Articles tagged: tutorial

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Posted by Ville Koskinen (September 16, 2019)

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. [...]

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Posted by Ville Koskinen (May 17, 2019)

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 [...]

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Posted by Richard Jacob (March 15, 2019)

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 [...]

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Posted by Patrick Emery (October 15, 2018)

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 [...]

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Posted by David Creasy (August 17, 2018)

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 [...]

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Posted by Richard Jacob (July 16, 2018)

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 [...]

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Posted by John Cottrell (April 17, 2017)

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 [...]

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Posted by John Cottrell (March 15, 2017)

Mascot Security: privacy settings

It is perfectly possible to share a single Mascot Server between individuals or groups who require privacy for their searches. Mascot Security provides the mechanism to limit access to result reports, databases, and even custom modifications. Mascot security is not designed to be highly secure – a determined hacker could probably find ways around it without too much difficulty – [...]

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Posted by John Cottrell (November 11, 2014)

Using Mascot security to share search results

How can you share Mascot result reports with external colleagues or customers? There is a help page that describes some off-line solutions, but it doesn’t cover the most flexible solution, which is to use Mascot security to provide external users with limited access to your Mascot Server. In a typical configuration, these users would be able to view their own [...]

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Posted by John Cottrell (February 26, 2014)

How long should a search take? – Data and search parameters

An earlier article discussed how hardware choices affect search speed. This article looks at the influence of the peak list and the search parameters. It’s important to distinguish between the time spent on the search itself and the time spent loading the result report; different factors apply to these two steps. It is not unknown for loading the result report [...]

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