Jacek R Wisniewski

..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...

..Supplementary material is available at http://iec01.mie.utoronto.ca/~thodoros/Bukhman/...

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

..MED-FASP offers efficient exploration of previously unused sample material, increasing depth of proteomic analyses and sequence coverage...

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

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

..It enables characterization of entire proteomes with unprecedented sensitivity and precision, providing platforms for identification of biomarkers and drug targets...

..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...

..In the focus are approaches allowing large scale mapping rather than analytical methods suitable for studying individual proteins or non-complex mixtures...

..N(epsilon)-lysine formylation in chromosomal proteins is relatively abundant, suggesting that it may interfere with epigenetic mechanisms governing chromatin function, which could lead to deregulation of the cell and disease...

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

..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...

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

..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...

..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...

..Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type...

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

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

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

..The N-glycoproteome contains a plethora of modification sites on factors important in development, organ-specific functions, and disease...

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

..The methods applied here can be directly applied to studying nerve systems and their disorders...

..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...

..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...

..The entire procedure allows processing and preparation of samples of minute amounts as 10-20 mg tissue and therefore can be extremely helpful for proteomic profiling of small pieces of tissue and clinical material...

..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...

..NARR only partially colocalizes with fibrillarin, the pre-ribosomal RNA-processing protein, positioning NARR in a separate niche within the rDNA cluster...

..Here, we describe an analytical workflow for analysis of laser-capture microdissected formalin-fixed and paraffin-embedded samples that allows studying proteomes to a depth of 10 000 proteins per sample...

..The combination of quantifying the secretome of cancer cell lines and of human plasma with a super-SILAC approach appears to be a promising new approach for finding markers of disease...

..Our work now allows in-depth study of brain membrane proteomes, such as of mouse models of neurological disease...

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