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Articles tagged: tutorial
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 [...]
Back to basics 3: Quantitation statistics
Mascot Server and Distiller support a number of different quantitation methods. These methods are carried out at the peptide level, the peptides are then grouped into protein families, and the peptide quantitation results used to calculate protein ratio values. Mascot and Distiller perform a number of statistical procedures and tests to give you an indication of the quality and reliability [...]
Back to Basics 2: Common mistakes
When a search on our public web fails, we are often contacted to provide some help. These are some of the common mistakes we have seen. Most of the focus here is on Peptide Mass Fingerprint (PMF) searches, which are still very popular on our public web site. If you are new to database searching, you may find this tutorial [...]
Back to Basics: Optimize your search parameters
Every now and then you need to determine good search parameters for a data set. They may be different from the normal ones you use due to a change in instrumentation, you may be analyzing data from a public resource like PRIDE/Proteome exchange or it could be data from a collaborator. Whatever the reason, here’s a quick overview on how [...]
Mascot Security: priority settings
An earlier article looked at privacy settings in Mascot security. This article looks at priority settings; the settings that allow one user group to run bigger or longer or more complex searches than another. Many aspects of searches can be limited by user group. The important ones are: SEARCH: Allow msms no enzyme searches SEARCH: Maximum number of concurrent searches [...]