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Posted by John Cottrell (May 17, 2017)

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 ion series is no better than [...]

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Posted by Patrick Emery (August 18, 2016)

Not Better Together: Processing and searching combined CID+ETD datasets with Mascot Distiller 2.6

Many modern mass spectrometers will produce raw datasets containing more than one type of scan data. For example, a common experiment using a Thermo Orbitrap instrument is to select the most abundant precursor ions and either independently fragment them using both ETD and CID fragmentation, or use a decision tree to select different fragmentation methods depending on, for example, the [...]

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Posted by John Cottrell (December 17, 2012)

High mass accuracy: fragments

In an earlier post, we looked at the implications for database search of very accurate precursor m/z. In this post, we discuss what to expect from high accuracy measurement of fragment m/z. It can come as a surprise that the accuracy of the fragment m/z values in an MS/MS spectrum has only a modest effect on the score for a [...]

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