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Sample Complexity (sample + complexity)
Selected AbstractsOn the sample-complexity of ,, identificationINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 7 2001S. R. Venkatesh Abstract In this paper we derive the sample complexity for discrete time linear time-invariant stable systems described in the ,, topology. The problem set-up is as follows: the ,, norm distance between the unknown real system and a known finitely parameterized family of systems is bounded by a known real number. We can associate, for every feasible real system, a model in the finitely parameterized family that minimizes the ,, distance. The question now arises as to how long a data record is required to identify such a model from noisy input,output data. This question has been addressed in the context of l1, ,2 and several other topologies, and it has been shown that the sample-complexity is polynomial. Nevertheless, it turns out that for the ,, topology the sample-complexity in the worst case can be infinite. Copyright © 2001 John Wiley & Sons, Ltd. [source] Analysis of nuclear proteome in C57 mouse liver tissue by a nano-flow 2-D-LC,ESI-MS/MS approachJOURNAL OF SEPARATION SCIENCE, JSS, Issue 17 2006Jie Zhang Abstract The analysis of whole cell or tissue extracts is too complex for current protein identification technology and not suitable for the study of proteins with low copy levels. To concentrate and enrich low abundance proteins, organelle proteomics is a promising strategy. This approach can not only reduce the protein sample complexity but also provide information about protein location in cells, organs, or tissues under analysis. Nano-flow two-dimensional strong-cation exchange chromatography (SCX),RPLC,ESI-MS/MS is an ideal platform for analyzing organelle extracts because of its advantages of sample non-bias, low amounts of sample required, powerful separation capability, and high detection sensitivity. In this study, we apply nano-scale multidimensional protein identification technology to the analysis of C57 mouse liver nuclear proteins. Organelle isolation has been optimized to obtain highly pure nuclei. Evaluation of nucleus integrity and purity has been performed to demonstrate the effectiveness of the optimized isolation procedure. The extracted nuclear proteins were identified by five independent nano-flow on-line SCX,RPLC,ESI-MS/MS analyses to improve the proteome coverage. Finally, a total of 462 proteins were identified. Corresponding analyses of protein molecular mass and pI distribution and biological function categorization have been undertaken to further validate our identification strategy. [source] A novel approach and protocol for discovering extremely low-abundance proteins in serumPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2006Yoshinori Tanaka Abstract The proteomic analysis of serum (plasma) has been a major approach to determining biomarkers essential for early disease diagnoses and drug discoveries. The determination of these biomarkers, however, is analytically challenging since the dynamic concentration range of serum proteins/peptides is extremely wide (more than 10,orders of magnitude). Thus, the reduction in sample complexity prior to proteomic analyses is essential, particularly in analyzing low-abundance protein biomarkers. Here, we demonstrate a novel approach to the proteomic analyses of human serum that uses an originally developed serum protein separation device and a sequentially linked 3-D-LC-MS/MS system. Our hollow-fiber-membrane-based serum pretreatment device can efficiently deplete high-molecular weight proteins and concentrate low-molecular weight proteins/peptides automatically within 1,h. Four independent analyses of healthy human sera pretreated using this unique device, followed by the 3-D-LC-MS/MS successfully produced 12,000,13,000 MS/MS spectra and hit around 1800,proteins (>95% reliability) and 2300,proteins (>80% reliability). We believe that the unique serum pretreatment device and proteomic analysis protocol reported here could be a powerful tool for searching physiological biomarkers by its high throughput (3.7,days per one sample analysis) and high performance of finding low abundant proteins from serum or plasma samples. [source] Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteomePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2005Tao Liu Abstract Automated multidimensional capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been increasingly applied in various large scale proteome profiling efforts. However, comprehensive global proteome analysis remains technically challenging due to issues associated with sample complexity and dynamic range of protein abundances, which is particularly apparent in mammalian biological systems. We report here the application of a high efficiency cysteinyl peptide enrichment (CPE) approach to the global proteome analysis of human mammary epithelial cells (HMECs) which significantly improved both sequence coverage of protein identifications and the overall proteome coverage. The cysteinyl peptides were specifically enriched by using a thiol-specific covalent resin, fractionated by strong cation exchange chromatography, and subsequently analyzed by reversed-phase capillary LC-MS/MS. An HMEC tryptic digest without CPE was also fractionated and analyzed under the same conditions for comparison. The combined analyses of HMEC tryptic digests with and without CPE resulted in a total of 14,416 confidently identified peptides covering 4294 different proteins with an estimated 10%,gene coverage of the human genome. By using the high efficiency CPE, an additional 1096 relatively low abundance proteins were identified, resulting in 34.3% increase in proteome coverage; 1390,proteins were observed with increased sequence coverage. Comparative protein distribution analyses revealed that the CPE method is not biased with regard to protein Mr,, pI, cellular location, or biological functions. These results demonstrate that the use of the CPE approach provides improved efficiency in comprehensive proteome-wide analyses of highly complex mammalian biological systems. [source] Cysteine-reactive covalent capture tags for enrichment of cysteine-containing peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 21 2009Priscille Giron Considering the tremendous complexity and the wide dynamic range of protein samples from biological origin and their proteolytic peptide mixtures, proteomics largely requires simplification strategies. One common approach to reduce sample complexity is to target a particular amino acid in proteins or peptides, such as cysteine (Cys), with chemical tags in order to reduce the analysis to a subset of the whole proteome. The present work describes the synthesis and the use of two new cysteinyl tags, so-called cysteine-reactive covalent capture tags (C3T), for the isolation of Cys-containing peptides. These bifunctional molecules were specifically designed to react with cysteines through iodoacetyl and acryloyl moieties and permit efficient selection of the tagged peptides. To do so, a thioproline was chosen as the isolating group to form, after a deprotection/activation step, a thiazolidine with an aldehyde resin by the covalent capture (CC) method. The applicability of the enrichment strategy was demonstrated on small synthetic peptides as well as on peptides derived from digested proteins. Mass spectrometric (MS) analysis and tandem mass spectrometric (MS/MS) sequencing confirmed the efficient and straightforward selection of the cysteine-containing peptides. The combination of C3T and CC methods provides an effective alternative to reduce sample complexity and access low abundance proteins. Copyright © 2009 John Wiley & Sons, Ltd. [source] | ||||||||||