Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies
Philipp E. Geyer,Philipp E. Geyer,Eugenia Voytik,Peter V. Treit,Sophia Doll,Sophia Doll,Alisa Kleinhempel,Lili Niu,Johannes Müller,Marie-Luise Buchholtz,Jakob M. Bader,Daniel Teupser,Lesca M. Holdt,Matthias Mann,Matthias Mann +14 more
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TLDR
Sample quality‐associated proteins are determined, many of which have been reported as biomarker candidates as revealed by a comprehensive literature survey, and sample preparation guidelines and an online resource are provided to assess overall sample‐related bias in clinical studies and to prevent costly miss‐assignment of biomarkers.Citations
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Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection.
Christoph B. Messner,Vadim Demichev,Vadim Demichev,Daniel Wendisch,Laura Michalick,Matthew White,Anja Freiwald,Kathrin Textoris-Taube,Spyros I. Vernardis,Anna Sophia Egger,Marco Kreidl,Daniela Ludwig,Christiane Kilian,Federica Agostini,Aleksej Zelezniak,Aleksej Zelezniak,Charlotte Thibeault,Moritz Pfeiffer,Stefan Hippenstiel,Andreas C. Hocke,Christof von Kalle,Archie Campbell,Caroline Hayward,David J. Porteous,Riccardo E. Marioni,Claudia Langenberg,Claudia Langenberg,Kathryn S. Lilley,Wolfgang M. Kuebler,Michael Mülleder,Christian Drosten,Norbert Suttorp,Martin Witzenrath,Florian Kurth,Florian Kurth,Leif E. Sander,Markus Ralser,Markus Ralser +37 more
TL;DR: A platform for ultra-high throughput serum and plasma proteomics that builds on ISO13485 standardisation and high-flow liquid chromatography to facilitate implementation in clinical laboratories and identifies 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19.
Journal ArticleDOI
Genetics meets proteomics: perspectives for large population-based studies.
TL;DR: How combining genetics with plasma proteomics is providing notable insights into human disease is described, and the challenges faced by currently available technologies are highlighted and perspectives relevant to their future application in large-scale biobank studies are provided.
Journal ArticleDOI
Recent advances in mass spectrometry based clinical proteomics: applications to cancer research.
TL;DR: Improvements in MS-based clinical proteomics not only solidify their integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
Journal ArticleDOI
Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona.
John E. Blume,William C. Manning,Greg Troiano,Daniel Hornburg,Michael Figa,Lyndal K. Hesterberg,Theodore L. Platt,Xiaoyan Zhao,Rea A. Cuaresma,Patrick A. Everley,Marwin Ko,Hope Liou,Max Mahoney,Shadi Ferdosi,Eltaher M. Elgierari,Stolarczyk Craig,Behzad Tangeysh,Hongwei Xia,Ryan W. Benz,Asim Siddiqui,Steven A. Carr,Philip Ma,Robert Langer,Vivek F. Farias,Omid C. Farokhzad +24 more
TL;DR: A highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for efficient proteomic profiling and biomarker discovery is developed.
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Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease
Jakob M. Bader,Philipp E. Geyer,Philipp E. Geyer,Johannes Müller,Maximilian T. Strauss,Manja Koch,Frank Leypoldt,Peter Koertvelyessy,Peter Koertvelyessy,Daniel Bittner,Carola G. Schipke,Enise I. Incesoy,Oliver Peters,Oliver Peters,Nikolaus Deigendesch,Mikael Simons,Majken K. Jensen,Majken K. Jensen,Henrik Zetterberg,Matthias Mann,Matthias Mann +20 more
TL;DR: A highly reproducible mass spectrometry (MS)‐based proteomics workflow for the in‐depth analysis of CSF from minimal sample amounts is presented and a consistent glycolytic signature across cohorts and a recent study suggests clinical utility of this proteomic signature.
References
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Jiirgen Cox,Matthias Mann +1 more
TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
Journal ArticleDOI
Mass spectrometry-based proteomics
Ruedi Aebersold,Matthias Mann +1 more
TL;DR: The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
Journal ArticleDOI
The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova,Tikira Temu,Pavel Sinitcyn,Arthur Carlson,Marco Y. Hein,Tamar Geiger,Matthias Mann,Jürgen Cox +7 more
TL;DR: The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
Journal ArticleDOI
Andromeda: a peptide search engine integrated into the MaxQuant environment
Jürgen Cox,Nadin Neuhauser,Annette Michalski,Richard A. Scheltema,Jesper V. Olsen,Matthias Mann +5 more
TL;DR: A novel peptide search engine using a probabilistic scoring model that can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.
Journal ArticleDOI
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
TL;DR: A new intensity determination and normalization procedure called MaxLFQ is developed that is fully compatible with any peptide or protein separation prior to LC-MS analysis, which accurately detects the mixing ratio over the entire protein expression range, with greater precision for abundant proteins.
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