Cutting Edge Proteomics Lectures and Interviews from the Best

Abstract: Ten years ago the first Orbitrap™ based mass spectrometer, the LTQ Orbitrap, came to market. A lot has happened in 10 years. Alexander Makarov, the inventor of the Orbitrap, describes how the Orbitrap mass analyser works and its developmental history and compares it with other types of mass analysers. He describes the current generations of Orbitrap based mass spectrometers and describes some performance records in terms of, for example, mass resolution and m/z range. Quantitative capabilities and strategies in the Orbitrap are also discussed. Look out for the Orbitrap MS made from children’s building blocks! That is something you need to see.

Abstract: What can proteomics investigate that genomics and transcriptomics cannot? Prof. Mann describes sample preparation, LC-MS and bioinformatics workflows and tools and approaches for optimal, rapid, in-depth analysis of the human proteome. He describes a minimalistic, automated proteomics approach and what can be achieved. Prof. Mann then describes several examples of the utility of these approaches. Firstly, his lab has revisited, with state-of-the-art mass spectrometry technology such as the Thermo Scientific™ Q Exactive™ HF quadrupole orbitrap mass spectrometer, proteomic plasma analysis. Working from a finger prick (5 micolitres of blood) within approx 3 hours LC-MS analysis of the sample can be achieved with more than 1000 proteins identifiable in that timeframe. Next Prof. Mann describes interactome proteomics experiments working from a simplifying experimental perspective of protein enrichment. He describes approaches to reduce LC-MS time greatly while maintaining high numbers of protein identifications with a goal to studying 96 interactomes per day. Lastly Prof. Mann discusses practical issues with phosphoproteomics to drastically simplify the experimental approach. He exemplifies this improved approach with an ultra deep, time-resolved analysis of the mouse liver phosphoproteome and implications for diabetes research.

Abstract: Prof. Albert Heck describes his work on stem cell biology. He talks about induced Pluripotent Stem cells (iPSCs), the ability to transform fibroblasts into iPSCs and their potential in personalized medicine. Prof Heck describes his extensive investigations into iPSC biology using proteomics and other tools.

Abstract: Prof. Albert Heck describes his work with native mass spectrometry using the Thermo Scientific™ Exactive™ Plus EMR mass spectrometer - the 'Jumbo' Orbitrap. He describes the development work that was needed to optimize the mass spectrometer for analysis of intact proteins and complexes. Examples of analysis include antibody drug conjugates, protein reaction monitoring, for example of kinase-substrate on the intact protein (Bora/AurorA/PLK), and intact viruses.

Abstract: Bernard Kuster, Professor of Proteomics and Bioanalytics at the TUM, Germany, the leader of one of the two recent public efforts to publish a draft map of the human proteome, speaks about his proteomics research. He describes optimised protocols for shotgun proteomics and phosphoproteomics. Following, Prof. Kuster suggests that while the last ten years have been dominated by developments in mass spec technology the next ten years will be dominated by informatics or by a combination of informatics and information driven mass spec. He describes a number of interesting examples to make his point and describes much of the work on the human proteome project and ProteomicsDB. Prof. Kuster announces a new effort to synthesize more than 1 million peptides to build spectral libraries, develop proteomics assays and so forth. Prof. Kuster finishes by stating that it would be highly desirable if we knew the complete protein binding spectrum of a drug molecule. This leads to knowledge about target deconvolution, selectivity profiling, mechanism of action and biomarker discovery. He illustrates this, for example, with a description of the 1000 kinase inhibitor project which allows for the definition of new targets and new uses of drugs and to predict toxic side effects and the technique of cellular thermal shift assays for discovery and measurement of protein-drug interactions (drug induced stabilization/destabilization).

Abstract: Dr. Ian Pike, COO of Proteome Science, describes their work on developing new approaches to stratified medicine and bringing their mass spectrometry based proteomics approaches into the clinic. For example he describes SysQuant, a hybrid proteomic/phosphoproteomic approach to stratifying mechanisms of disease in individual patients with pancreatic cancer, TMT Calibrator™ for low level identification of tissue derived biomarkers in body fluids and work on a CSF biomarker panel for Alzheimer’s disease.

Abstract: Ken Miller, VP of Marketing, Life Science Mass Spectrometry, very briefly introduces Thermo Fisher Scientific and briefly describes the first ten years of Orbitrap™ M. S. Happy 10.0000^th birthday to Orbitrap™ MS.He also describes mass spectrometry technologies for targeted and holistic quantitative approaches. Quantitation transformed. He finishes by describing more qualitative approaches using Orbitrap MS such as the ’Universal Method’ on the Thermo Scientific™ Orbitrap™ Fusion™ Tribrid™ MS and also describes recent developments in the Q Exactive™ group of products.

