Blog
Articles tagged: tutorial
Adding a custom AI/ML adapter to Mascot
Mascot Server 3.0 and later ship with MS2Rescore for predicting retention time and spectral similarity. What if you wanted to use a different AI/ML system for predictions? Mascot Server has an application programming interface (API) exactly for this purpose. The tutorial below includes a fully working Python script that you can use as a starting point for your own adapter. [...]
Mascot workflow for LC-MS/MS data
Data analysis in mass spectrometry proteomics is complex and, nowadays, almost entirely software driven. Processing a raw file, peptide identification by database searching, protein inference and protein quantitation all have many steps and built-in assumptions, not to mention a huge number of parameters. Software continues to evolve as does best practice. Whether you are new to mass spectrometry proteomics or [...]
Tutorial: Creating custom reports in Mascot Distiller
Mascot Distiller 2.8 reports are written in Python, a commonly used programming language, and use Mascot Parser to access the search and quantitation results. We supply a range of standard reports, including reports for quality, clustering and statistical analysis, which we took a look at in an earlier blog article. In addition to these, you can develop your own reports [...]
ABRF iPRG 2023 crosslinking study
One of the great things about the Association of Biomolecular Resource Facilities (ABRF) is their technical studies involving real samples and data. The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year the iPRG group has put together a crosslinking study. The goal is to teach [...]
Solving a puzzle with Mascot Distiller de novo
Have you tried either of the MS/MS interpretation challenges organised by EUPA and LBMSDG? Maybe you are expert enough to read off the peptide sequence, directly. If so, you can stop reading right here! If your interpretation skills and mental arithmetic are a bit rusty, we thought it might be useful to walk through how Mascot Distiller plus a bit [...]
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 [...]
Common myths about protein scores
Mascot Server is used in many different application areas by both mass spectrometry experts and non-experts. Over the years, we’ve spotted a few recurring misconceptions about how protein scores are interpreted and used. All the examples come from recent peer-reviewed papers. Protein scores in PMF searches The very first thing to check is, what type of experiment is being reported. [...]
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 [...]
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 [...]