---
title: "Spectronaut功能升级历史（截止24.09）"
author: "omicsolution"
account: "omicsolution"
published_at: "2024-09-17T17:37:07+08:00"
captured_at: "2026-08-27T10:51:43.806807+08:00"
source_url: "https://mp.weixin.qq.com/s?__biz=MzI2MTI5NDAzNg==&mid=2247495100&idx=1&sn=7209327de6f0eb1129fec1624f9f8dda&chksm=ea5e3f07dd29b6111df2aeb3d1c54f645639ae07ac4ab552fc530b2e4404765d15297d3124f0#rd"
---

# Spectronaut功能升级历史（截止24.09）
![图片 1](images/001.png)

[更新 19.2.240905.62635]

- 修复了 plexDIA 工作流程中 “In-Silico 生成缺失通道 ”选项的问题（该问题在 19.1 中引入）

- 添加了 “PEP.AllOccuringOrganisms ”报告列

- 为 manageSNE 命令添加了不创建带有时间戳的输出子文件夹的选项

- 添加了对多通道 (plexDIA) PTM 定位的支持

- 添加了始终从 directDIA 搜索生成光谱库 (.kit) 的选项

[小更新 19.1.240806.62635］

- 修正了为透视报告生成损坏的 Parquet 文件的问题

- 修复了 XICGraph 无法显示标签重/轻图对的小问题

[更新 19.1.240724.62635］

- 修复了使用 “生成标签库 ”向导时修改注释被破坏的问题。

- 修复了使用 Spectronaut >= 19.0 生成的 SNE 文件合并失败的问题

- 修正了交错窗口方法的 “分析视角”->“分析摘要图 ”中的 DPPP 估计值

- 修复了双通道 plexDIA 实验的比率调节分析

- 为 manageSNE 命令添加了覆盖条件设置的可能性

- 添加了在 JSON 文件中提供设置的选项，以便在命令行模式下生成 Pulsar 库

- 添加了在 Apache Parquet 中导出报告的功能

[小更新 19.0.240606.62635］

- 修复了发行版安装程序中缺失的 HTRMS 转换器二进制文件

[Spectronaut 19 - 发行说明］

1. directDIA 的主要改进

- 改进了评分：基于大量不同的 DIA 数据集，蛋白质组平均增加 10%，前体增加 13

- 改进量化：基于大量不同的受控定量实验，真正的候选蛋白增加了 11%。

2. 以人工智能为动力

- 深度学习模型的关键性能指标最多可提高 40%

- 可选择使用基于深度学习的干扰校正算法 deepQuant

- 改进了对二甲基化、泛素化、mTRAQ 等一系列修饰的推断。

3. 显著的计算性能

- 与 Spectronaut 18.0 相比，directDIA 对 timsTOF 和 Astral 数据的处理速度提高了 40%

- 减少 directDIA 内存使用量：内存增长减少 90%。使用 directDIA 加 SNECombine 工作流程，理论上 512 GB 内存可处理 10,000 个样品。

- Spectronaut 保存的实验 (.SNE) 文件大小最多可减少 80%

- 临时硬盘需求降低达 86%（directDIA 来自 HTRMS）

- 临时硬盘需求降低达 50%（从原始 Vendor 格式导入 directDIA） .

4. 支持新的采集方法

- 布鲁克公司 timsTOF 平台上的对角-PASEF 支持 directDIA 和基于库的分析

- 分析视角中对角-PASEF 的新可视化功能

5. 改进了对标记 DIA 工作流程的支持

- 增加了对运行级通道 q 值的支持

- 在通道级注释生物条件

6. 分析翻译后修饰的新功能

- 通过将富集实验与非富集实验连接，实现输入归一化

- 支持位点占有率计算

- 分析和分析后视角的新可视化功能 .