Abstract: Prof. Mathias Uhlén, director of the SciLifeLab in Stockholm, speaks about the human protein atlas: a resource generating spatial proteomics data with antibody-based analysis giving single cell resolution and in the context of neighbouring cells. He goes on to discuss the integration of transcriptomics and proteomics data; targeted proteomics approaches such as PrEST-SILAC and Immuno-SILAC; generating a large resource for targeted proteomics with thousands of protein assays and absolute quantification using high resolution/accurate mass Orbitrap™ mass spectrometry approaches. Prof. Uhlen asks do we need proteomics? The answer is yes. ‘There is a great need for proteome-wide quantitative protein assays.’

Abstract: Dr. Matsson talks about biomarkers and their utility in healthcare such that biomarker information can be interpreted and acted on with clinical utility. His goal is to reduce development time for biomarkers from 17 to 7 years. He discusses single- to multi-plexing, the impact of multiplexing on complexity and the impact of informatics to reduce complexity and describes examples, opportunities and hurdles to overcome to achieve a reduced time in bringing biomarkers to the clinic. He describes the EIT health consortium opportunity for collaboration.

Abstract: Dr. Huhmer talks about the science that has been driven by technology improvements in proteomics over recent years. Full proteomes are accessible using modern high resolution/accurate mass MS technology. What was the effect of orbitrap technology development on, for example, depth and speed of proteomic analysis? Dr Huhmer asks and answers many important questions. Where are we today in terms of the human proteome? How can proteomics be used to annotate the genome? What is the degree of transcriptional versus translational control of protein expression? He discusses PTM dynamics and dynamic protein networks. He further discusses the need for multiplexing in proteomics, for example, using tandem mass tags.

Abstract: Dr. Myriam Demant, product specialist for the Orbitrap Fusion, describes the Universal Method for optimized proteomic data acquisition on the Orbitrap Fusion which delivers maximum protein identification irrespective of the sample amount loaded on-column.

Abstract: Ken Miller, VP of Research Product Marketing at Thermo Fisher Scientific gives a brief perspective of what it was like working with the original LTQ Orbitrap in 2005 and developments since then.

Abstract: Dr. Michaela Scigelova talks about the latest version of the Thermo Scientific™ Proteome Discoverer™ with performance enhancements particularly in the area of multiplexed quantitation, for example with 10-plex tandem mass tags. Other enhancements include the addition of study design management and improved handling of huge datasets. Dr. Scigelova also describes progress with development of the Orbitrap since 2005.

Abstract: Prof. Kathryn Lilley talks about her work over the last ten years to develop broadly applicable, multiplexed Orbitrap based mass spectrometry workflows for the high resolution characterization of sub-cellular protein localization and protein isoforms.

Abstract: Prof. Neil Kelleher talks about top down proteomics workflows using Orbitrap based mass spectrometers. What is possible using Orbitrap based mass spectrometers in 2015 in terms of identifying and quantitating intact proteoforms.

Abstract: Claire Dauly, Sales Support Manager, describes glycoproteomic and glycan analysis workflows utilizing Orbitrap based mass spectrometers such as the Orbitrap Fusion and optimized chromatography.

Abstract: Prof. Albert Heck talks about new methods in proteomics and how to apply them to the clinic. Proteomics data is very biologically relevant and relevant to the patient. Genomics, transcriptomics and proteomics together help us better understand biological processes.

Abstract: Dr. Shannon Eliuk describes the Universal Method on the Orbitrap Fusion, a self-optimizing method for data acquisition of proteomics samples in a range of concentrations and complexities. The Universal method uses dynamic scan management to modify injection times directly on the fly during acquisition.

Abstract: Dr. Christof Lenz describes managing a mass spectrometry core facility and his experience of Orbitrap mass spectrometers. He describes, for example, supporting pathologists in their investigations of lung cancer sub-types using proteomics approaches to identify characteristic protein profiles and the robustness of the Q Exactive mass spectrometer.

Abstract: Prof. Andrea Sinz describes her research using the Orbitrap Fusion in chemical cross-linking mass spectrometry to map protein-protein interactions and better understand protein 3D structure.

Abstract: Prof. Henning Urlaub talks about method development, the proteome of the synapse, Xenopus oocytes and protein-protein interaction research using protein cross-linking and protein-nucleic acid interactions.

Abstract: Dr. Yue Xuan describes data independent acquisition (DIA) mass spectrometry approaches on Orbitrap based mass spectrometers such as the Q Exactive and Orbitrap Fusion.

Abstract: Dr. Jeroen Krijgsveld describes his research working on chromatin biology and transcriptional regulation and method development to optimize proteomic workflows.

Abstract: Dr. Madalina Oppermann describes ways to standardize high performance in shotgun proteomics across a wide dynamic range with short and long gradients and with and without upfront sample fractionation. Once performance of the LCMS has been verified high quality analysis of biological samples can follow with confidence. She discusses the recent draft human proteome maps.

Abstract: Prof. Bruno Domon talks about Parallel Reaction Monitoring (PRM) in proteomics relative to SRM and the ability to analyze low abundance proteins with PRM accurately and precisely.

Abstract: Bernard Delanghe talks about the recent release of Proteome Discoverer 2.0. The software has improved data processing capabilities for handling large data sets and is now enabled with study management tools, for example, to work with TMT 10-plex data sets. Additional database searching tools and visualization capabilities have been added.