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1 Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis Palma, S. Di; Boersema, P. J.; Heck, A. J. R.; Mohammed, S. 2011
2 Universal and confident phosphorylation site localization using phosphoRS. Kaus, T.; Köcher, T.; Pichler, P.; Paschke, C.; Schmidt, A.; Henrich, C.; Mechtler, K. 2011
3 Ultra Acidic Strong Cation Exchange Enabling the Efficient Enrichment of Basic Phosphopeptides Hennrich, M. L.; van den Toorn, H. W. P.; Groenewold, V.; Mohammed, S.; Heck, A. J. R. 2012
4 Trends in ultrasensitive proteomics Altelaar, A. F. M.; Heck, A. J. R. 2012
5 Towards a human proteomics atlas Gonnelli, G.; Hulstaert, N.; Degroeve, S.; Martens, L. 2012
6 TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. Junker, J.; Bielow, C.; Bertsch, A.; Sturm, M.; Reinert, K.; Kohlbacher, O. 2012
7 thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files Colaert, N.; Barsnes, H.; Vaudel, M.; Helsens, K.; Timmerman, E.; Sickmann, A.; Gevaert, K.; Martens, L. 2011
8 The toxin-antitoxin proteins relBE2Spn of Streptococcus pneumoniae: Characterization and association to their DNA target Moreno-Cordoba, I.; Diago-Navarro, E.; Barendregt, A.; Heck, A. J. R.; Alfonso, C.; Diaz-Orejas, R.; Nieto, C.; Espinosa, M. 2012
9 The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator Jungmichel, S.; Clapperton, J. A.; Lloyd, J.; Hari, F. J.; Spycher, C.; Pavic, L.; Li, J. J.; Haire, L. F.; Bonalli, M.; Larsen, D. H.; Lukas, C.; Lukas, J.; MacMillan, D.; Nielsen, M. L.; Stucki, M.; Smerdon, S. J. 2012
10 The Effect of Peptide Identification Search Algorithms on MS2-Based Label-Free Protein Quantification Degroeve, S.; Staes, A.; Bock, P. J. De; Martens, L. 2012
11 Targeted analysis of tyrosine phosphorylation by immuno-affinity enrichment of tyrosine phosphorylated peptides prior to mass spectrometric analysis. Zoumaro-Djayoon, A. D.; Heck, A. J. R.; Muñoz, J. 2011
12 Sigpep: Calculating unique peptide signature transition sets in a complete proteome background Helsens, K.; Mueller, M.; Hulstaert, N.; Martens, L. 2012
13 Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues Lundby, A.; Secher, A.; Lage, K.; Nordsborg, N. B.; Dmytriyev, A.; Lundby, C.; Olsen, J. V. 2012
14 Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation. Soufi, B.; Soares, N. C.; Ravikumar, V.; Macek, B. 2012
15 Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation Weinert, B. T.; Wagner, S. A.; Horn, H.; Henriksen, P.; Liu, W. R.; Olsen, J. V.; Jensen, L. J.; Choudhary, C. 2011
16 PredAlgo, a new subcellular localization prediction tool dedicated to green algae Tardif, M.; Atteia, A.; Specht, M.; Cogne, G.; Rolland, N.; Brugiere, S.; Hippler, M.; Ferro, M.; Bruley, C.; Peltier, G.; Vallon, O.; Cournac, L. 2012
17 Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment Kelstrup, C. D.; Hekmat, O.; Francavilla, C.; Olsen, J. V. 2011
18 Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer Kelstrup, C. D.; Young, C.; Lavallee, R.; Nielsen, M. L.; Olsen, J. V. 2012
19 MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation Gatto, L.; Lilley, K. S. 2012
20 Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of "noncanonical" proteotypic peptides. Jacuinod, M.; Trauchessec, M.; Huillet, C.; Louwagie, M.; Lebert, D.; Picard, G.; Adrait, A.; Dupuis, A.; Garin, J.; Brun, V.; Bruley, C. 2012
21 jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions. Helsens, K.; Brusniak, M. Y.; Deutsch, E.; Moritz, R. L.; Martens, L. 2011
