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Posted by Ville Koskinen (July 13, 2023)

Get better HCD results by matching internal fragments

Mascot ships with several instrument definitions, which define the fragment ion series used for matching and scoring. All of them enable b ions and most enable y ions, and a few like ETD-TRAP also enable c and z+1. Mascot can also match internal fragments, which are formed by double backbone cleavage, a combination of a/b type and y type. Of [...]

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Posted by Ville Koskinen (February 16, 2022)

Single-cell peptide fragmentation spectra

More single-cell proteomics studies are published each year as instruments become more sensitive and sample preparation is optimised. A recent publication in the Journal of Proteome Research, Features of Peptide Fragmentation Spectra in Single-Cell Proteomics, highlights potential challenges to protein and peptide identification by database searching. Boekweg et al. computationally examined the fragmentation spectra of peptides from bulk samples, 2ng [...]

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Posted by Patrick Emery (January 17, 2020)

The Third Column: MS/MS fragment ion decharging in Mascot Server 2.7

In the Mascot Generic (mgf) peak list format, MS/MS fragment ions are typically defined as pairs of values. The first value is the m/z of the fragment ion peak and the second the intensity of the peak. However, a third value can also be supplied – the charge state of the fragment ion. In Mascot 2.6 or earlier, the fragment [...]

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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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