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Items: 20


A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.


Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing.

Gillet LC, Leitner A, Aebersold R.

Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):449-72. doi: 10.1146/annurev-anchem-071015-041535. Epub 2016 Mar 30. Review.


An open-source computational and data resource to analyze digital maps of immunopeptidomes.

Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R.

Elife. 2015 Jul 8;4. doi: 10.7554/eLife.07661.


Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.

Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R.

Cell Host Microbe. 2015 Jul 8;18(1):96-108. doi: 10.1016/j.chom.2015.06.001. Epub 2015 Jun 18.


Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.

Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R.

Nat Med. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. Epub 2015 Mar 2.


Building high-quality assay libraries for targeted analysis of SWATH MS data.

Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R.

Nat Protoc. 2015 Mar;10(3):426-41. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12.


Quantitative variability of 342 plasma proteins in a human twin population.

Liu Y, Buil A, Collins BC, Gillet LC, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R.

Mol Syst Biol. 2015 Feb 4;11(1):786. doi: 10.15252/msb.20145728.


Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.

Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R.

Mol Cell Proteomics. 2015 Mar;14(3):739-49. doi: 10.1074/mcp.M113.035550. Epub 2015 Jan 5.


Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.

Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R.

Mol Syst Biol. 2014 Dec 9;10:767. doi: 10.15252/msb.20145112.


Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness.

Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R.

Mol Cell Proteomics. 2014 Jul;13(7):1753-68. doi: 10.1074/mcp.M114.038273. Epub 2014 Apr 16.


Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics.

Toprak UH, Gillet LC, Maiolica A, Navarro P, Leitner A, Aebersold R.

Mol Cell Proteomics. 2014 Aug;13(8):2056-71. doi: 10.1074/mcp.O113.036475. Epub 2014 Mar 12.


Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.

Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R.

Nat Methods. 2013 Dec;10(12):1246-53. doi: 10.1038/nmeth.2703. Epub 2013 Oct 27.


Virulence factors of Candida albicans isolates from the oral cavities of HIV-1-positive patients.

Menezes TO, Gillet LC, Menezes SA, Feitosa RN, Ishak MO, Ishak R, Marques-da-Silva SH, Vallinoto AC.

Curr HIV Res. 2013 Jun;11(4):304-8.


Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS.

Liu Y, Hüttenhain R, Surinova S, Gillet LC, Mouritsen J, Brunner R, Navarro P, Aebersold R.

Proteomics. 2013 Apr;13(8):1247-56. doi: 10.1002/pmic.201200417. Epub 2013 Mar 11.


Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.

Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. doi: 10.1074/mcp.O111.016717. Epub 2012 Jan 18.


In-cell selectivity profiling of serine protease inhibitors by activity-based proteomics.

Gillet LC, Namoto K, Ruchti A, Hoving S, Boesch D, Inverardi B, Mueller D, Coulot M, Schindler P, Schweigler P, Bernardi A, Gil-Parrado S.

Mol Cell Proteomics. 2008 Jul;7(7):1241-53. doi: 10.1074/mcp.M700505-MCP200. Epub 2008 Mar 24.


Crosslinking of the NER damage recognition proteins XPC-HR23B, XPA and RPA to photoreactive probes that mimic DNA damages.

Maltseva EA, Rechkunova NI, Gillet LC, Petruseva IO, Schärer OD, Lavrik OI.

Biochim Biophys Acta. 2007 May;1770(5):781-9. Epub 2007 Jan 25.


Molecular mechanisms of mammalian global genome nucleotide excision repair.

Gillet LC, Schärer OD.

Chem Rev. 2006 Feb;106(2):253-76. Review. No abstract available.


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