7. 改进的命令行界面

- 新增 SNEMerge 选项，便于批量或并行处理：将多个 SNE 文件合并为一个 SNE 文件

- 新增输入规范化选项

- 如果命令出错，可立即优雅退出

- 每个管道都有单独的命令，选项范围明确

- 增强了 POSIX 兼容性

8. 新的可视化和可报告功能

- 洗脱组级别 -> EG.InputNormalizationFactor

- 洗脱组级别 -> EG.QuantityPerProtein

- PTM 位点报告 -> PTM.QuantityPerProtein

- PTM位点报告 -> PTM.输入规范化因子

- PTM 位点报告 -> PTM.Stoichiometry

- 新的 R.PTMSites 类别列出每个 PTM 的所有已识别位点

- 多肽与蛋白质数量对比图

- 分析后分析概览 定位的 PTM 平均值

- 实验设置中的样本链接页面

9. 新的和已更改的分析设置

- DIA 分析 -> PTM 工作流程 -> 输入归一化策略

- DIA 分析 -> PTM 工作流程 -> PTM 定位 -> 化学计量学计算策略

- DIA 分析 -> 定量 -> DeepQuant 校正 [Beta]

- DIA 分析 -> 工作流程 -> 混合（DDA + DIA）库

- directDIA -> Pulsar Search -> Speed-up -> diaPASEF Processing -> Fast

- directDIA -> 脉冲星搜索 -> 识别 -> directDIA 工作流程 -> RT 采样减少

- Spectronaut 19 仅使用 MS2 定量进行丰度差异分析。之前的默认值是同时使用 MS1 和 MS2

[小更新 18.7.240506.55695］

- 更改了 XIC DB 导出，以便为每个原始文件生成一个 sqlite db 文件

[更新 18.7.240325.55695］

- 大幅提高了 DirectDIA 处理 Astral DIA 数据的速度，最高可达 50%

- 添加了在实验层面合并 SNE 文件的新功能

- 修正了第三方库中的已知漏洞

- 修正了从 .psar 文件生成标记库时修改注释的问题

- 修正了用户界面和 CMD 生成的 PDF 之间 “CV 低于 X ”条形图的差异

- 修正了文库生成过程中 “识别重要前体 ”过程中的罕见崩溃问题

- 修正了加载某些 Astral DIA 数据时 “不是有效 DIA 方法 ”的错误

- 修复了未切换 N 端蛋氨酸时识别未知肽的错误

- 修复了之前的许可证过期时无法激活 Spectronaut 的错误

[更新 18.6.231227.55695]

- 为 Spectronaut Linux 添加了导入和导出自定义消化规则的可能性

- 修正了 PCA 图中不正确的颜色（未使用选定的条件颜色）

- 修正了处理包含自定义修改的 PSAR 文件时的崩溃问题

- 修正了尝试分析 timsTOF DDA 数据以生成库时的崩溃问题

- 修正了修改数据库中 Hex(1)HexNAc(1)成分不正确的问题

- 修复了 GO 注释数据库条目损坏导致的启动崩溃问题

[更新 18.5.231110.55695]

- 修正了从管道角度使用 directDIA 重复分析同一文件时的崩溃问题

- 修复了在导出规范化报告时出现的停滞情况

- 添加了允许将所有 XIC 导出到 SQLite 数据库文件的功能

- 推出了更方便用户使用的新版命令行应用程序接口（API）

- 当使用 MaxLFQ 时，修正了报告中 PEP.UsedForProteinGroupQuantity 标志的错误分配

[小更新 18.4.231017.55695］

- 修复了从 HTRMS 执行 directDIA 时的崩溃（18.4.231011 中引入）。

[更新 18.4.231011.55695］

- 修复了 timsTOF .d 文件的文件监控问题

- 添加了顶点的 MS2 扫描编号作为报告列 (FG.MS2ApexScanIndex)

