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Posted by Richard Jacob (December 5, 2023)

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 [...]

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Posted by John Cottrell (October 19, 2020)

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 [...]

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Posted by John Cottrell (June 17, 2020)

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 [...]

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Posted by John Cottrell (May 19, 2020)

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 [...]

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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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