PC specification for Mascot Distiller
Introduction
Mascot Distiller integrates with Mascot Server using a client-server architecture. The two possible configurations are:
- Mascot Server runs on PC 1 and Mascot Distiller runs on PC 2.
- Mascot Server and Mascot Distiller run on the same PC.
In case #1, check PC specification for Mascot Server for PC 1. The rest of this document provides recommendations for PC 2.
In case #2, you will need more RAM on the one PC. These are noted below where appropriate.
Quick reference
Any recent, high specification PC containing either Intel or AMD Ryzen processor(s) should make a suitable platform for Mascot. A GPU is not required.
For processing DIA experiments, we recommend a system with 16-24 processor cores with high ‘turbo’ clock speed (at least 4 GHz), at least 32GB of RAM and the largest SSD or NVMe disks available (at least 2TB). For DIA experiments with more than 20 raw files, we recommend at least 128GB of RAM and 32 processor cores.
For processing DDA experiments, a processor with 8-16 cores is sufficient.
If you are running Mascot Server on the same PC, check the Mascot Server requirements for processor and memory requirements. We recommend reserving 32GB for Mascot Server and 32GB for Mascot Distiller, for a total of 64GB of RAM.
Hardware virtualisation is discussed in Hardware virtualisation.
Speed versus throughput
Speed and throughput are related but different goals. Speed refers to the duration taken to process a file, while throughput is the number of files processed in a unit of time (say files per hour).
You can increase speed by adding more CPU cores/threads to the PC. However, as you add more threads, processing can hit other limiting factors such as code synchronisation points, file and memory access. Exactly when the increase in performance tails off will depend on the CPU type, workload and type of data.
Increasing throughput requires a system-level perspective. In Mascot DIA and Mascot DDA, processing is split between Mascot Server and Mascot Distiller. An easy way to increase throughput is to add more PCs running Mascot Distiller. This way, multiple experiments can be processed in parallel and database searching can share a single Mascot Server instance. Check the Mascot Server PC specification for how to increase database searching throughput.
Processor (CPU)
The two main PC processor manufacturers are Intel and AMD. Matrix Science does not currently support Mascot Distiller on other processor architectures.
Processor speed
The Geekbench CPU benchmark is a fairly good guide to the performance you can expect from Mascot Distiller. Because Mascot Distiller can use all the cores made available to it, it’s important to look at the multi-threaded performance of the CPU, not just the single-thread performance.
If you are running Mascot Server on the same PC, we recommend AMD Threadripper or AMD EPYC. These processors have both excellent single-thread performance and excellent multi-threaded performance.
Number of cores
Mascot Distiller will use all available cores for processing. Unless you plan to run Mascot Server on the same PC, it is rarely beneficial to use a processor with more than 64 cores. Scalability is better achieved by distributing raw file processing across multiple Distiller clients running on separate PCs.
If you plan to run Mascot Server on the same PC, you should choose a processor that satisfies both requirements. For Small or Medium Mascot Server licence, we recommend getting a processor with double the number of cores.
Intel Hybrid Architectures
Recent Intel processor families for desktop and mobile have a hybrid core architecture, starting from the 12th generation Intel Core processors. For example, Intel Core i7 12700 has 8 ‘ P’ performance and 4 ‘E’ efficiency cores.
Mascot Distiller can be run on both P and E cores, but do note that E cores are typically much slower than P cores. It is better to buy a processor with at least 8 P cores, preferably more. Alternatively, choose Intel Xeon or AMD processors which do not have this limitation.
64-bit
Mascot Distiller requires 64-bit processor architecture. All modern Intel and AMD processors are 64-bit or, in Intel terms, have “Intel EM64T” technology. All recent versions of Windows are fully 64-bit.
Hyper-Threading or Simultaneous Multithreading technology
Hyper-Threading is available on Intel processors. Recent AMD processors (Zen microarchitecture) have similar technology called Simultaneous Multithreading. Hyper-Threading works by duplicating certain sections of the processor – those that store the architectural state – but not duplicating the main execution resources. This allows a Hyper-Threading equipped processor to pretend to be two “logical” processors to the host operating system, allowing the operating system to schedule two threads or processes simultaneously.
When HT is enabled, 2 logical “processors” per core will be visible to Mascot Distiller. So, for example, a single physical Intel Xeon® Gold 5210 with 14 cores and HT will appear to have 28 logical processors. A single physical AMD Ryzen 9 5900X with 12 cores and Simultaneous Multithreading will appear to have 24 logical processors.
Hyper-threading can give 10-20% performance increase.
Random Access Memory (RAM)
Peak memory usage depends on the experiment structure and the number of MS and MS/MS scans (a function of LC gradient length and instrument scan speed).
If you are processing one raw file at a time, you will rarely need more than 16GB of RAM. This is the case with TMT/iTRAQ quantitation (DDA) and label-free quantitation using the ‘Average’ protocol (DIA, DDA).
If you are processing a multi-file project, such as label-free quantitation using the ‘Replicate’ protocol, peak memory usage depends on the number of raw files. As a point of reference, processing an Orbitrap Astral DIA experiment with 10 raw files will fit in 64GB of RAM.
If Mascot Server is running on the same PC as Mascot Distiller, you will need more RAM. This is because the processing is interleaved with database searching, and several items are kept in RAM simultaneously. It is best to allocate 32GB to Mascot Server and at least 32GB to Mascot Distiller, for a total of at least 64GB.
Hard Disk Storage
The Mascot Distiller program files require little disk space in comparison to native (“raw”) files from the mass spectrometer and Distiller project files.
The Distiller project file stores the peak list file (MGF) derived from the raw file, the database search results and any quantitation results. A project file will be typically of similar size to the raw file.
Processing speed is improved by keeping the raw file and the project file (.rov) on an NVMe drive. We recommend at least 2TB NVMe storage. It is beneficial to have cheaper SSD or HDD drives for bulk storage so older projects can be archived.
If you are running Mascot Server on the same PC, check Mascot Server requirements. You will need enough space for both.
Operating System
Microsoft Windows
The following versions of Windows are supported:
| Operating System | Max processor sockets | Max cores | Max RAM |
|---|---|---|---|
| Windows 10 Pro – 64 bit | 2 | 256 | 2 TB |
| Windows 10 Enterprise – 64 bit | 2 | 256 | 6 TB |
| 2016 Server Standard – 64 bit | 64 | unlimited | 24 TB |
| 2016 Server Datacenter – 64 bit | 64 | unlimited | 24 TB |
| 2019 Server Standard – 64 bit | 64 | unlimited | 24 TB |
| 2019 Server Datacenter – 64 bit | 64 | unlimited | 24 TB |
| 2022 Server Standard – 64 bit | 64 | unlimited | 256 TB |
| 2022 Server Datacenter – 64 bit | 64 | unlimited | 256 TB |
| 2025 Server Standard – 64 bit | 64 | unlimited | 256 TB |
| 2025 Server Datacenter – 64 bit | 64 | unlimited | 256 TB |
| Windows 11 Pro – 64 bit | 2 | 256 | 2 TB |
| Windows 11 Enterprise – 64 bit | 2 | 256 | 6 TB |
- Windows Server Core editions are not supported
- Windows Home Basic and Starter editions are not supported
- If you need to run Mascot Distiller on an earlier version of Windows, your licence allows running any earlier version of Mascot Distiller that supported the target Windows version
Linux
Mascot Distiller is not available on Linux.
Web Server Software
Mascot Distiller does not require a web server. If you are running Mascot Server on the same PC, check Mascot Server requirements.