- 进一步提高了 Pulsar psar 文件合并管道的内存效率

- 修正了 MaxLFQ 稀疏蛋白质矩阵线性求解器中的一个错误

- 改进了 HTRMS 转换器中对布鲁克 .d 文件夹的监控

- 改进了 SN 管道视角中对布鲁克 .d 文件夹的监控

- 改进 IT-DIA 的数据分析，用于中心化 IT 采集

[更新 18.3.230830.50606］

- 库生成和搜索档案合并过程中的内存进一步改善

- 改进了对混合 DIA 方法（DIA 加 PRM）的支持/自动检测

- 修正了某些 SNE-Combine 场景中的空引用异常

[更新 18.2.230802.55695］

- 对 timsTOF 数据的性能略有改进

- 修复了报告视角中缺少 PG.FastaHeader 的问题

- 修正了 directDIA+ 中对无 IM 维度的 timsTOF 数据的校准问题

- 添加了命令行激活或停用失败时的特定退出代码

- 删除了命令行启动时的激活密钥提示

- 修正了 Linux 上的忽略条件设置

- 改进了库生成和搜索归档合并过程中的内存管理

[更新 18.1.230626.50606］

- 修正了 timsTOF API 文件路径中的非字符串问题

- 修正库生成工作流程中解析 .d 原始文件的问题

- 修正了使用 directDIA+ 处理 dia-PASEF 时偶尔出现的冻结/崩溃问题

- 修正了某些高分辨率显示器设置下的用户界面渲染问题（链接消失

- 在管道视角中添加了测试版工作监控器

[Spectronaut 18 - 发行说明］

- 大大改进了定量分析（CV<10% 的蛋白质增加了 12%）

- 通过命令行支持 Linux（直接加载布鲁克和赛默公司文件，通过 HTRMS 支持 Sciex）

- 改进蛋白质鉴定（平均提高 5%）

- 为 directDIA+ 添加了搜索档案支持

- 命令行功能大幅扩展

- 简化并改进了云安装许可

- 为 SNE-Combine 添加了 MaxLFQ 支持

- 所有方框图的小提琴图选项

- 改进了管道处理过程中的错误和警告反馈

- 在分析概览中添加了 “量化 ”汇总节点

- 在常规 DIA 分析中直接使用搜索档案 (.psar)

- 在运行级别上添加每个周期的鉴定概览图

- 将所有以 .XLS 导出的文件更改为 .TSV

- 新的默认定量设置（通过 DIA 分析 -> 定量 -> 定量窗口）

[更新 17.7.230531.55965］

- 修正了不包含无标记通道（directDIA+）的标记工作流问题

[小更新 17.6.230428.55965］

- 修复了许可证过期系统的启动崩溃问题

[更新 17.5.230413.55965］

- 提高了 directDIA dia-PASEF 的处理速度

- 添加了全球蛋白质覆盖率报告字段 (PG.Coverage (Global))

- 修复了已损坏的报告字段 PEP.AllOccuringProteinAccessions

[小更新 17.4.230317.55965］

- 修正了 directDIA+ 与 diaPASEF 中可能导致管道无限重复的罕见崩溃问题

[更新 17.4.230316.55965］

- 修正了较重元素（> 氩）质量表（0.0Da 质量）中的错误

- 修正了为修改定义加载完整周期表用户界面的问题。

- 修正了高分辨率系统中罕见的启动问题

- 改进了 directDIA 搜索的临时存储要求

- 修正了羟脯氨酸修饰的定义。

- 更改了条件 UI 标签的默认值，使其不再缩短

[更新 17.3.230224.55965］

- 修正了 SN17.2 中引入的从 HTRMS 文件运行 directDIA 时的崩溃问题

- 修复了显示具有共同标签的条件的 PCA 图的问题

- 修正了 IM-Calibration 中的罕见错误

- 修正了带有 “非 C 端 ”位置定义（例如 GlyGly (K)）的模式的 PTM 定位错误

[更新 17.2.230208.55965］

- 改进了对 directDIA+ 的修改支持

- 改进了对 directDIA / directDIA+ 中不同 FAIMS 采集模式的支持。

- 修正了 SNE-Combine 中的错误，该错误会导致每批最后一次运行的鉴定结果为 0。

- 修正了 SILAC 蛋白质数量计算中导致所有通道数量默认为 0 的罕见错误

- 修正了方法评估管道量化不一致的问题

- 修正了错误的用户手册链接

[Update 17.1.221229.55965]

