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Articles tagged: Mascot Daemon
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 [...]
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 [...]
Complementary reporter ion clusters in TMT/TMTpro labeling
We recently received a support request about complementary ions in TMTpro labeling. Complementary ions are formed during fragmentation, where the precursor loses the reporter ion and carbon monoxide, leaving behind the peptide and the balance region of the label. Complementary ion spacing is similar to reporter ions but the mass varies depending on peptide mass. The customer was concerned that [...]
Using the Quantitation Summary to create reports and charts
An earlier article described how to create a Quantitation Summary in Mascot Daemon. This is a spreadsheet-like text file, where the rows correspond to proteins and the columns contain expression data for various samples in the form of abundances or ratios of abundances. A Quantitation Summary can be opened and manipulated in a spreadsheet program such as Excel, and it [...]
Tabulate expression data from multiple analyses with Mascot Daemon
Studies that use mass spectrometry-based quantitation often contain large numbers of individual analyses: samples from different sources or treatments or time points, possibly fractionated, with replicates and so forth. Using statistical methods to combine the analyses, extract meaningful information, and report it as charts and tables is a complex task that usually requires custom scripting in a language such as [...]
How to set up remote working
There are times when you unexpectedly find yourself having to work from home. Fear not: data analysis doesn’t need to stop when you’re away from the lab. Mascot Server has a client-server architecture, and the client PC can be located anywhere. Distiller and Daemon can also be used remotely, or they can be run on a remote client PC and [...]
Disaster recovery
There are a number of potential issues that can cause your Mascot Server or other computer infrastructure to stop working. In the worst case, you may need to do a full recovery from backups. This can be an involved procedure, but it is straightforward as long as you have backed up key configuration and data files. For disk or storage [...]
Back to basics 4: Mascot Daemon
Mascot Daemon is a client to Mascot Server that can automate the processing of raw data to peak lists and submit multiple searches to a central Mascot Server. It is included with the Mascot Server licence and can be installed on as many computers in the lab as you like. Processing raw data files will use CPU resources, so you [...]
Using a shared TaskDB with Mascot Daemon
Mascot Daemon is our automation client for Mascot Server. The client was introduced with Mascot Server version 1.6 and has been continually developed ever since. The licensing for Mascot Daemon allows as many copies of Daemon to be installed in your lab as you like. By default, each copy of Daemon uses its own task database, TaskDB, to store information [...]
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 [...]