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Articles tagged: DIA
Probabilistic spectrum-centric scoring for DIA
In DIA analysis, it feels like far too much attention is devoted to maximising the number of identified proteins and too little on the quality of results. We’re working on a universal spectrum-centric solution for the analysis of DIA data, called Mascot DIA. The key focus is on using all the peak information in the MS/MS scan, without prior assumptions [...]
You’ve got to pick a precursor or two: Precursor detection in Mascot DIA
We’re working on a universal spectrum-centric solution for the analysis of DIA data, called Mascot DIA. A preview was presented at our ASMS 2025 Breakfast Meeting, the slides from which are free to download. Last month’s blog article outlines the spectrum-centric search approach for DIA data and compares it to the more common peptide-centric approach. One thing that is essential [...]
The promise of spectrum-centric DIA
We’re working on a universal spectrum-centric solution for the analysis of DIA data, called Mascot DIA. A preview was presented at our ASMS 2025 Breakfast Meeting, whose slides are free to download. But what is spectrum-centric searching and what is it meant to solve? Complementary approaches “Peptide-centric” and “spectrum-centric” analysis are broad technical terms that are mainly of interest to [...]
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 [...]
Generating high quality spectral libraries for DIA-MS
Using Mascot Daemon, Mascot Distiller and Mascot Server A recent paper from Manda et al.[1] describes a pipeline to generate high quality spectral libraries from Data-Dependent Acquisition (DDA) experiments for use in searching Data-Independent Acquisition (DIA) data, starting from the raw data, through to generating the library from the search results. The pipeline uses a collection of different tools in [...]
Searching DIA data, especially Swath
DIA-Umpire is a new, open source Java program that enables untargeted peptide and protein identification and quantitation using DIA data. A detailed description can be found in Nature Methods. The DIA-Umpire signal extraction module deconvolutes the DIA data to create a conventional DDA-type peak list, suitable for database searching. The software is intended to be applicable to DIA from any [...]