- Changed targeting framework of HTRMS-Converter to .NET6

- Improved PTM search for directDIA+

大版本更新[Spectronaut 17 - Release Notes] 2022.12.07

- 全新directDIA+算法，相对上个版本显著提升鉴定深度

- 相对于Spectronaut 16，提升 dia-PASEF 约50%母离子鉴定量

- 相对于Spectronaut 16，提升 Orbitrap-dia 约50%母离子鉴定量

- 相对于Spectronaut 16，提升 IonTrap-dia 约100%母离子鉴定量

- 相对于Spectronaut 16，提升 ZenoTOF-SWATH 约150%母离子鉴定量

- 添加directDIA的 FAST 和 DEEP 模式检索

- 改进保留时间和离子淌度的AI预测模型

- 添加支持 1F Slice dia-PASEF 检测模式

- 改进热图渲染效率

- 改进Gene水平蛋白质整合算法

- 后台框架升级到 .NET6

- 添加Run-level Protein Group PEP 过滤 (Posterior Error Probability)

大版本更新[Spectronaut 16 - Release Notes]

More Identifications

- Improved identifications with new machine learning framework

- Improved identifications with new DeepLearning score models

- Up to 17% more precursor and 10% more protein groups identifications for directDIA

- Up to 25% more precursor and 15% more protein groups identifications for library based DIA analysis

- New "1-step" hybrid library workflow via directDIA enrichment

Pulsar Database Search Engine

- 30% faster directDIA and DDA searches

- Improved machine learning and scoring

Deep-learning Augmented Improvements

- Added DeepXIC scoring model for improved identifications

- Novel Deep PSM scoring model for spectrum centric analysis

New Post Analysis Features

- Ranked protein groups in post analysis perspective now reflects quantity IQR per protein

- Added principal component contribution bar plot to PCA plot

Improved User Experience and Visualization

- Streamlined settings for clarity with new advanced category

- Streamlined quantification settings by replacing q-value sparse with new imputation strategy “Use Background Signal”

- Added condition box plot in the protein grid view

- Added mass error histogram at run level in analysis perspective

- Added DIA acquisition method overview at run level in analysis perspective

- Improved data completeness plot to easily tell how many proteins, precursors were identified in x% of samples

- Library ion mobility 1/k0 distribution plot in library perspective

- Export peptide precursor list from library via right-click option

- Switched to 2-color (Green and Red) system for identification status annotation

- Swapped heatmap colors in analysis protein grid view (red = high, blue = low) based on user feedback

- Added condition box plot in analysis protein grid view

DIA Analysis Settings Changes

- JSON settings override for more flexible pipeline integration

- Changed default quantification setting back to q-value without imputation based on user feedback

directDIA Analysis Settings Changes:

- Improved flexibility for directDIA analysis settings

- Added option to disable MS2 Index filtering

New Downloadable Content

- Added a high-quality Hela search archive as a resource for Hela DIA analysis

- Added search archive from our new plasma publication (Tognetti et al., 2022, JPR)

- Added Uniprot protein databases from January 2022

[Update 15.6.211220.50606]

- Added support for report schemas being provided via command line interface (-rs [path to schema])

- Added functionality to remember user selected columns in analysis grid-view

- Added support for "Is Gene Specific" peptide filtering for quantification

- Added report column "PEP.IsGeneSpecific" on peptide level

- Added "Is Gene Specific" annotation to protein coverage plot

[Update 15.5.211111.50606]

- Added support for PTM Site report in SNE combine workflow

- Updated Pulsar search-engine corresponding with SpectroMine 3 release

- Improved analysis speed for Pulsar searches (including directDIA) with many modifications

- Improved fragmentation prediction model for Pulsar

- Improved handling of large FASTA files in Pulsar

- Ion Mobility prediction for libraries from all instrument platforms

[Update 15.3.210906.50606]

