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MATRIXSCIENCE.COM
GETTING THE MOST OUT OF YOUR MASCOT SERVER HARDWARE A Mascot Server needs a minimum of 16GB of RAM on a standalone computer or the head node of a cluster. Less than 16GB may mean Mascot is not able to bring very large databases on line. For larger Mascot Server licenses, with 3 or more CPU’s, we recommend an additional 1GB of RAM per a core. If the Mascot Server has insufficient RAM the MASS-TOLERANT VS ERROR TOLERANT The frequency distributions for the bins illustrated in Figure 2 of the paper are narrow Gaussians, but some of the other bins with high counts extend over a very wide mass range and are not well fitted by a Gaussian, so have been labelled artefact. DOES PROTEIN FDR HAVE ANY MEANING? Does protein FDR have any meaning? Its easy to grasp the concept of using a target/decoy search to estimate peptide false discovery rate. You search against a decoy database where there are no true matches available, so the number of observed matches provides a good estimate of the number of false matches in the results from the target. VARIABLE MODIFICATIONS IN MASCOT 2.7SEE MORE ON MATRIXSCIENCE.COM NCBINR IS DEAD, LONG LIVE NCBIPROT NCBInr is dead, long live NCBIprot. NCBI recently dropped gi number identifiers, as explained in this blog article.This change breaks the old database definition, NCBInr, so we have created a new definition for accession.version identifiers, NCBIprot; now available on thissite.
INSTRUMENT SPECIFIC MS/MS ION SERIES MATCHING 2 Ion series in Mascot 1.7 •a, b, and y ions •Neutral loss of 17 from all ions •2+ ions if precursor was 2+ or higher Room for improvement? •More ion series, esp. high energy fragments •Internal fragments •Neutral loss of 17 or 18 is composition dependent In Mascot 1.7, all MS/MS data was matched and scored using the a, b, and y ion series. PHOSPHORYLATION SITE ANALYSIS 3 ASMS 2004 Search for phosphorylation, May 13 2004 - 656 messages One of the best sources of information on phosphorylation is the ABRF email discussion group. STEP AWAY FROM THE IODOACETAMIDE Step away from the iodoacetamide. In our July newsletter, we featured a paper from Torsten Müller and Dominic Winter, University of Bonn, concerning alkylation artefacts.Some of their findings were quite shocking. For example, differences of more than 9 fold in numbers of identified methionine-containing peptides for in-gel digested samples between iodine- and non-iodine-containing ION SERIES FOR ETHCD Ion series for EThcD. The ion series considered during a Mascot search are selected by choosing an instrument type. If you have Mascot Server in-house, you can edit existing instrument types and create new ones. There are 17 ion series available, and Mascot takes an iterative approach to scoring. If the number of matched peaks in a particular BACK TO BASICS 5: PEPTIDE-SPECTRUM MATCH STATISTICSSEE MORE ONMATRIXSCIENCE.COM
GETTING THE MOST OUT OF YOUR MASCOT SERVER HARDWARE A Mascot Server needs a minimum of 16GB of RAM on a standalone computer or the head node of a cluster. Less than 16GB may mean Mascot is not able to bring very large databases on line. For larger Mascot Server licenses, with 3 or more CPU’s, we recommend an additional 1GB of RAM per a core. If the Mascot Server has insufficient RAM the MASS-TOLERANT VS ERROR TOLERANT The frequency distributions for the bins illustrated in Figure 2 of the paper are narrow Gaussians, but some of the other bins with high counts extend over a very wide mass range and are not well fitted by a Gaussian, so have been labelled artefact. DOES PROTEIN FDR HAVE ANY MEANING? Does protein FDR have any meaning? Its easy to grasp the concept of using a target/decoy search to estimate peptide false discovery rate. You search against a decoy database where there are no true matches available, so the number of observed matches provides a good estimate of the number of false matches in the results from the target. VARIABLE MODIFICATIONS IN MASCOT 2.7SEE MORE ON MATRIXSCIENCE.COM NCBINR IS DEAD, LONG LIVE NCBIPROT NCBInr is dead, long live NCBIprot. NCBI recently dropped gi number identifiers, as explained in this blog article.This change breaks the old database definition, NCBInr, so we have created a new definition for accession.version identifiers, NCBIprot; now available on thissite.
INSTRUMENT SPECIFIC MS/MS ION SERIES MATCHING 2 Ion series in Mascot 1.7 •a, b, and y ions •Neutral loss of 17 from all ions •2+ ions if precursor was 2+ or higher Room for improvement? •More ion series, esp. high energy fragments •Internal fragments •Neutral loss of 17 or 18 is composition dependent In Mascot 1.7, all MS/MS data was matched and scored using the a, b, and y ion series. PHOSPHORYLATION SITE ANALYSIS 3 ASMS 2004 Search for phosphorylation, May 13 2004 - 656 messages One of the best sources of information on phosphorylation is the ABRF email discussion group. ION SERIES FOR ETHCD Ion series for EThcD. The ion series considered during a Mascot search are selected by choosing an instrument type. If you have Mascot Server in-house, you can edit existing instrument types and create new ones. There are 17 ion series available, and Mascot takes an iterative approach to scoring. If the number of matched peaks in a particular NEW FEATURES IN MASCOT SERVER 2.8 New features in Mascot Server 2.8 New statistical model for error tolerant searches. The Error Tolerant Search finds unsuspected modifications, peptides with non VARIABLE MODIFICATIONS IN MASCOT 2.7 Variable modification permutation in Mascot 2.7. Modification iteration in Mascot 2.7 uses a single, consistent method – it no longer switches between two methods. This is controlled by 3 user definable parameters, described in table 1 below, with default values which give similar depth and speed of search to Mascot 2.6 or earlier: SOLVING A PUZZLE WITH MASCOT DISTILLER DE NOVO Under Peak profile, set all three width values to 0.02. Choose Process scan from the Processing menu or the toolbar. You should now have something similar to this: Click to view full size image. From the Tools menu, choose Preferences, Sequence tag / De Novo. Since we cannot assume this is a tryptic peptide, set Enzyme to Specific andnon-specific.
NCBINR IS DEAD, LONG LIVE NCBIPROT NCBInr is dead, long live NCBIprot. NCBI recently dropped gi number identifiers, as explained in this blog article.This change breaks the old database definition, NCBInr, so we have created a new definition for accession.version identifiers, NCBIprot; now available on thissite.
COMMON MYTHS ABOUT PROTEIN SCORES A paper might say the authors accepted “all proteins with score > 51″ or “protein scores greater than 67 (p* Home
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