使用完全卷积神经网络进行精确的de novo序测序
Kaiyuan Liu1, Yuzhen Ye1, Sujun Li1,2
1Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, 47408, IN, USA.
Nature communications
|December 2, 2023
概括
佩普网通过使用一种新型神经网络提高了新的序列测序的准确性和速度. 该工具从质谱中识别出新型,改进了蛋白质组学研究.
科学领域:
- 蛋白质组学和生物信息学
- 计算生物学 计算生物学
- 质谱分析分析 质谱分析
背景情况:
- 在不依赖数据库的情况下识别新型的过程中,新测序至关重要.
- 现有的 de novo 测序算法面临着准确性和覆盖范围的挑战,限制了它们在蛋白质组学中的使用.
- 需要更准确,更高效的de novo测序方法.
研究的目的:
- 介绍PepNet,一个完全卷积的神经网络,旨在高精度的de novo序列.
- 评估PepNet的性能与当前最先进的算法对比.
- 为了证明PepNet作为大规模蛋白质组学数据分析的补充工具的实用性.
主要方法:
- 佩普网使用完全卷积神经网络架构.
- 该模型将MS / MS光谱作为输入,并输出最佳的序列与信心分数.
- 培训涉及300万个高能碰撞解离MS/MS光谱来自人类库.
主要成果:
- 佩普网在酸水平和位置水平的准确性方面显著优于PointNovo和DeepNovo等现有算法.
- 佩普网成功地对大量的光谱进行了测序,而传统的数据库搜索引擎却忽略了这一点.
- 佩普网表现出卓越的计算效率,在GPU上运行速度分别比PointNovo和DeepNovo快3倍和7倍.
结论:
- 佩普网在新测序精度和效率方面取得了重大进展.
- 该算法可以有效地识别新,并补充蛋白质组学中现有的数据库搜索方法.
- 由于PepNet的速度和准确性,它非常适合分析大规模的蛋白质组学数据集.
相关概念视频
01:33Peptide Identification Using Tandem Mass Spectrometry
6.5K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
6.5K
03:21RNA-seq
10.0K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
03:00Next-generation Sequencing
89.0K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
89.0K