Titlebook: Introduction to Proteomics; Tools for the New Bi Daniel C. Liebler Book 2002 Springer Science+Business Media New York 2002 Proteomics.prote

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Overview of Analytical Proteomicsound one essential fact: most peptide sequences of approximately six or more amino acids are largely unique in the proteome of an organism. Put another way, a typical six amino acid peptide maps to a single gene product. Thus, if we can obtain the sequence of the peptide or if we can accurately meas

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Protein Digestion Techniquess simply by measuring the masses of intact proteins? Unfortunately, intact mass measurements are of relatively little use for three reasons. First, as good as MS instruments are, there are still errors in the measurements they produce. The greater the mass of the protein, the greater the absolute ma

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Protein Identification by Peptide Mass Fingerprintingein then is identified by matching the measured peptide masses to corresponding peptide masses from protein or nucleotide sequence databases. Peptide mass fingerprinting works well for analytical proteomics because it combines a conceptually simple approach with robust, high-throughput instrumentati

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Peptide Sequence Analysis by Tandem Mass SpectrometryWhen we searched a human/mouse protein sequence database, we found two “perfect” hits for this peptide, both of which had ./. 1529.7384 for the [M+H]. ion. Both corresponded to hemoglobin alpha peptides that are highly conserved between mice and men:

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Protein Identification with Tandem Mass Spectrometry Datad by BLAST searching of the sequence against a sequence database to identify the protein. This is a perfectly reasonable approach—as long as there are only a few spectra to deal with. Manual . interpretation of an individual MS-MS spectrum takes between half an hour and a couple of days, depending o

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SALSA: An Algorithm for Mining Specific Features of Tandem MS Data come from?” Sequest and similar programs are well-suited to the task of protein identification from peptide MS-MS data. However, the proposition becomes a bit different if we want to do something other than simply identify what proteins are present in a sample. Consider the following scenarios:

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Protein Expression Profilingrated that gene-expression patterns in cells are also changing constantly. Indeed, one can use either old or new technologies to observe regular changes in the status of many enzymes during the daily life cycle of an organism or in the cycle of a cell. All this suggests that the proteomes of cells a