Blog
Articles tagged: fragmentation
Best MS2PIP model for Thermo Orbitrap
Mascot Server 3.0 greatly improves protein and peptide identification rates with Thermo Orbitrap instruments. The new version ships with MS2PIP, which provides fragment intensity predictions. When the database search results are correlated with predicted spectra, it boosts the number of statistically significant matches even with straightforward tryptic digests. CID and HCD models For qualitative work and label-free quantitation, Mascot Server [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]