Oktoberfest:基于 Prosit 的开源光谱库生成和恢复管道
Mario Picciani1, Wassim Gabriel1, Victor-George Giurcoiu1
1Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
Proteomics
|September 6, 2023
概括
Oktoberfest 是一个新的开源 Python 包,用于生成光谱库和恢复蛋白质组学数据. 它使先进的机器学习可访问性质预测,以便在蛋白质组学分析中更广泛地使用.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
背景情况:
- 像Prosit这样的机器学习 (ML) 和深度学习 (DL) 模型能够高质量的in silico性质预测.
- 这些预测对于数据独立获取 (DIA) 分析和搜索引擎结果在蛋白质组学中的重搜等应用至关重要.
研究的目的:
- 介绍Oktoberfest,一个开源的Python包用于光谱库生成和性质预测.
- 提供一个搜索引擎不可知工具,将最先进的ML/DL模型集成到蛋白质组学分析管道中.
- 促进对蛋白质组学研究的先进ML/DL工具的采用和本地安装.
主要方法:
- 开发Oktoberfest,一个Python包,集成光谱库生成和rescoring功能.
- 从ML/DL模型中利用在线性质预测.
- 在两个截然不同的复刻用例上展示该包的性能.
主要成果:
- Oktoberfest成功地复制并增强了之前的复制分析结果.
- 该包是搜索引擎不可知,促进更广泛的适用性.
- 通过PyPI成功进行本地安装得到确认.
结论:
- Oktoberfest 民主化了对基于 ML/DL 的先进蛋白质组学性质预测的访问.
- 该开源包简化了光谱库生成和数据分析.
- 它使研究人员能够提高蛋白质组学研究的准确性和效率.
相关概念视频
01:06Sampling Methods: Overview
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A sample refers to a smaller subset representative of a larger population. In analytical chemistry, studying or analyzing an entire population is often impractical or impossible. Therefore, samples are used to draw inferences and generalize the whole population. The sampling method selects individuals or items from a population to create a sample. Standard sampling methods include random, judgemental, systematic, stratified, and cluster sampling.
In analytical chemistry, the choice of...
In analytical chemistry, the choice of...
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01:23Mass Spectrum
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A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x axis represents the ratio of the mass of the charged fragment to the elementary charge it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal...
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01:23Sampling Plans
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Sampling is a crucial step in analytical chemistry, allowing researchers to collect representative data from a large population. Common sampling methods include random, judgmental, systematic, stratified, and cluster sampling.
Random sampling is a method where each member of the population has an equal chance of being selected for the sample. It involves selecting individuals randomly, often using random number generators or lottery-type methods. For example, when analyzing the properties of a...
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208
01:24Mass Spectrum: Interpretation
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An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a low-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.
To...
To...
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01:17Bandpass Sampling
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In signal processing, bandpass sampling is an effective technique for sampling signals that have most of their energy concentrated within a narrow frequency band. This type of signal is known as a bandpass signal. The key principle of bandpass sampling involves sampling the signal at a rate that is greater than twice the signal's bandwidth to prevent aliasing.
A bandpass signal has a spectrum with a lower frequency limit, denoted as ω1, and an upper frequency limit, denoted as ω2....
A bandpass signal has a spectrum with a lower frequency limit, denoted as ω1, and an upper frequency limit, denoted as ω2....
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01:20Raman Spectroscopy: Overview
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The underlying principle of Raman spectroscopy is based on the interaction between light and matter, specifically molecules' inelastic scattering of photons. When a monochromatic beam of light, typically from a laser source, interacts with a sample, most scattered light has the same frequency as the incident light. This is known as Rayleigh scattering.
However, a small fraction of the scattered light exhibits a frequency shift due to the exchange of energy between the incident photons and...
However, a small fraction of the scattered light exhibits a frequency shift due to the exchange of energy between the incident photons and...
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