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Articles tagged: chimeric spectra
Finding unsuspected modifications in narrow-window DIA data using the Mascot Error Tolerant Search
Mascot’s spectrum-centric approach doesn’t have the constraints on variable modifications, missed cleavages and protein sequences that are required by peptide-centric DIA tools. In fact, it’s nearly trivial to identify unsuspected variable modifications in narrow-window DIA data using the Mascot Error Tolerant Search. There can be many reasons for failing to get a significant sequence match to an MS/MS spectrum. Three [...]
Spectrum-centric searching of narrow window DIA data with Mascot Server
Data-independent acquisition (DIA) can be broadly separated into narrow window and wide window strategies depending on the size of the isolation window. There are also two data analysis strategies – peptide-centric and spectrum-centric. Wide window DIA typically requires a peptide-centric approach, but narrow window DIA data can be analysed either way. Mascot Server is spectrum-centric, and it’s possible to run [...]
Identifying peptides from chimeric spectra (DDA, DIA)
Many traditional search engines assume the MS/MS spectrum of a peptide is produced by a single precursor. This is often true when you run a single-species tryptic digest in data dependent acquisition (DDA) mode with a narrow isolation window. Once you change the acquisition strategy or analyse a complex mixture, like an environmental sample, it’s possible for two or more [...]
How many of you are there in there? Processing and searching chimeric MS/MS spectra with Mascot Distiller and Mascot Server
In the typical shotgun proteomics experiment, the assumption is that each MS/MS spectrum is derived from a single precursor selected by the Mass Spectrometer for fragmentation. However, in practice, near isobaric precursors can co-elute and undergo co-fragmentation resulting in chimeric MS/MS spectra containing fragments from multiple different precursor peptides. With high resolution data, it is possible for these overlapping isotope [...]