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Dedicated Software Enhancing Data-independent Acquisition Methods in Mass Spectrometry.

Bilbao A, Lisacek F, Hopfgartner G.

Chimia (Aarau). 2016;70(4):293. doi: 10.2533/chimia.2016.293. No abstract available.


Comparative Proteomic Profiling of Ehrlichia ruminantium Pathogenic Strain and Its High-Passaged Attenuated Strain Reveals Virulence and Attenuation-Associated Proteins.

Marcelino I, Ventosa M, Pires E, Müller M, Lisacek F, Lefrançois T, Vachiery N, Coelho AV.

PLoS One. 2015 Dec 21;10(12):e0145328. doi: 10.1371/journal.pone.0145328. eCollection 2015.


Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search.

Alocci D, Mariethoz J, Horlacher O, Bolleman JT, Campbell MP, Lisacek F.

PLoS One. 2015 Dec 14;10(12):e0144578. doi: 10.1371/journal.pone.0144578. eCollection 2015.


Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries.

Horlacher O, Lisacek F, Müller M.

J Proteome Res. 2016 Mar 4;15(3):721-31. doi: 10.1021/acs.jproteome.5b00877. Epub 2015 Dec 31.


SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

Mariethoz J, Khatib K, Alocci D, Campbell MP, Karlsson NG, Packer NH, Mullen EH, Lisacek F.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1243-50. doi: 10.1093/nar/gkv1247. Epub 2015 Nov 17.


Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.

Bilbao A, Zhang Y, Varesio E, Luban J, Strambio-De-Castillia C, Lisacek F, Hopfgartner G.

J Proteome Res. 2015 Nov 6;14(11):4581-93. doi: 10.1021/acs.jproteome.5b00394. Epub 2015 Oct 14.


The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition.

Zhang Y, Bilbao A, Bruderer T, Luban J, Strambio-De-Castillia C, Lisacek F, Hopfgartner G, Varesio E.

J Proteome Res. 2015 Oct 2;14(10):4359-71. doi: 10.1021/acs.jproteome.5b00543. Epub 2015 Sep 3.


MzJava: An open source library for mass spectrometry data processing.

Horlacher O, Nikitin F, Alocci D, Mariethoz J, Müller M, Lisacek F.

J Proteomics. 2015 Nov 3;129:63-70. doi: 10.1016/j.jprot.2015.06.013. Epub 2015 Jun 30.


Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies.

Zhang Y, Bottinelli D, Lisacek F, Luban J, Strambio-De-Castillia C, Varesio E, Hopfgartner G.

Anal Biochem. 2015 Sep 1;484:40-50. doi: 10.1016/j.ab.2015.05.007. Epub 2015 May 15.


Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding.

Zhang Y, Muller M, Xu B, Yoshida Y, Horlacher O, Nikitin F, Garessus S, Magdeldin S, Kinoshita N, Fujinaka H, Yaoita E, Hasegawa M, Lisacek F, Yamamoto T.

Proteomics. 2015 Aug;15(15):2568-79. doi: 10.1002/pmic.201400454. Epub 2015 May 3.


Uncovering intense protein diversification in a cone snail venom gland using an integrative venomics approach.

Biass D, Violette A, Hulo N, Lisacek F, Favreau P, Stöcklin R.

J Proteome Res. 2015 Feb 6;14(2):628-38. doi: 10.1021/pr500583u. Epub 2015 Jan 22.


Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.

Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V.

BMC Genomics. 2014;15 Suppl 9:S1. doi: 10.1186/1471-2164-15-S9-S1. Epub 2014 Dec 8.


Processing strategies and software solutions for data-independent acquisition in mass spectrometry.

Bilbao A, Varesio E, Luban J, Strambio-De-Castillia C, Hopfgartner G, Müller M, Lisacek F.

Proteomics. 2015 Mar;15(5-6):964-80. doi: 10.1002/pmic.201400323. Epub 2015 Feb 2. Review.


Animal board invited review: advances in proteomics for animal and food sciences.

Almeida AM, Bassols A, Bendixen E, Bhide M, Ceciliani F, Cristobal S, Eckersall PD, Hollung K, Lisacek F, Mazzucchelli G, McLaughlin M, Miller I, Nally JE, Plowman J, Renaut J, Rodrigues P, Roncada P, Staric J, Turk R.

Animal. 2015 Jan;9(1):1-17. doi: 10.1017/S1751731114002602. Epub 2014 Oct 31. Review.


GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination.

Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F.

Bioinformatics. 2014 Nov 1;30(21):3131-3. doi: 10.1093/bioinformatics/btu425. Epub 2014 Jul 10.


Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.


NETTAB 2012 on "Integrated Bio-Search".

Romano P, Lisacek F, Masseroli M.

BMC Bioinformatics. 2014;15 Suppl 1:S1. doi: 10.1186/1471-2105-15-S1-S1. Epub 2014 Jan 10.


Toolboxes for a standardised and systematic study of glycans.

Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F.

BMC Bioinformatics. 2014;15 Suppl 1:S9. doi: 10.1186/1471-2105-15-S1-S9. Epub 2014 Jan 10.


Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information.

Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Rechenmann F, Lisacek F, Romano P.

BMC Bioinformatics. 2014;15 Suppl 1:S2. doi: 10.1186/1471-2105-15-S1-S2. Epub 2014 Jan 10. Review.


UniCarbKB: building a knowledge platform for glycoproteomics.

Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D215-21. doi: 10.1093/nar/gkt1128. Epub 2013 Nov 13.

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