- Added Avg. PPM Mass Tolerances meta field per run level in the search archive

[Update 15.2.210819.50606]

- Improved dynamic mass tolerances for diaPASEF

- Added PEP cutoff indicator to scoring histograms

大版本更新[Spectronaut 15 - Release Notes]

To see all of the changes, please visit here:

https://biognosys.com/spectronaut15-releasenotes

New Features

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 localization

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 settings

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

[Update 14.11.210528.47784]

- Spectronaut version that was used to create a Pulsar search archive is now saved to the archive

- Improved support for iRT-Kit calibration and QC in multi-CV FAIMS DIA

[Update 14.10.201222.47784]

- Added Posterior Error Probability (PEP) filter for identification confidence

- Added imputation strategies for "Qvalue complete" filter strategy

- Added Run level report column "R.MS1 Average Tolerance (ppm)"

- Added Run level report column "R.MS2 Average Tolerance (ppm)"

- Added Run level report column "R.Average XIC Width

- Added Run level report column "R.Average IM Width"

[Update 14.9.201124.47784]

- Improved loading performance for search archives using Pulsar

- Added normalization filter option based on source FASTA

- Added normalization filter option based on source library

[Update 14.8.201029.47784]

- Improved automatic method detection for Pulsar

- Improved raw scan processing for Waters TOF instruments

- Added auto-detection for MS2 demultiplexing in all workflows

[Update 14.6.201001.47784]

- Changed default setting for PTM localization in DIA/directDIA to FALSE

- Improved speed of searching PASEF data by up to 30% for library generation

- Updated NN model for fragmentation and iRT prediction

- Added EG.UsedInNormalizationSet column to standard and pivot report

- Added TIC overlay plot to post analysis perspective

- Improved memory efficiency for SONAR XIC extraction

[Update 14.4.200727.47784]

- Improved library generation from PASEF with Pulsar

- Performance improvement when building libraries from Pulsar

[Important Update 14.3.200701.47784]

- Added support for library generation from MQLive DDA files with Pulsar

- Added support for library generation from HTRMS files with Pulsar (HTRMS from 14.2 or newer)

[Update 14.1.200615.47784]

- Added option for MS2 demultiplexing of staggered windows in directDIA

- Added option for MS2 demultiplexing to Pulsar library generation for DIA

- Added HTRMS files as option for directDIA

- Changed library precursor charge filter to allow min/max filtering

大版本更新Spectronaut 14 Release Notes

To see all of the changes, please visit here: https://biognosys.com/spectronaut14-releasenotes

directDIA 2.0

-Deep learning augmented spectrum-centric DIA analysis

Ion Mobility support

- Improved Bruker dia-PASEF support

- Improved Thermo FAIMS Pro support

- Waters HDMSE support

- directDIA support for ion mobility data

- Improved PTM localization in ion mobility data

SNE combine

- Analyze huge experiments by analysis of partial datasets and merging of multiple .sne

files into a single report file

Quant 3.0

- Improved differential abundance analysis using MS1 and MS2 level quantification

- New unpaired t-test option is new default

Deep-learning-augmented library generation and peptide identification

- Deep learning predicted decoys is new default

- Deep learning assisted iRT regression is new default

- Deep learning augmented scoring in Pulsar

New Visualizations

- Protein coverage plot

- LFQbench plot

- Ion Mobility method overview

- Ion Mobility calibration

- MS1 base peak chromatogram

- MS2 base peak and TIC chromatogram per window

- Digest specificity bar plot

New method support

- RTwinDIA [Li , 2019]

- Demultiplexing of overlapping windows (via HTRMS converter) [Amodei, 2019]

- dia-PASEF with multiple MS1 full scans in a cycle

Library Generation

-View library settings in library perspective (for new libraries only)

- [Pulsar] Improved identification performance (with project DDA libraries as well as in

directDIA)

