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Thermo Fisher Scientific Inc.. (7/20/10). "Press Release: Superiority of Data-dependent Decision Tree Logic Demonstrated. Combined Intelligent ETD and CID Fragment Approaches for Tyrosine Phosphorylation Site Determination". San José, CA.

Region Region Utrecht
  Country Netherlands
Organisations Organisation Thermo Fisher Scientific Inc. (NYSE: TMO)
  Group Thermo Fisher (Group)
  Organisation 2 University of Utrecht, Biomolecular Mass Spectrometry and Proteomics Group (Heck Lab)
  Group University of Utrecht (Utrecht University)
Products Product LTQ Orbitrap XL™ mass spectrometer
  Product 2 Proteome Discoverer software
Index term Index term Thermo Fisher–Univ Utrecht: mass spectrometry, –201007 collab developm application note ETD + CID with LTQ Orbitrap XL using Proteome Discoverer s/w
Person Person Heck, Albert J. R. (Univ Utrecht 199809– Prof + Head Biomolecular Mass Spec & Proteomics Group)

Combined Intelligent ETD and CID Fragmentation Approaches for Tyrosine Phosphorylation Site Determination Available on the LTQ Orbitrap XL ETD Mass Spectrometer

Thermo Fisher Scientific Inc., the world leader in serving science, today announced a new application note entitled "Enhancing Phosphotyrosine Proteome Coverage using a Combined ETD and CID Approach on a LTQ Orbitrap XL ETD". The application note is a result of the cooperation with the Netherlands Proteomic Centre and in particular the Biomolecular Mass Spectrometry and Proteomics Group at Utrecht University, headed by Albert Heck. It demonstrates how electron transfer dissociation (ETD) and collision induced dissociation (CID) are complementary fragmentation techniques, that when used together on the Thermo Scientific LTQ Orbitrap XL ETD mass spectrometer, provide significantly greater phosphoproteome coverage than mass spectrometry (MS) methods relying on CID alone. By using intelligent data-dependent decision tree (DDDT) logic to choose whether to perform ETD or CID in real-time, significantly more phosphopeptide can be identified, along with unambiguous determination of the phosphorylation sites. The application note is available for download via

Reversible tyrosine phosphorylation plays an important role in many cellular processes such as growth, differentiation and migration. Because aberrant tyrosine phosphorylation has been shown to affect the course of many cancers, the detection and site-specific localization of tyrosine phosphorylation are important to understanding cancer mechanisms. Low abundances (compared with non-phosphorylated peptides) and the dynamic nature of tyrosine phosphorylation make it difficult to detect. A variety of strategies, including immuno-affinity enrichment of phosphoproteins and phosphopeptide enrichment prior to MS, have been developed to overcome underrepresentation of tyrosine phosphorylation. Despite advances in these approaches, characterization of the tyrosine phosphoproteome is far from comprehensive and ongoing method development is needed.

The application note compares two approaches to identify and localize tyrosine phosphorylation in a phospho-tyrosine peptide immuno-affinity purification of pervanadate treated HeLa cells. One is the traditional approach of fragmenting every peptide by both ETD and CID. The other approach is to use DDDT logic in real time to choose the most effective dissociation technique (ETD or CID) depending on the peptide's mass-to-charge ratio (m/z) and its charge state (z).

The LTQ Orbitrap XL ETD* acquires high-resolution full-scan spectra in the Orbitrap* mass analyzer, and then uses the linear ion trap to perform either ETD or CID. Its superior mass resolution enables DDDT logic to use the information in the full-scan spectra to make real-time decisions about which fragmentation method to use. Data was processed with the Thermo Scientific Proteome Discoverer software, which is specifically designed to handle raw data with CID and ETD spectra. It provides search algorithms for ETD data and combines results from multiple search engines and dissociation techniques.

Compared with the traditional approach, 30% more tyrosine phosphopeptides were identified when using intelligent DDDT logic. In both approaches, a significant number of phosphopeptides were identified only by ETD or CID, demonstrating that the techniques are truly complementary. ETD is most effective for peptides with three or more charges, while CID is most effective for those doubly charged. The nearly complete fragment ion series produced from complementary ETD and CID spectra generated using real-time DDDT logic enabled unambiguous determination of the tyrosine phosphorylation sites.

For more information or to download the application note, please call 1-800-532-4752, e-mail or visit

Thermo Scientific is part of Thermo Fisher Scientific, the world leader in serving science.

About Thermo Fisher Scientific

Thermo Fisher Scientific Inc. (NYSE: TMO) is the world leader in serving science. Our mission is to enable our customers to make the world healthier, cleaner and safer. With revenues of more than $10 billion, we have approximately 35,000 employees and serve customers within pharmaceutical and biotech companies, hospitals and clinical diagnostic labs, universities, research institutions and government agencies, as well as in environmental and process control industries. We create value for our key stakeholders through two premier brands, Thermo Scientific and Fisher Scientific, which offer a unique combination of continuous technology development and the most convenient purchasing options. Our products and services help accelerate the pace of scientific discovery, and solve analytical challenges ranging from complex research to routine testing to field applications. Visit

Record changed: 2016-03-19


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