Articles tagged: benchmark

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Posted by Ville Koskinen (September 22, 2021)

Identify more HLA peptides

Endogenous peptides are challenging to identify by database searching. A Mascot no-enzyme search matches every subsequence of a protein to the observed spectrum, which makes a very large search space even if precursor tolerance is tight. As a result, Mascot score thresholds tend to be conservative and sensitivity is reduced. Mascot ships with Percolator, which often improves discrimination between true [...]

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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 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 (June 14, 2019)

What are you inferring?

Benchmarking protein inference is notoriously difficult. Artificial samples of known content tend to be too simple while real samples lack ground truth. An interesting approach was adopted for the ABRF iPRG 2016 study, and has been the subject of a publication from The et al. A collection of human Protein Epitope Signature Tags (PrESTs) were expressed in E. coli and [...]

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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 (November 14, 2016)

Benchmarking your Mascot Server

In an earlier blog post we talked about choosing the right hardware for a Mascot Server and mentioned that the major performance bottle neck is the CPU performance. We also looked at the PassMark PerformanceTest CPUBenchmark as a way of predicting the performance of a Mascot Server. In this article we will look at how to measure Mascot Server performance [...]

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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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Posted by Richard Jacob (December 14, 2014)

Running Mascot Server on a supercomputer

A supercomputer comprises a large number of dedicated processors, typically hundreds to thousands, that are situated close together in racks and cabinets and connected by a fast network. An individual computational node might look like a normal server or may be a more specialized blade server or a bare bones system of the sort Google and Facebook sometimes use. Their [...]

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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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Posted by John Cottrell (January 20, 2014)

How long should a search take? – Hardware and configuration

This question comes up quite frequently. Sometimes in the form of "How large a licence do I need?" and sometimes as "My searches seem slower since I re-installed Mascot / updated to the new version / moved to new hardware." Resisting the temptation to reply "How long is a piece of string?", let’s review some of the factors that influence [...]

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