Case No.PC-11089A customer who viewed our website asked us about a PC for proteomics analysis.
The software to be used is DIA-NN, MaxQuant, FragPipe, Skyline, and MS-DIAL, and is also expected to be used for other Omics analyzes such as NGS analysis.
You requested a large number of physical CPU cores, but some software requires speed, so a well-balanced configuration is ideal.
The overall conditions are as follows.
・CPU: It is preferable to have a large number of cores, but I would like a product that has a good balance with speed. ・Memory: 128GB or more ・OS: Ubuntu 22.04 ・Software used: DIA-NN 1.8.1, MaxQuant, FragPipe, Skyline, MS-DIAL, etc. ・Budget: About 100 million yen |
Based on the information we received, we have proposed the following structure.
CPU | Intel Xeon W7-2475X (2.60GHz 20 cores) |
memory | 128GB REG ECC |
Storage 1 | 2TB M.2 SSD |
Storage 2 | 2TB M.2 SSD |
Storage 3 | 16TB HDD S-ATA |
video | NVIDIA T400 4GB |
network | on board (2.5GbE x1, 10GbE x1) |
Housing + power supply | Tower type housing + 1000W |
OS | Microsoft Windows 11 Pro for WS 64bit |
OS | Ubuntu 22.04 dual boot configuration |
We have proposed a configuration suitable for your desired conditions and the software you plan to use.
Of the software you plan to use, Skyline is Windows-only software.Therefore, we have a dual boot configuration of Windows 11 + Ubuntu 22.04, but please let us know so we can suggest an OS environment that suits your needs.
The CPU is equipped with the latest Xeon W-2023 series as of October 10.
Considering the balance between the number of cores and operating speed, we selected the 2.60-core model Intel Xeon W20-7X with a basic operating frequency of 2475GHz.
The memory capacity is 128GB, but it can be expanded, so please contact us if you need a larger memory capacity.
The storage configuration includes two 2TB M.2 SSDs for dual-boot OS and a 2TB S-ATA HDD as the data HDD.You can also change the storage type, capacity, number of installed devices, etc.
It is also likely that the software you plan to use does not require advanced drawing capabilities.Therefore, we chose the NVIDIA T400 4GB video card, which is a product for entry-class workstations.
The configuration of this case study is based on the conditions given by the customer.
We will flexibly propose machines according to your conditions, so please feel free to contact us even if you are considering different conditions than what is listed.
■ Keywords・What is Omics analysis? Omics analysis is a data-driven approach widely used in biology and medicine. Omics is a general term for technologies for collecting and analyzing biological data, such as genomics, proteomics, and transcriptomics. ・What is DIA-NN? DIA-NN is DIA (Data Independent Analysis) software for proteomics data processing.Using high-throughput experimental methods, it is possible to perform large-scale experiments that are reliable, robust, and quantitatively accurate. ・What is MaxQuant? MaxQuant is a software package for quantitative proteomics.Designed for analyzing large mass spectrometry data sets.In addition to focusing on high-resolution mass spectrometry data, it also supports several labeling methods and label-free quantitative methods. ・What is FragPipe? FragPipe is a graphical user interface (GUI) that enables comprehensive analysis of mass spectrometry-based proteomics data.It includes MSFragger, an ultra-fast database search tool for peptide identification in mass spectrometry-based proteomics, and Philosopher, a toolkit for shotgun proteomics data analysis. ・What is Skyline? Skyline is an open source software for targeted proteomics and metabolomics data analysis.It supports methods such as selected reaction monitoring (SRM), multiple reaction monitoring (MRM), parallel reaction monitoring (PRM), and data independent analysis (DIR/SWATH).
・What is MS-DIAL? MS-DIAL is software for non-targeted proteomics announced as the result of joint research by a group from RIKEN and the University of California, Davis.Spectral deconvolution is supported in both gas chromatograph-mass spectrometers (GC/MS) and data-independent tandem mass spectrometers (MS/MS). |
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