Bogdán István A, Rivers Jenny, Beynon Robert J, Coca Daniel
Department of Automatic Control & Systems Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK.
Bioinformatics. 2008 Jul 1;24(13):1498-502. doi: 10.1093/bioinformatics/btn216. Epub 2008 May 3.
Peptide mass fingerprinting (PMF) is a method for protein identification in which a protein is fragmented by a defined cleavage protocol (usually proteolysis with trypsin), and the masses of these products constitute a 'fingerprint' that can be searched against theoretical fingerprints of all known proteins. In the first stage of PMF, the raw mass spectrometric data are processed to generate a peptide mass list. In the second stage this protein fingerprint is used to search a database of known proteins for the best protein match. Although current software solutions can typically deliver a match in a relatively short time, a system that can find a match in real time could change the way in which PMF is deployed and presented. In a paper published earlier we presented a hardware design of a raw mass spectra processor that, when implemented in Field Programmable Gate Array (FPGA) hardware, achieves almost 170-fold speed gain relative to a conventional software implementation running on a dual processor server. In this article we present a complementary hardware realization of a parallel database search engine that, when running on a Xilinx Virtex 2 FPGA at 100 MHz, delivers 1800-fold speed-up compared with an equivalent C software routine, running on a 3.06 GHz Xeon workstation. The inherent scalability of the design means that processing speed can be multiplied by deploying the design on multiple FPGAs. The database search processor and the mass spectra processor, running on a reconfigurable computing platform, provide a complete real-time PMF protein identification solution.
肽质量指纹图谱（PMF）是一种蛋白质鉴定方法，即通过特定的裂解方案（通常用胰蛋白酶进行蛋白水解）将蛋白质裂解，这些产物的质量构成一个“指纹”，可与所有已知蛋白质的理论指纹进行比对。在PMF的第一阶段，对原始质谱数据进行处理以生成肽质量列表。在第二阶段，利用该蛋白质指纹在已知蛋白质数据库中搜索最佳的蛋白质匹配项。尽管当前的软件解决方案通常能在较短时间内给出匹配结果，但一个能够实时找到匹配项的系统可能会改变PMF的应用和展示方式。在 earlier we presented a hardware design of a raw mass spectra processor that, when implemented in Field Programmable Gate Array (FPGA) hardware, achieves almost 170-fold speed gain relative to a conventional software implementation running on a dual processor server. In this article we present a complementary hardware realization of a parallel database search engine that, when running on a Xilinx Virtex 2 FPGA at 100 MHz, delivers 1800-fold speed-up compared with an equivalent C software routine, running on a 3.06 GHz Xeon workstation. The inherent scalability of the design means that processing speed can be multiplied by deploying the design on multiple FPGAs. The database search processor and the mass spectra processor, running on a reconfigurable computing platform, provide a complete real-time PMF protein identification solution. 中我们展示了一种原始质谱处理器的硬件设计，当在现场可编程门阵列（FPGA）硬件中实现时，相对于在双处理器服务器上运行的传统软件实现，其速度提升了近170倍。在本文中，我们展示了一种并行数据库搜索引擎的补充硬件实现，当在100 MHz的Xilinx Virtex 2 FPGA上运行时，与在3.06 GHz至强工作站上运行的等效C软件程序相比，速度提高了1800倍。该设计固有的可扩展性意味着通过在多个FPGA上部署该设计，处理速度可以成倍提高。在可重构计算平台上运行的数据库搜索处理器和质谱处理器提供了一个完整的实时PMF蛋白质鉴定解决方案。 （你提供的原文中“earlier we presented...”部分存在重复表述未完整，请检查原文准确性，以上是按照完整可理解部分翻译的）
