Journal ArticleDOI
Next-generation proteomics: towards an integrative view of proteome dynamics
Reads0
Chats0
TLDR
MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis, and to highlight recent applications.Abstract:
Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the interconnectivity of proteins into complexes and signalling networks that are highly divergent in time and space. Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis. Here we describe this emerging next generation of proteomics and highlight recent applications.read more
Citations
More filters
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
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.
Journal Article
Interactome networks and human disease
TL;DR: Why interactome networks are important to consider in biology, how they can be mapped and integrated with each other, what global properties are starting to emerge from interactome network models, and how these properties may relate to human disease are detailed.
Journal ArticleDOI
Methods of integrating data to uncover genotype–phenotype interactions
TL;DR: The emerging approaches for data integration — including meta-dimensional and multi-staged analyses — which aim to deepen the understanding of the role of genetics and genomics in complex outcomes are explored.
Journal ArticleDOI
Searching molecular structure databases with tandem mass spectra using CSI:FingerID.
TL;DR: This work presents CSI:FingerID, which combines fragmentation tree computation and machine learning for searching molecular structure databases using tandem MS data of small molecules, and is shown to improve on the competing methods for computational metabolite identification by a considerable margin.
References
More filters
Journal ArticleDOI
The Cell in an Era of Systems Biology
Paul Nurse,Jacqueline Hayles +1 more
TL;DR: The increasing use of high-throughput technologies and computational modeling is revealing new levels of biological function and organization, which are influencing the authors' view of the cell.
Journal ArticleDOI
aPKC phosphorylates NuMA-related LIN-5 to position the mitotic spindle during asymmetric division
Matilde Galli,Javier Muñoz,Vincent Portegijs,Mike Boxem,Stephan W. Grill,Albert J. R. Heck,Sander van den Heuvel +6 more
TL;DR: A quantitative mass spectrometry approach for in vivo identification of protein kinase substrates is described and it is found that depletion of the polarity kinase PKC-3 results in markedly decreased levels of phosphorylation of a cluster of four LIN-5 serine residues.
Journal ArticleDOI
Proteomic snapshot of the EGF-induced ubiquitin network
Elisabetta Argenzio,Tanja Bange,Barbara Oldrini,Fabrizio Bianchi,Raghunath Peesari,Sara Mari,Pier Paolo Di Fiore,Matthias Mann,Simona Polo +8 more
TL;DR: The results unveil the complex impact of growth factor signaling on Ub‐based intracellular networks to levels that extend well beyond what might have been expected and are proof of principle of the biological relevance of the EGF‐Ubiproteome.
Journal ArticleDOI
Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)
Angus I. Lamond,Mathias Uhlén,Stevan Horning,Alexander Makarov,Carol V. Robinson,Luis Serrano,F. Ulrich Hartl,Wolfgang Baumeister,Anne Katrin Werenskiold,Jens S. Andersen,Ole Vorm,Michal Linial,Ruedi Aebersold,Matthias Mann,Matthias Mann +14 more
TL;DR: A perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new “third generation” proteomics strategy that offers an indispensible tool for cell biology and molecular medicine is presented.
Journal ArticleDOI
Highly sensitive proteome analysis of FACS-sorted adult colon stem cells.
Serena Di Palma,Daniel E. Stange,Marc van de Wetering,Hans Clevers,Albert J. R. Heck,Shabaz Mohammed +5 more
TL;DR: This work applies a highly sensitive multidimensional chromatographic strategy based on a combination of hydrophilic interaction liquid chromatography and reversed phase chromatography to the analysis of a limited number of FACS-sorted colon stem cells extracted from mouse intestine, obtaining a proteome coverage comparable to current methods that generally require 100-fold more starting material.
Related Papers (5)
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Jiirgen Cox,Matthias Mann +1 more