Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years


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Posted by Ville Koskinen (February 16, 2024)

How to run the public Mascot service

The public Mascot service running on this website recently had its 25th birthday: the service was launched in November 1998. The purpose is to let you evaluate the product before buying, but it’s also useful for small data sets and proteomics training courses. We’re a small company and our main activity is software development. The secrets to running the public [...]

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Posted by Ville Koskinen (April 25, 2023)

Get more search speed with SplitNumberOfQueries

Mascot Server has several parameters and options that have an effect on database search duration. One of them is SplitNumberOfQueries, which specifies how many queries (MS/MS spectra) are searched at a time. The default is 1000 queries, which is reasonable, but like all defaults, it isn’t optimal. On most hardware, increasing it to 2000 will yield an immediate 10-20% performance [...]

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Posted by Ville Koskinen (January 17, 2023)

Mascot in the Cloud

Cloud computing is the IT paradigm of our times. More and more business services and applications are delivered as a subscription service, where the software runs in a data centre somewhere, operated by a third-party cloud platform. We are often asked whether you can run Mascot Server “in the cloud” and if so, whether it’s the right solution. The answers [...]

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Posted by Ville Koskinen (April 19, 2022)

NCBI nr in Mascot Server 2.8.1

Mascot Server 2.8.01 patch was released in March 2022. One of the big improvements is optimising the compression speed of the NCBI nr database, available as the NCBIprot predefined definition. We’ve greatly decreased the time it takes to bring the database online, as well as removed an inadvertent limitation on database size. The patch is available to download on the [...]

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Posted by Patrick Emery (October 25, 2021)

Choosing hardware for Mascot Distiller

One question which comes up frequently with regards to Mascot Distiller is what is a good specification for the workstation it’s going to be installed on. By that, we’re really interested in what sort of CPU you should be getting, how much RAM the workstation should have, and what sort of disk drives (SSD or HDD) should you be getting. [...]

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Posted by Ville Koskinen (August 16, 2021)

Addressing disk bottlenecks

One of the improvements in Mascot Server 2.8 is reducing the overall search time. We’ve benchmarked the new version with a variety of data sets of different sizes on a range of PCs and servers, and the typical reduction in run time is 20-35%. The incremental improvement is achieved by addressing disk access bottlenecks at the beginning, during and at [...]

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Posted by Ville Koskinen (June 17, 2021)

NCBI nr tips

NCBI nr is the comprehensive database of non-identical protein sequences compiled by the National Center for Biotechnology Information. The database is available in Mascot Server as the NCBIprot predefined definition. If possible, nr should be used as the database of last resort due to its huge size. The January 2021 version contains 338 million protein sequences and the FASTA file [...]

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Posted by Richard Jacob (December 22, 2020)

How large a Mascot Server licence do I need?

One frequent question from new customers is how many CPUs do I need to licence for my Mascot Server? This is actually two questions. First, Mascot is licensed in CPU units, where 1 CPU is good for 4 cores. The computer can have more than one processor, and each processor can have more than 4 cores, but only the number [...]

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Posted by John Cottrell (September 18, 2018)

Mascot Server cluster mode

Most modern Intel processors have at least 4 cores and some models have 12 cores or more. Mascot Server is licenced by the CPU, where each CPU corresponds to 4 physical cores, so a single PC is perfectly sufficient for licences of 1 or 2 CPU. If you have a larger licence, there comes a point where it is not [...]

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Posted by Richard Jacob (September 14, 2016)

Getting the most out of your Mascot Server hardware

A Mascot Server search consists of a number of separate stages. Once the input file has been uploaded to the server, Mascot starts by sorting the peak list by peptide molecular mass. Unless the peak list is very small, it also divides the peak list into chunks limited in size by either the number of bytes or the number of [...]

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