Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra. by de Graaf, E, Altelaar, A, van Breukelen, B, Mohammed, S, Heck, A

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. by Cappadona, S, Muñoz, J, Spee, W, Low, T, Mohammed, S, van Breukelen, B, Heck, A

LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation. by van Breukelen, B, Georgiou, A, Drugan, M, Taouatas, N, Mohammed, S, Heck, A

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. by Pinkse, M, Mohammed, S, Gouw, J, van Breukelen, B, Vos, H, Heck, A

Protease bias in absolute protein quantitation. by Peng, M, Taouatas, N, Cappadona, S, van Breukelen, B, Mohammed, S, Scholten, A, Heck, A

Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. by Helbig, A, Gauci, S, Raijmakers, R, van Breukelen, B, Slijper, M, Mohammed, S, Heck, A

Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites. by Mohammed, S, Lorenzen, K, Kerkhoven, R, van Breukelen, B, Vannini, A, Cramer, P, Heck, A

Database independent proteomics analysis of the ostrich and human proteome. by Altelaar, A, Navarro, D, Boekhorst, J, van Breukelen, B, Snel, B, Mohammed, S, Heck, A

RockerBox: analysis and filtering of massive proteomics search results. by van den Toorn, H, Muñoz, J, Mohammed, S, Raijmakers, R, Heck, A, van Breukelen, B

Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo. by Lemeer, S, Pinkse, M, Mohammed, S, van Breukelen, B, den Hertog, J, Slijper, M, Heck, A

Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. by Helbig, A, Rosati, S, Pijnappel, P, van Breukelen, B, Timmers, M, Mohammed, S, Slijper, M, Heck, A

Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. by Binai, N, Bisschops, M, van Breukelen, B, Mohammed, S, Loeff, L, Pronk, J, Heck, A, Daran-Lapujade, P, Slijper, M

Large Scale Multiplex Stable Isotope Dimethyl Labeling Applied to the Quantitative Analysis of Tyrosine Phosphorylation by Boersema, P, Foong, L, Ding, V, Lemeer, S, Mohammed, S, Raijmakers, R, van Breukelen, B, Boekhorst, J, Choo, A, Heck, A

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis by Low, T, vanHeesch, S, vandenToorn, H, Giansanti, P, Cristobal, A, Toonen, P, Schafer, S, Hübner, N, vanBreukelen, B, Mohammed, S, Cuppen, E, Heck, A, Guryev, V

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. by Low, T, van Heesch, S, van den Toorn, H, Giansanti, P, Cristobal, A, Toonen, P, Schafer, S, Hübner, N, van Breukelen, B, Mohammed, S, Cuppen, E, Heck, A, Guryev, V