Abstract
Mass spectrometric technology has improved tremendously in the last few years in all key parameters. Here I discuss the use of the linear ion trap - orbitrap and ICR instruments in proteomics experiments. Using 'lock mass' ions and integration over LC peaks, a mass precision of significantly less than one ppm can now be achieved. This mass accuracy, particularly in conjunction with SILAC, allows determination of the chemical composition of small peptides and a reasonable 'guess' to the identity of larger peptides, even without sequencing. Very recently, the addition of "Higher Energy Dissociation" has allowed the recording of full mass range fragmentation spectra with 'triple quadrupole like' characteristics. These capabilities, combined with label-free or SILAC based quantitation allow the majority of the proteome to be analyzed.  Several recent examples of relevance in cell signaling and clinical proteomics will be described.
 
 - Olsen JV, de Godoy LM, Li G, Macek B, Mortensen P, Pesch R, Makarov A, Lange O, Horning S, Mann M: Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap. Mol Cell Proteomics 2005, 4(12):2010-2021.
 - Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M: Higher-Energy C-trap Dissociation (HCD) for precise peptide modification analysis. Nature Methods 2007, in the press.
 - Cox, J. and Mann M: Is genomics the new proteomics?, Cell, August issue Macek B, Waanders LF, Olsen JV, Mann M: Top-down Protein Sequencing and MS3 on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer. Mol Cell Proteomics 2006, 5(5):949-958.
 - Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M: Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks. Cell 2006, 127(3):635-648.


Background
Professor Matthias Mann (born 1959) is a scientist in the area of mass spectrometry and proteomics. Born 1959 in Germany he studied mathematics and physics at the University of Goettingen. He received his Ph.D. in 1988 at Yale University were he worked in the group of the later Nobel laureate John Fenn. After a postdoctoral fellowship at the University of Southern Denmark in Odense he became group leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg. Later he went back to Odense as a Professor for Bioinformatics. Since 2005 he is a director at the Max Planck Institute of Biochemistry in Munich. In addition, he will also become a principal investigator at the newly founded "Novo Nordisk Foundation Center for Protein Research" in Copenhagen.

His work has impact in various fields of mass spectrometry-based proteomics. For example, the peptide sequence tag approach developed at the EMBL was one of the first methods for the identification of peptides based on mass spectra and genome data. A recently developed metabolic labeling technique called SILAC (stable isotope labeling with amino acids in cell culture) is now used by many labs in quantitative proteome research.