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Knowledge Base Articles

An Information System Enabling the Organization and Automatic Annotation of Proteomic Experiments with User-specific Proteins

Devin Lee Drew1, Daniel Lopez-Ferrer1, Emanuela Milani2, Jacob Poder3, Martin Damsbo3, Bernd Wollscheid2 and Andreas FR Hühmer1International Hupo 2016Purpose: Researchers studying engineered proteins or other proteins not defined in public sequence r...

Pushing the Limits of Bottom-Up Proteomics with State-Of-The-Art Capillary UHPLC and Orbitrap Mass Spectrometry for Reproducible Quantitation of Proteomes

Daniel Lopez-Ferrer1, Michael Blank1, Stephan Meding2, Aran Paulus1, Romain Huguet1, Remco Swart2, Andreas FR Huhmer1 Application Note 639Describes a higher-performing quantitative proteomics workflow compared to current methods using a Thermo Scient...

Multiplexed protein quantification using the isobaric TMT method: Improving reproducibility and protein coverage with Proteome Discoverer 2.1

Rosa VinerMultiplexed protein quantification using the isobaric TMT method relies on robust software algorithms for the consistent retrieval and interpretation of the report ion signal to report relative protein amounts across the quantification chan...

How to do TMT experiments on Orbitrap based mass spectrometers. From sample preparation to data acquisition and data processing.

Xiaoyue Jiang and Rosa Viner A presentation providing an overview of multiplexed isobaric labeling, the basics of Tandem Mass Tags and the SPS MS3 technique. The presentation also covers sample prep. Specifically summary of the steps involved for a c...

Breaking the 2000-Protein Barrier in a Standard LC Run Using a New Orbitrap Benchtop Instrument and Multiple Search Engines

Paschke C, Kellmann M, Xuan Y, Damoc E, Ueckert T, Grensemann H, Comberg U, Delanghe B.Scientific PosterGetting a comprehensive view of the protein content of a complex sample is still a challenge in proteomics; accomplishing it in one analytical run...

Evaluation of the deuterium isotope effect in zwitterionic hydrophilic interaction liquid chromatography separations for implementation in a quantitative proteomic approach

Di Palma S, Raijmakers R, Heck AJ, Mohammed S.Anal Chem. 2011 Nov 1;83(21):8352-6. Quantitative methodologies for the global in-depth comparison of proteomes are frequently based on chemical derivatization of peptides with isotopically distinguishabl...

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