- [Pulsar] Improved speed of many modifications search when using high-resolution DDA

data

- [Pulsar] ETD/EThcD support

- [Pulsar] Faster PASEF and dia-PASEF database search

- [Pulsar] Improved identifications for DDA and DIA runs

- [Proteome Discoverer] PD 2.4 support

- [Proteome Discoverer]Library generation for FAIMS DDA results

- [Proteome Discoverer]Protein group FDR is taken into account for library generation

Other features

- All proteins protein inference strategy

- Protein quantity reported separately for each channel in labelling experiments

- XIC Graph plot improvements

- iBAQ protein quantities

- Updated downloadable content: FASTA protein databases

[Update 13.14.200423.43655]

- Added support for library generation from MaxQuant 1.6.14

[Update 13.13.200417.43655]

- Added individual channel quantities for protein group and peptide level in report [Beta]

[Update 13.12.200217.43655]

- Added ability to copy the download link in the update notification

[Update 13.10.191212.43655]

- Added pipeline mode reporting settings options to directDIA analysis settings

[Update 13.9.191106.43655]

- Improved FAIMS library generation pipeline

- Added Labelled workflow support for XIC graph

- Enabled manual override of peptide selection for quantification

- Improved UI response for settings page

- Added support for Hybrid SONAR method

[Update 13.8.190930.43655]

- Added PTM Protein sequence locations to export columns (EG.ProteinPTMLocations)

- Added EG.StartIRT and EG.EndIRT columns to report

- Added EG.PeakWidth (iRT) and EG.ExtractionWindowWidth (iRT) columns to report

- Added support for repeated pasef scans in diaPASEF

[Update 13.7.190916.43655]

- Beta support for diaPASEF acquired with Bruker timsTOF Pro

- Beta support for generating ion mobility enhanced spectral library from PASEF using Pulsar search engine

[Update 13.5.190902.43655]

- Added option to disable run clustring in heatmap

- Minor memory improvements with large libraries

[Update 13.4.190802.43655]

- Enabled delta mass modified sequence representation in report (EG.IntPMID, TG.IntMID)

[Update 13.3.190726.43655]

- Added PG.MolecularWeight to list of available report columns (long format)

- Added Protein-FDR histogram to automatic reports in pipeline/cmd mode

- Added settings option for optimized processing of In-Silico libraries (Settings -> Workflow)

[Update 13.2.190705.43655]

- Allow imported decoys to be used in calibration

- Changed default behaviour for automatic condition setup parsing from raw file names

[Update 13.1.190621.43655]

- Improved scalability for PTM localization and many modifications

- Added normalization option to XIC Graph

- Added option to attach custom descriptions to a library

- Added option assigning a custom icon to a library

- Added XIC peak start and end RT to report

- Improved LDA stability in machine learning

- Improved detection for QC peptides

大版本更新[Release Notes]What is new in Spectronaut™ 13

Features

- PTM localization for targeted DIA analysis

- PTM localization optimized library generation

- PTM localization details plot in Analysis perspective

- PTM localization filtering for library generation

- Export as batch file option after experiment setup

- New Quantification imputing strategies

- Protein abundance rank plot in post analysis

- Support for BoxCar DIA analysis

Improvements

- Improved memory scalability for external library import

- Improved scalability for very large (> 1000 runs) DIA experiments

- Improved overall memory management

- Improved command line support

Changes

- Changed default normalization strategy to "Global Median Normalization"

[Update 12.0.20491.22]

- Improved support for segmented DIA methods

- Added fragment level reportable to indicate whether a fragment was shared between multiple channels

- Fixed issue with opening SNE files from window file explorer

- Added theoretical MS1 isotopic pattern to report (FG.IsotopicPatternTheoretical)

- Added measured MS1 isotopic pattern to report (FG.IsotopicPatternMeasured)

- Added measured MS1 isotope quantities to report (FG.IsotopeQuantities)

- Added theoretical MS2 isotopic pattern to report (F.IsotopicPatternTheoretical)

[Update 12.0.20491.18]

- Added support for Proteome Discoverer 2.3

- Added Explained TIC plot to cmd/pipeline exported reports

- Added PTM localization filter for library generation with pulsar

[Update 12.0.20491.17]

