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Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling. Russell MR, Lilley KS. J Proteomics. 2012 

Popular computational methods to assess multi-protein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Armean IM, Lilley KS, Trotter MW. Mol Cell Proteomics. 2012 

Putative glycosyltransferases and other plant golgi apparatus proteins are revealed by LOPIT proteomics. Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Plant Physiol. 2012 

MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. Fan J, Mohareb F, Bond NJ, Lilley KS, Bessant C. OMICS 2012 

Isobaric tagging approaches in quantitative proteomics: the ups and downs. Christoforou AL, Lilley KS. Anal Bioanal Chem. 2012 

Evaluation and properties of the budding yeast phosphoproteome. Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Mol Cell Proteomics. 2012 

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Gatto L, Lilley KS Bioinformatics. 2012 Jan 15;28(2):288-9. Epub 2011 Nov 22.