Matthias Mann

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..Developments discussed in this Perspective will soon enable complete proteome analysis of mammalian cells, as well, with profound impact on biology and biomedicine...

..abstract:..

..abstract:..

..More than half of the detected proteins were not previously identified at the protein level, thus confirming the existence of proteins only known as genomic sequences previously...

..maxquant.org )...

..For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites...

..Little is known about the protein composition of tear fluid but its deregulation is associated with disease states, such as diabetic dry eyes. This makes this body fluid an interesting candidate for in-depth proteomic analysis...

..Substantially increased coverage of the yeast proteome appears feasible with further development in software and instrumentation...

..When combined with quantitative proteomics methodologies, it should be useful for studies of fertilization, male infertility, and prostatic and testicular cancers...

..The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future...

..Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible...

..Huge challenges and opportunities remain in technology development for proteomics; thus, this is not "the beginning of the end" but surely "the end of the beginning."..

..Our data demonstrate that the regulatory scope of lysine acetylation is broad and comparable with that of other major posttranslational modifications...

..Of the 243 amino acids, at least 36 can be modified with a total of 57 posttranslational modifications. Thus, NUCKS appears to have the highest ratio of modified to unmodified residues of any protein so far described...

..Our results demonstrate that system-wide mapping of peptide-protein interactions sites is possible, and suggest shared and unique roles of ErbB-receptor family members in downstream signaling...

..In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells...

..Our assay is streamlined and generic and could become a useful tool in kinase drug development...

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..The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation...

..Our results establish Ser/Thr/Tyr phosphorylation as a common posttranslational modification in Eubacteria, present since the onset of cellular life...

..Finally, we devised a triple labeling strategy comprising control cells, stimulated cells, and phosphatase treated cells to derive an upper bound on phosphorylation occupancy...

..In conclusion, the straightforward experimental procedures described here enable different implementations of kinase-selective proteomics with considerable potential for future signal transduction and kinase drug target analysis...

..In 16 proteins we identified a hydrophobic cluster SUMOylation motif (HCSM). SUMO conjugation of RanGAP1 and ZBTB1 via HCSMs is remarkably efficient...

..Our data are consistent with a change in the role of Sos from Ras-dependent signaling to actin remodeling/endocytic signaling events by a proline-SH3 domain switch...

..Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology...

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..Availability of the C. elegans phosphoproteome should add a novel dimension to functional data obtained by genetic screens in this organism...

..The 5' region of the mRNA of DGCR-8/Pasha, a component of the microprocessor complex, specifically interacts with components of the translational machinery, suggesting that it contains an internal ribosome entry site...

..Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover...

..Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies...

..g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net ...

..We conclude that a Src/FAK signaling unit inhibits differentiation to promote tumorigenesis downstream of β1 integrin and independent of β1 integrin tyrosine phosphorylation...

..Advantages of the in-gel format include better reliability and robustness. Considering its superior performance, diminished sample and work-up requirements, peptide IEF will become a method of choice for sample preparation in proteomics...

..Finally, we present evidence for a complex containing insulin receptor substrate-4 and ShcA in signaling by the fibroblast growth factor receptor...

..Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer...

..The software is freely available at the MaxQuant home page...

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..Moreover, THRAP3 depletion causes cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair...

..Many N-glycosylated proteins coevolved with the rise of extracellular processes that are specific within corresponding phylogenetic groups and essential for organismal development, body growth, and organ formation...

..High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities...

..We conclude that HCD in the new configuration is now a viable method for large-scale phosphoproteome analysis alongside collisional induced dissociation, (CID) and electron capture/transfer dissociation (ECD/ETD)...

..More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools...

..Our analysis ties biochemistry, cell biology, and genomics into a common framework for organelle analysis...

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..We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com)...

..Our analysis highlights a connection of Ptp61F to cytoskeletal regulation through GTPase regulating proteins and focal adhesion components...

..Apart from defining the chromatin interaction landscape in mouse tissues, our workflow can be used for peptides with different modifications and cell types of any organism...

..This study defines the cellular response to Hsp90 inhibition at the proteome level and sheds light on the mechanisms by which it can be used to target cancer cells...

..It includes the selection and preparation of the spike-in SILAC standard, the sample preparation procedure, and analysis and evaluation of the results...

..Our data reveal a highly adapted interplay between chromatin marks and their associated protein complexes. Reading specific trimethyl-lysine sites by specialized complexes appears to be a widespread mechanism to mediate gene expression...

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..Together with the glycosylation sites from a recent large-scale study, they can confirm or correct predicted membrane topologies of these proteins, as we show for the examples calcium channels and glutamate receptors...

..We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides...

..Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities...

