Spectronaut 15 带着众多性能改进、功能更新于6月15日晚正式发布。在新一代深度学习算法的加持下，DIA数据分析的性能和DDA的差距进一步扩大。

新版本详细介绍视频（中文校正版）：

Mann课题组单细胞DIAPASEF介绍（中文自动翻译）及Q&A：

Spectronaut 15 主要更新内容如下

• 定性能力提升： 谱图库DIA和directDIA结果均有明显提升

• 定量改进：整合MaxLFQ算法，提升定量准确性

• 全面的PTM分析功能：PTM位点分析全面升级，你想要的都有了

• 改善用户体验：增加大量DIA数据可视化功能

• 深度学习：改进机器学习算法显著提升免疫多肽和离子淌度数据分析能力

  
  

定性能力提升

相对于Spectronaut14来说，新版本在显著提升了DIA-PASEF数据的定性能力，基于谱图库或directDIA均有15-30%的提升。非DIA-PASEF数据实现了5%-20%的提升。

提升灵敏度的同时，SN15引入基于单个run的FDR控制算法，能够大显著改进FDR的准确性同时不牺牲灵敏度。

定量改进

DIA分析的核心痛点是定量的准确性。Spectronaut15中加入了MaxLFQ算法，在CV不变的情况下，进一步提升了可定量的母离子比例。

全面的PTM分析功能

PTM定量分析，位点置信度及位点定量分析是目前蛋白质组学中的核心关切点，而大部分分析软件都依赖于研究者自行进行位点拆分、定量和解读。

SN15的PTM专属分析流程为您带来一键式的位点置信度、定量、差异分析功能，同时全部支持可视化查看，为您的修饰定量插上翅膀。

相关详细介绍可以参考官方简介视频：

DIA数据可视化改进

对于商业化数据分析软件来说，可视化界面的使用体验是其相对于免费软件的重要优势之一。

在SN15中，我们加入了全新的以蛋白为核心的结果查看、差异展示和离子淌度可视化界面。

详细用户界面改进参见官方视频介绍：

Spectronaut用户请连接上互联网后点击About界面自行更新。

如需进一步帮助欢迎和我们联系。

详细更新日志：

More Identifications 

• Improved identification with new scores, especially for short gradients

• Up to 35% more precursor identifications for directDIA with diaPASEF

• Up to 10% more precursor identifications for directDIA in general

• Up to 30% more precursor identifications for short gradient DIA analysis with library

• Up to 10% more precursor identifications for DIA analysis with library in general

Accurate Quantification

• Improved default settings for quantification

• New MaxLFQ based protein quantification

• Up to 15% more protein identifications with CVs below 10% in controlled quantitative experiments

Improved Ion Mobility Support 

• Ion Mobilogram visualization for dia-PASEF

• Ion Mobilogram based manual peak refinement

• Up to 30% faster processing of dia-PASEF data

• Added optimal support for high-sensitive py5 dia-PASEF method 

General DIA Analysis

• New Run-wise protein FDR calculation and filtering

• New peptide posterior error probability (PEP) filtering

• Improved flexibility for directDIA search settings

• Improved multi-channel quantity summarization

• Command line support for SNECombine workflow

• New “Method Evaluation” workflow with directDIA

Comprehensive PTM Analysis

• Site collapse calculation

• Site regulation analysis

• Modification specific normalization filter for enrichment workflows

• New PTM site report

Pulsar Database Search Engine

• Improved performance for large protein databases (> 2 GB) with Pulsar

• Improved identification and performance for unspecific searches

Deep-learning Augmented Improvements

• Prediction for ion mobility (1/K0) during library generation

• Improved fragment prediction for unspecific peptides

New Post Analysis Features

• Added PCA analysis

• Added custom selection for protein rank plot

• Added custom selection for volcano plots

• New PTM Analysis node

Improved User Experience and Visualization

• Improved Protein Coverage plot

• PTM support

• Peptide tooltip and highlighting

• New sub-perspective “Protein Grid View” in the analysis perspective

• Improved XIC Alignment plots with support for unlimited number of runs

• Detachable perspective and plots for side-by-side visualization

• Improved XIC grid overview plots

• One-Click tree navigation in plots

• Improved plot and tree filter selection

• Quick-Action bar for analysis perspective

• Improved warning messages with actionable links

• Improved UI for analysis log

• Updated Analysis Summary plot for easier access

Other Changes

• Report Perspective Changes

• New PTM site level report when performing PTM localizationPage

• DIA Analysis Settings Changes

• Default row filtering for quantification changed from Q-value to Q-value Sparse

• Default quantification strategy changed from Quant 2.0 to Auto, where it will use MaxLFQ if analyzing less than 500 runs

• Default normalization strategy changed from Global Normalization to Auto, where it will use Local Normalization if analyzing less than 500 runs

• New PTM workflow node in the setting

• directDIA Analysis Settings Changes:

• New Method Evaluation setting in directDIA settings → Workflow → Method Evaluation

• Distinguish between Pulsar and DIA analysis settings for directDIA for more flexibility