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Articles tagged: scoring
Back to basics 5: Peptide-spectrum match statistics
Mascot can identify peptides in uninterpreted MS/MS data. Observed spectra are submitted to Mascot as search queries. A query specifies the precursor ion m/z and charge state as well as the MS/MS peak list. Mascot digests protein sequences from the chosen database and selects peptide sequences whose mass is within the specified tolerance of the query’s precursor mass. The software [...]
Mascot workflows in Proteome Discoverer
For many users of Thermo instruments, Proteome Discoverer (PD) is their primary user interface for database searching, and Mascot is represented by a node in the workflow. This article collects together a few tips and observations concerning Proteome Discoverer 2.3 and Mascot Server 2.6. Proteome Discoverer Configuration Under Administration; Mascot Server, the setting Max. MGF File Size [MB] has a [...]
Some peaks are more equal than others
When you look at the details of a peptide match in the Mascot Peptide View report, only a small number of the peaks may be labelled in the spectrum graphic and highlighted in the table of fragment masses. We often got challenged about this: "Why haven’t you labelled these other peaks that clearly match?". So, in Mascot 2.3, we added [...]
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 [...]
High mass accuracy: precursors
High performance instruments can deliver low ppm accuracy for both precursors and fragments. How does this impact database search? In this post, the first of two, we’ll look at the implications of very accurate precursor m/z. High mass accuracy and high resolution have transformed mass spectrometry over the last few years. Apart from increasing file sizes, and maybe the time [...]