- Switched all encryption algorithms to be FIPS compliant

- Enabled peptide precursor Pvalue (EG.Pvalue) in report for all versions

- Enabled protein group Pvalue (P.Pvalue) in report for all versions

[Update 12.0.20491.16]

- Improved performance of some protein summary plots for large protein groups

[Update 12.0.20491.14]

- Added export option for imported GO Anntoations

- Added export option for imported Gene Onthologies

- Added ProteinGroup report field for molecular weight

- Added ProteinGroup report field for sequence coverage

- Added option to exclude deamidated peptides from calibration

[Update 12.0.20491.13]

- Added SN-10 Unify Peptide Peaks algorithm

[Update 12.0.20491.11]

- Improved Pulsar scoring function for library generation and directDIA workflow

- Introduced calibration settings option to skip iRT-Kit based calibration step if iRT-Kit was not present in sample

- Minor performance improvements during experiment post processes

[Update 12.0.20491.9]

- Enabled report columns for FWHM

- Improved protein-group peptide overview plot for > 20 peptide cases

[Update 12.0.20491.7]

- Improved performance for report export

- Added support for library generation from MaxQuant 1.6.2.3

- Improved messaging for iRT calibration during speclib generation

[Update 12.0.20491.6]

- Improved fragment selection when generating libraries with Pulsar

- Run identifications bar-plot in post analysis perspective

- Minor memory improvements during library import

- Improved sampling rate for scoring sensitivity plot

[Update 12.0.20491.5]

- Added data-matrix export option for sample correlation matrix

[Update 12.0.20491.4]

- Improved UI freeze issues in certain hardware configurations

- Improved UI freeze issue with some remote desktop configurations

- Enabled HTRMS file merging for gas-phase fractionation in HTRMS Converter

- Added automatic SNE storage to pipeline process (Settings -> Global -> Reporting)

- Improved logging and error feedback for SN from command line

[Update 12.0.20491.3]

- Improved performance for pivot report

[Update 12.0.20491.2]

- Improved memory handling during regulation analysis

- Improved memory handling during profiling

- Added PEP.IsProteotypic to Pivot report

- Added PEP.IsProteinGroupSpecific to Pivot report

- Added PEP.AllOccurringProteinAccessions to Pivot report

大版本更新[Release Notes]What is new in Spectronaut™ Pulsar X

- Support for Hybrid Library workflows

- Added pulsar search archives

- Added of source-specific iRT calibration

- Improved library generation from DIA data

- Improved directDIA™ workflow

- Improved protein-FDR estimation

- Added peptide-FDR filtering for library generation

- Added GO clustering to post analysis

- Added support for Waters DDA in library generation

- Added direct loading of Waters SONAR

- Improved experiment setup

- Improved loading / saving of SNE files

- Improved support for spike-in workflows

- Improved support for Host Cell Proteome (HCP) workflows

- Improved user interface

[Update 11.0.15038.22]

[Update 11.0.15038.21]

- Updated user manual

[Update 11.0.15038.20]

- Improved HCP workflow with calibration carry-over

[Update 11.0.15038.19]

- Improved noise picking for XICs

- Added precursor selection window definition to report

- Added peptide peak start and end RT to report

- Added reference run columns (Name, Qvalue, Response) to kit export

- Improved TIC chart loading behaviour

[Update 11.0.15038.18]

- Added unpaired strategy for testing in Ultimate

[Update 11.0.15038.17]

- Added geometric mean option for Peptide/Protein-Group quantity

- Added median option for Peptide/Protein-Group quantity

[Update 11.0.15038.16]

- Improved performance for protein-inference in large datasets

[Update 11.0.15038.15]

- Improved robustness for Protein-FDR

- Improved automatic scaling for mirror plot in alignment view

[Update 11.0.15038.13]

- Improved experiment-wide machine learning option

- Enabled experiment-wide machine learning option for all versions

[Update 11.0.15038.12]

- Added logic to automatically center volcano plot x-axis around 0

- Added support for peptide FDR filtering for library generation from PD 2.0 or higher.

