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Items: 30

1.

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

Soste M, Charmpi K, Lampert F, Gerez JA, van Oostrum M, Malinovska L, Boersema PJ, Prymaczok NC, Riek R, Peter M, Vanni S, Beyer A, Picotti P.

Cell Syst. 2019 Sep 11. pii: S2405-4712(19)30267-4. doi: 10.1016/j.cels.2019.07.010. [Epub ahead of print]

2.

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

Gerez JA, Prymaczok NC, Rockenstein E, Herrmann US, Schwarz P, Adame A, Enchev RI, Courtheoux T, Boersema PJ, Riek R, Peter M, Aguzzi A, Masliah E, Picotti P.

Sci Transl Med. 2019 Jun 5;11(495). pii: eaau6722. doi: 10.1126/scitranslmed.aau6722.

PMID:
31167929
3.

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

Laferrière F, Maniecka Z, Pérez-Berlanga M, Hruska-Plochan M, Gilhespy L, Hock EM, Wagner U, Afroz T, Boersema PJ, Barmettler G, Foti SC, Asi YT, Isaacs AM, Al-Amoudi A, Lewis A, Stahlberg H, Ravits J, De Giorgi F, Ichas F, Bezard E, Picotti P, Lashley T, Polymenidou M.

Nat Neurosci. 2019 Jan;22(1):65-77. doi: 10.1038/s41593-018-0294-y. Epub 2018 Dec 17.

PMID:
30559480
4.

Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date.

Boersema PJ, Melnik A, Hazenberg BPC, Rezeli M, Marko-Varga G, Kamiie J, Portelius E, Blennow K, Zubarev RA, Polymenidou M, Picotti P.

J Proteome Res. 2018 Dec 7;17(12):4072-4084. doi: 10.1021/acs.jproteome.8b00401. Epub 2018 Sep 28.

PMID:
30137990
5.

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

Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M.

J Biol Chem. 2018 Apr 13;293(15):5600-5612. doi: 10.1074/jbc.RA117.001484. Epub 2018 Feb 16.

6.

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells.

Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R.

Nat Commun. 2017 Oct 31;8(1):1212. doi: 10.1038/s41467-017-01422-6.

7.

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

Schopper S, Kahraman A, Leuenberger P, Feng Y, Piazza I, Müller O, Boersema PJ, Picotti P.

Nat Protoc. 2017 Nov;12(11):2391-2410. doi: 10.1038/nprot.2017.100. Epub 2017 Oct 26.

PMID:
29072706
8.

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis.

Hartl M, Füßl M, Boersema PJ, Jost JO, Kramer K, Bakirbas A, Sindlinger J, Plöchinger M, Leister D, Uhrig G, Moorhead GB, Cox J, Salvucci ME, Schwarzer D, Mann M, Finkemeier I.

Mol Syst Biol. 2017 Oct 23;13(10):949. doi: 10.15252/msb.20177819.

9.

Dimethyl-Labeling-Based Quantification of the Lysine Acetylome and Proteome of Plants.

Lassowskat I, Hartl M, Hosp F, Boersema PJ, Mann M, Finkemeier I.

Methods Mol Biol. 2017;1653:65-81. doi: 10.1007/978-1-4939-7225-8_5.

PMID:
28822126
10.

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

Leuenberger P, Ganscha S, Kahraman A, Cappelletti V, Boersema PJ, von Mering C, Claassen M, Picotti P.

Science. 2017 Feb 24;355(6327). pii: eaai7825. doi: 10.1126/science.aai7825.

PMID:
28232526
11.

Proteomics beyond large-scale protein expression analysis.

Boersema PJ, Kahraman A, Picotti P.

Curr Opin Biotechnol. 2015 Aug;34:162-70. doi: 10.1016/j.copbio.2015.01.005. Epub 2015 Jan 28. Review.

PMID:
25636126
12.

Global analysis of protein structural changes in complex proteomes.

Feng Y, De Franceschi G, Kahraman A, Soste M, Melnik A, Boersema PJ, de Laureto PP, Nikolaev Y, Oliveira AP, Picotti P.

Nat Biotechnol. 2014 Oct;32(10):1036-44. doi: 10.1038/nbt.2999. Epub 2014 Sep 14.

PMID:
25218519
13.

The mitochondrial lysine acetylome of Arabidopsis.

König AC, Hartl M, Boersema PJ, Mann M, Finkemeier I.

Mitochondrion. 2014 Nov;19 Pt B:252-60. doi: 10.1016/j.mito.2014.03.004. Epub 2014 Apr 12.

PMID:
24727099
14.

