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Articles tagged: benchmark
Best MS2PIP model for Thermo Orbitrap
Mascot Server 3.0 greatly improves protein and peptide identification rates with Thermo Orbitrap instruments. The new version ships with MS2PIP, which provides fragment intensity predictions. When the database search results are correlated with predicted spectra, it boosts the number of statistically significant matches even with straightforward tryptic digests. CID and HCD models For qualitative work and label-free quantitation, Mascot Server [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]