22 Introducing AAA-MS, a Rapid and Sensitive Method for Amino Acid Analysis Using Isotope Dilution and High-Resolution Mass Spectrometry Louwagie, M.; Kieffer-Jaquinod, S.; Dupierris, V.; Coute, Y.; Bruley, C.; Garin, J.; Dupuis, A.; Jaquinod, M.; Brun, V. 2012
23 Improving SRM Assay Development: A Global Comparison between Triple Quadrupole, Ion Trap, and Higher Energy CID Peptide Fragmentation Spectra de Graaf, E. L.; Altelaar, A. F. M.; van Breukelen, B.; Mohammed, S.; Heck, A. J. R. 2011
24 Improving depth in phosphoproteomics by using an SCX-WAX-RP multidimensional separation approach Hennrich, M. L.; Groenewold, V.; Kops, G. J.; Heck, A. J. R.; Mohammed, S. 2011
25 Impact of phosphoproteomics on studies of bacterial physiology. Mijakovic, I.; Macek, B. 2011
26 Highly Sensitive Proteome Analysis of FACS-Sorted Adult Colon Stem Cells Palma, S. Di; Stange, D.; de Wetering, M. van; Clevers, H.; Mohammed, S.; Heck, A. J. R. 2011
27 Global detection of protein kinase D-dependent phosphorylation events in nocodazole-treated human cells. Franz-Wachtel, M.; Eisler, S. A.; Krug, K.; Wahl, S.; Carpy, A.; Nordheim, A.; Pfizenmaier, K.; Hausser, A.; Macek, B. 2012
28 Evaluation of the Deuterium Isotope Effect in Zwitterionic Hydrophilic Interaction Liquid Chromatography Separations for Implementation in a Quantitative Proteomic Approach. Palma, S. Di; Raijmakers, R.; Mohammed, S.; Heck, A. J. R. 2011
29 Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment Zhou, H.; Low, T. Y.; Hennrich, M. L.; den Toorn, H. van; Schwend, T.; Zou, H.; Mohammed, S.; Heck, A. J. R. 2011
30 Development of a Protein Standard Absolute Quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum. Adrait, A.; Lebert, D.; Trauchessec, M.; Dupuis, A.; Louwagie, M.; Masselon, C.; Jaquinod, M.; Chevalier, B.; Vandenesch, F.; Garin, J.; Bruley, C.; Brun, V. 2012
31 Data extraction from proteomics raw data: An evaluation of nine tandem MS tools using a large Orbitrap data set. Mancuso, F.; Bunkenborg, J.; Wierer, M.; Molina, H. 2012
32 Combining quantitative proteomics data processing workflows for greater sensitivity Colaert, N.; Huele, C. Van; Degroeve, S.; Staes, A.; Vandekerckhove, J.; Gevaert, K.; Martens, L. 2011
33 Collagen stimulation of platelets induces a rapid spatial response of cAMP and cGMP signaling scaffolds Margarucci, L.; Roest, M.; Preisinger, C.; Bleijerveld, O. B.; van Holten, T. C.; Heck, A. J. R.; Scholten, A. 2011
34 Chromatographic retention time prediction for posttranslationally modified peptides Moruz, L.; Staes, A.; Foster, J. M.; Hatzou, M.; Timmerman, E.; Martens, L.; Kall, L. 2012
35 Analysis of the Plasmodium falciparum proteasome using Blue Native PAGE and label-free quantitative mass spectrometry. Sessler, N.; Krug, K.; Nordheim, A.; Mordmüller, B.; Macek, B. 2012
36 Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients. Köcher, T.; Pichler, P.; Swart, R.; Mechtler, K. 2012
37 An analysis of the resolution limitations of peptide identification algorithms. Colaert, N.; Degroeve, S.; Helsens, K.; Martens, L. 2011
38 Accurate quantification of cardiovascular biomarkers in serum using protein standard absolute quantification (PSAQ (TM)) and selected reaction monitoring. Huillet, C.; Adrait, A.; Lebert, D.; Picard, G.; Trauchessec, M.; Louwagie, M.; Dupuis, A.; Hittinger, L.; Ghaleh, B.; Corvoisier, P. Le; Jaquinod, M.; Garin, J.; Bruley, C.; Brun, V. 2011
39 A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles Wagner, S. A.; Beli, P.; Weinert, B. T.; Nielsen, M. L.; Cox, J.; Mann, M.; Choudhary, C. 2011
40 A complex standard for protein identification, designed by evolution Vaudel, M.; Burkhart, J. M.; Breiter, D.; Zahedi, R. P.; Sickmann, A.; Martens, L. 2012