Blog
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 [...]
Mascot Distiller 20th anniversary
This year is the 25th anniversary of Matrix Science and 25 years of Mascot Server, but it’s also the 20th birthday of Mascot Distiller! Mascot Distiller 1.0 was released in June 2003 and it’s still under active development today. Distiller started as a GUI application for browsing and peak picking native (raw, binary) mass spectrometry data files. Let’s have a [...]
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 [...]
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 [...]
Mascot Daemon Export Extender
Mascot Daemon has two features to help with automation and creating pipelines. The first is the AutoExport feature that allows you to configure and export a report into a CSV file, mzIdentML file or other format that Mascot Server supports with the options you choose. This happens once the search is complete. The lesser known but more powerful feature is [...]
How old is the software in that publication?
Most proteomics data analysis requires complex and sophisticated software. When you read the methods section of a journal article, it should state the software name and version number, as this is the minimum required for reproducibility of the data analysis. Often it is useful to also know how old the software package is. If it’s Mascot Server, there is now [...]
Get more search speed with SplitNumberOfQueries
Mascot Server has several parameters and options that have an effect on database search duration. One of them is SplitNumberOfQueries, which specifies how many queries (MS/MS spectra) are searched at a time. The default is 1000 queries, which is reasonable, but like all defaults, it isn’t optimal. On most hardware, increasing it to 2000 will yield an immediate 10-20% performance [...]
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 [...]
25 years of Matrix Science
Happy 25th birthday, Matrix Science! A lot has happened since John Cottrell and David Creasy founded the company in 1998, and proteomics today certainly looks very different to the bleeding edge of science back then. The success of any company could be attributed to various causes, but the simple fact is that we would not be here without our loyal [...]
Mascot in the Cloud
Cloud computing is the IT paradigm of our times. More and more business services and applications are delivered as a subscription service, where the software runs in a data centre somewhere, operated by a third-party cloud platform. We are often asked whether you can run Mascot Server “in the cloud” and if so, whether it’s the right solution. The answers [...]
Peak picking intact crosslink spectra with Mascot Distiller
There are several important factors to take into account when carrying out peakpicking for an intact crosslinked dataset. You’ll typically be dealing with higher charge state precursors to handle the larger masses of the linked peptides, and the MS/MS spectra are inherently complex, chimeric spectra with fragments from the alpha and beta peptides. To look at the effects of adjusting [...]
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