Identifying Proteins with Tandem Mass Spectrometry Lectures识别和串联质谱蛋白质讲座.pptVIP

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Identifying Proteins with Tandem Mass Spectrometry Lectures识别和串联质谱蛋白质讲座.ppt

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* Forth so that the peaks shouldn’t align. They used this number, also called the Auto-Correlation, as their background. * This is another representation of the Cross Correlation and the Auto Correlation. * The XCorr score is the Cross Correlation divided by the average of the auto correlation over a 75 AMU range. The XCorr is high if the direct comparison is significantly greater than the background, which is obviously good for peptide identification. * And this is actually a pretty robust method for estimating how accurate the match is, and so far, there really haven’t been any significant improvements on it. The DeltaCn is another score that scientists often use, which measures how good the XCorr is relative to the next best match. As you can see, this is actually a pretty crude calculation. * Here’s another representation of that sentiment. The XCorr is a strong measure of accuracy, whereas the DeltaCn is a weak measure of relative goodness. * Obviously, there could be an alternative method that focuses more on the success of the relative score. Mascot and X! Tandem fit that bill. * Now the X! Tandem accuracy score is rather crude. It only considers B and Y ions and attaches these factorial terms with a very admittedly hand waving argument. * But instead of just considering the best match to the second best, it looks at the distribution of lower scoring hits, assuming that they are all wrong. This is somewhat based on ideas pioneered with the BLAST algorithm. Here, every bar represents the number of random matches at a given score. The X! Tandem creators found that the distribution decays (or slopes down) exponentially… * And the log of the distribution is relatively linear because of the exponential decay. * If the distribution represents the number of random matches at any given score, the linear fit should correspond to the expected number of random matches. * And from this, you can calculate the likelihood that the best match is random. In this