Journal ArticleDOI
Next-generation proteomics: towards an integrative view of proteome dynamics
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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
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Journal ArticleDOI
In vivo brain GPCR signaling elucidated by phosphoproteomics
Jeffrey J. Liu,Kirti Sharma,Luca Zangrandi,Chongguang Chen,Sean J. Humphrey,Yi-Ting Chiu,Mariana Spetea,Lee-Yuan Liu-Chen,Christoph Schwarzer,Matthias Mann,Matthias Mann +10 more
TL;DR: This work demonstrates the utility of combining phosphoproteomics with pharmacological tools and behavioral assessments as a general approach for studying GPCR signaling in vivo and identifies the signaling pathways associated with desired and undesired outcomes of KOR activation in vivo.
Journal ArticleDOI
NeuCode Labels for Relative Protein Quantification
Anna E. Merrill,Alexander S. Hebert,Matthew E. MacGilvray,Christopher M. Rose,Derek J. Bailey,Joel Chandler Bradley,William Wakefield Wood,Marwan El Masri,Michael S. Westphall,Audrey P. Gasch,Joshua J. Coon +10 more
TL;DR: It is demonstrated that incorporation of these molecules into the proteomes of actively growing cells does not affect cellular proliferation, and how to use the embedded mass signatures (neutron encoding (NeuCode) for multiplexed proteome quantification by means of high-resolution mass spectrometry is discussed.
Journal ArticleDOI
Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology.
Felix Meissner,Matthias Mann +1 more
TL;DR: Technical aspects of proteomics workflows, instrumentation as well as computational considerations to obtain high-quality proteomics data are described.
Journal ArticleDOI
High fidelity between saliva proteomics and the biologic state of salivary glands defines biomarker signatures for primary Sjögren's syndrome.
TL;DR: The aim of this study was to recapitulate the diagnosis of SS through noninvasive means and to define the biologic state of SS patients' salivary glands.
Journal ArticleDOI
Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution
TL;DR: This work reports a high-throughput, straightforward, and comprehensive label-free phosphoproteomics approach using the highly selective, reproducible, and sensitive Ti4+-IMAC phosphopeptide enrichment method, and demonstrates the applicability of this approach to Jurkat T cells stimulated by prostaglandin E2.
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