The Arabidopsis class II sirtuin is a lysine deacetylase and interacts with mitochondrial energy metabolism.

König AC, Hartl M, Pham PA, Laxa M, Boersema PJ, Orwat A, Kalitventseva I, Plöchinger M, Braun HP, Leister D, Mann M, Wachter A, Fernie AR, Finkemeier I.

Plant Physiol. 2014 Mar;164(3):1401-14. doi: 10.1104/pp.113.232496. Epub 2014 Jan 14.

15.

Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.

Boersema PJ, Geiger T, Wisniewski JR, Mann M.

Mol Cell Proteomics. 2013 Jan;12(1):158-71. doi: 10.1074/mcp.M112.023614. Epub 2012 Oct 22.

16.

Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex.

Li VS, Ng SS, Boersema PJ, Low TY, Karthaus WR, Gerlach JP, Mohammed S, Heck AJ, Maurice MM, Mahmoudi T, Clevers H.

Cell. 2012 Jun 8;149(6):1245-56. doi: 10.1016/j.cell.2012.05.002.

17.

Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants.

Mithoe SC, Boersema PJ, Berke L, Snel B, Heck AJ, Menke FL.

J Proteome Res. 2012 Jan 1;11(1):438-48. doi: 10.1021/pr200893k. Epub 2011 Dec 1.

PMID:
22074104
18.

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

Boekhorst J, Boersema PJ, Tops BB, van Breukelen B, Heck AJ, Snel B.

PLoS One. 2011;6(8):e23276. doi: 10.1371/journal.pone.0023276. Epub 2011 Aug 10.

19.

Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis.

Di Palma S, Boersema PJ, Heck AJ, Mohammed S.

Anal Chem. 2011 May 1;83(9):3440-7. doi: 10.1021/ac103312e. Epub 2011 Mar 28.

PMID:
21443167
20.

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells.

Ding VM, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJ, Choo A.

PLoS One. 2011 Mar 17;6(3):e17538. doi: 10.1371/journal.pone.0017538.

21.

MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway.

Sue Ng S, Mahmoudi T, Li VS, Hatzis P, Boersema PJ, Mohammed S, Heck AJ, Clevers H.

Biol Chem. 2010 Feb-Mar;391(2-3):171-80. doi: 10.1515/BC.2010.028.

PMID:
20128690
22.

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling.

Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ.

Mol Cell Proteomics. 2010 Jan;9(1):84-99. doi: 10.1074/mcp.M900291-MCP200. Epub 2009 Sep 21.

23.

Effect of chemical modifications on peptide fragmentation behavior upon electron transfer induced dissociation.

Hennrich ML, Boersema PJ, van den Toorn H, Mischerikow N, Heck AJ, Mohammed S.

Anal Chem. 2009 Sep 15;81(18):7814-22. doi: 10.1021/ac901108g.

PMID:
19689115
24.

Phosphopeptide fragmentation and analysis by mass spectrometry.

Boersema PJ, Mohammed S, Heck AJ.

J Mass Spectrom. 2009 Jun;44(6):861-78. doi: 10.1002/jms.1599. Review.

PMID:
19504542
25.

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics.

Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ.

Nat Protoc. 2009;4(4):484-94. doi: 10.1038/nprot.2009.21.

PMID:
19300442
26.

Straightforward and de novo peptide sequencing by MALDI-MS/MS using a Lys-N metalloendopeptidase.

Boersema PJ, Taouatas N, Altelaar AF, Gouw JW, Ross PL, Pappin DJ, Heck AJ, Mohammed S.

Mol Cell Proteomics. 2009 Apr;8(4):650-60. doi: 10.1074/mcp.M800249-MCP200. Epub 2008 Nov 29.

27.

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

Boersema PJ, Aye TT, van Veen TA, Heck AJ, Mohammed S.

Proteomics. 2008 Nov;8(22):4624-32. doi: 10.1002/pmic.200800297.

PMID:
18850632
28.

Hydrophilic interaction liquid chromatography (HILIC) in proteomics.

Boersema PJ, Mohammed S, Heck AJ.

Anal Bioanal Chem. 2008 May;391(1):151-9. doi: 10.1007/s00216-008-1865-7. Epub 2008 Feb 9. Review.

29.

Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy.

Boersema PJ, Divecha N, Heck AJ, Mohammed S.

J Proteome Res. 2007 Mar;6(3):937-46. Epub 2007 Jan 27.

PMID:
17256977
30.

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

Föcking M, Boersema PJ, O'Donoghue N, Lubec G, Pennington SR, Cotter DR, Dunn MJ.

Proteomics. 2006 Sep;6(18):4914-31.

PMID:
16927420

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