidou, Magdalini, Picotti, Paola

Journal:

Journal of Proteome Research

Year:

2018

Language:

english

File:

PDF, 666 KB

english, 2018

29

Phosphorylation of nuclear Tau is modulated by distinct cellular pathways

Ulrich, Giorgio, Salvadè, Agnese, Boersema, Paul, Calì, Tito, Foglieni, Chiara, Sola, Martina, Picotti, Paola, Papin, Stéphanie, Paganetti, Paolo

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.18 MB

english, 2018

30

TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies and neurotoxic effects reflecting disease progression rates

Laferrière, Florent, Maniecka, Zuzanna, Pérez-Berlanga, Manuela, Hruska-Plochan, Marian, Gilhespy, Larissa, Hock, Eva-Maria, Wagner, Ulrich, Afroz, Tariq, Boersema, Paul J., Barmettler, Gery, Foti, Sa

Journal:

Nature Neuroscience

Year:

2019

Language:

english

File:

PDF, 4.60 MB

english, 2019

31

A cullin-RING ubiquitin ligase targets exogenous α-synuclein and inhibits Lewy body–like pathology

Gerez, Juan A., Prymaczok, Natalia C., Rockenstein, Edward, Herrmann, Uli S., Schwarz, Petra, Adame, Anthony, Enchev, Radoslav I., Courtheoux, Thibault, Boersema, Paul J., Riek, Roland, Peter, Matthia

Journal:

Science Translational Medicine

Year:

2019

Language:

english

File:

PDF, 2.25 MB

english, 2019

32

Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity

Soste, Martin, Charmpi, Konstantina, Lampert, Fabienne, Gerez, Juan Atilio, van Oostrum, Marc, Malinovska, Liliana, Boersema, Paul Jonathan, Prymaczok, Natalia Cecilia, Riek, Roland, Peter, Matthias,

Journal:

Year:

2019

Language:

english

File:

PDF, 3.38 MB

english, 2019

33

Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity

Soste, Martin, Charmpi, Konstantina, Lampert, Fabienne, Gerez, Juan Atilio, van Oostrum, Marc, Malinovska, Liliana, Boersema, Paul Jonathan, Prymaczok, Natalia Cecilia, Riek, Roland, Peter, Matthias,

Journal:

Year:

2019

File:

PDF, 3.38 MB

2019

34

Transcriptomic characterization of culture-associated changes in murine and human precision-cut tissue slices

Bigaeva, Emilia, Gore, Emilia, Simon, Eric, Zwick, Matthias, Oldenburger, Anouk, de Jong, Koert P., Hofker, Hendrik S., Schlepütz, Marco, Nicklin, Paul, Boersema, Miriam, Rippmann, Jörg F., Olinga, Pe

Journal:

Archives of Toxicology

Year:

2019

Language:

english

File:

PDF, 4.18 MB

english, 2019

35

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

Cappelletti, Valentina, Hauser, Thomas, Piazza, Ilaria, Pepelnjak, Monika, Malinovska, Liliana, Fuhrer, Tobias, Li, Yaozong, DÃ¶rig, Christian, Boersema, Paul, Gillet, Ludovic, Grossbach, Jan, Dugourd

Journal:

Year:

2020

File:

PDF, 8.74 MB

2020