..With further development, single-run analysis has the potential to radically simplify many proteomic studies while maintaining a systems-wide view of the proteome...

..Furthermore, Nce102 inhibits Pkh kinase signaling and is required for plasma membrane organization. Therefore, Nce102 might act as a sensor of sphingolipids that regulates plasma membrane function...

..For example, whereas methylation sites are frequent in tissues, this type of modification was much less abundant in cultured cells and escaped detection. Our study significantly extends the known spectrum of linker histone variability...

..Thus, intracellular activation of RTKs by oncogenic mutations in the biosynthetic route may exploit cellular architecture to initiate aberrant signaling cascades, thus evading negative regulation...

..Thus, FFPE biobank material can be analyzed by quantitative proteomics at the level of proteins and post-translational modifications...

..We compared the proteome with a recently published map of chromatin states of promoters in ES cells and found excellent correlation between protein expression and the presence of active and repressive chromatin marks...

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..Thus, optimal de novo sequencing algorithms should be able to obtain substantial sequence information in at least half of all cases...

..In vivo comparison of organellar proteomes can thus directly address functional questions in metabolism...

..Our results assign an important role to the integrin/ILK complex for caveolar trafficking to the cell surface...

..These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification...

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..Thus, the group II chaperonins may have facilitated the evolution of the highly complex proteomes characteristic of eukaryotic cells...

..MAPU 2.0 is a model for a database specifically designed for high-accuracy proteomics and a member of the ProteomExchange Consortium. It is available on line at http://www.mapuproteome.com...

..The approach is robust, sensitive, and specific and offers the potential for high-throughput determination of TF binding profiles...

..The use of filters with these relatively large cutoffs facilitates depletion of detergents...

..Importantly the MS-based strategies described here are entirely generic and can be used to address the poorly understood aspects of cellular PTP function...

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..The combination of quantitative phosphoproteomics with cell culture models provides a powerful strategy to dissect the insulin signaling pathways in intact cells...

..The SILAC-mouse approach is a versatile tool by which to quantitatively compare proteomes from knockout mice and thereby determine protein functions under complex in vivo conditions...

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..SILAC combined with modification-based affinity purification is a useful approach to detect specific and functional protein-protein interactions...

..Since RELMalpha is expressed by adipose tissue and it is a secreted factor, our findings suggest that RELMalpha may be involved in the control of the adipogenesis as well as in the process of muscle differentiation...

..MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates...

..These results provide a vastly extended knowledge base for functional studies on kinases and their regulation through site-specific phosphorylation...

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..This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico prediction of acetylated lysine residues...

..Peptides eluted after digestion on the filter were pure, allowing single-run analyses of organelles and an unprecedented depth of proteome coverage...

..We also provide a generic protocol for combining FASP with StageTip-based ion exchange fractionation, which is generally applicable to proteome analysis...

..Collectively, our results indicate that tyrosine-phosphorylation sites of bacterial effector proteins have evolved as versatile interaction modules that can recruit a rich repertoire of cellular SH2 domains...

..Our data and analysis can serve as a model for cellular proteomics. The adipocyte proteome is available as supplemental material and from the Max-Planck Unified Proteome database...

..4. In H1.0 five less abundant (<1% of H1.0) sites were identified. Analysis of patient matched pairs of cancer and adjacent normal breast demonstrated high variation in H1 methylation between individuals...

..In common with other recent reports, our data furthermore hint at non-SH2 or phosphotyrosine-binding domain-mediated phosphotyrosine binding...

..By decoupling the labeling from the measurement, this super-SILAC method broadens the scope of SILAC-based proteomics...

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..Our results demonstrate that membrane proteins can be analyzed as efficiently as soluble proteins...

..The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome...

..The QUBIC approach enables biologists with access to high resolution mass spectrometry to perform small and large-scale protein interactome mappings...

..Direct proteomic analysis of functionally distinct cellular structures opens up perspectives in physiology and pathology...

..These results show that FASP is suitable for the low level analysis of microdissected tissue and that it has the potential for exploration of clinical samples for biomarker and drug target discovery...

..3%, transmembrane domains were predicted. For potential application in toxicology or clinical studies, we demonstrate that it is possible to consistently identify more than 1000 proteins in a single run...

..Our finding that SUMO can be modified may point to an additional level of complexity through modifying a protein-modifier...

..To our knowledge, this is the first report of RNA-insertion editing in humans and may be an example of the type of discoveries possible with modern proteomics methods...

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..We demonstrate three principal advantages of this system: nearly continuous MS utilization, duplicate analysis without requirement for additional sample, and targeting of important but undersampled features in the replay run...

..The CSF proteome has only partial overlap with the plasma proteome, thus it is produced locally rather than deriving from plasma. Our work offers insights into CSF composition and origin...