[Update 11.0.15038.10]

- Added support for removal of large number of runs from experiment in review perspective

[Update 11.0.15038.9]

- Enabled decoy generation settings for all Spectronaut versions

- Added license key link to About perspective

[Update 11.0.15038.8]

- Added speclib support for ProteomeDiscoverer 2.2

- Improved Pulsar PSM score

- Improved loss-type fragment matching in Pulsar

- Added option to perform multiple-testing correction in regulation analysis per condition pairing

[Update 11.0.15038.6]

- Improved DDA MS1 feature detection for Pulsar

- Added import option for precursor user comments in library

- Added support for speclib generation from Mascot search results from SCIEX data

- Added Multi-EG PDF plot export

[Update 11.0.15038.5]

- Improved robustness for MS1 mass calibration

- Improved DDA MS2 feature detection for Pulsar

- Improved Protein FDR decoy sampling

[Update 11.0.15038.4]

- Added protein-group specific peptide filtering as alternative for proteotypic quantification (when using isoforms)

- Improved robustness for mass calibration in low iRT-Kit situations

- Improved memory efficiency in experiment setup when using large spectral libraries

[Update 11.0.15038.3]

- Added CMID mutation decoy generation strategy

- Improved robustness for iRT-Kit detection

[Update 11.0.15038.2]

- Further memory improvements for directDIA

- Allow protein inference on other than accession ID in Pulsar

[Update 11.0.15038.1]

- Added Protein Qvalue to reportable values

- Improved experiment setup speed from SCIEX wiff files

大版本更新[Release Notes]What is new in Spectronaut™ Pulsar and Spectronaut™ 11

- Support for directDIA processing (only in Spectronaut™ Pulsar)

- Integrated Protein-FDR control

- No more iRT-Kit requirement for DIA analysis (only in Spectronaut™ Pulsar)

- Library generation from DDA/DIA using Pulsar (only in Spectronaut™ Pulsar)

- Improved analysis processes for centroided DIA

- Support for library based Waters SONAR™ analysis

- Library generation from Mascot™

- GO Enrichment in post analysis

- Improved memory efficiency

- Un-supervised centroid algorithm in HTRMS converter

- Improved UI performance

[Update 10.0.12817.12]

- Added "PG.NrOfStrippedSequencesUsedForQuantification" column to report

- Added "PG.NrOfModifiedSequencesUsedForQuantification" column to report

- Added "PG.NrOfPrecursorsUsedForQuantification" column to report

- Added "# of Ratios" column to candidates list

- Added qvalue based filtering options for cross run normalization

[Bug Fixes 10.0.12817.11]

- Added "Carry-over Peak Boundaries" option to iRT-Profiling strategy

- Added "HCP Cleanup Profiling" settings schema

[Bug Fixes 10.0.12817.10]

- Added new MSStats report for version 3.7.3

- Added protein-fdr corrected numbers in run overview

[Bug Fixes 10.0.12817.8]

- Made Bucket ID PAP plot relative

[Bug Fixes 10.0.12817.7]

- Trigger correct PAP refresh on volume correction changed

- Trigger correct PAP refresh on fraction setup changed

- Trigger correct PAP refresh on enable/disable ProteinFDR filtering

[Bug Fixes 10.0.12817.6]

- Added basic quantification values for FG level in report

- Added experimental Protein-FDR filtering

- Added Protein-FDR Histogram plot

[Bug Fixes 10.0.12817.4]

- Changed ratio columns in candidates list to utilize more accurate QUANT 2.0 (old columns marked [DEPRECATED])

- Added "Save as Vector Graphic" option to chart framework

- Added "Re-extract all XICs" option to review perspective (to repopulate iontraces for SNE file saved without XIC data)

- Improved generation and merging of labeled libraries

[Bug Fixes 10.0.12817.2]

- Improved caching during the calibration process

[Bug Fixes 10.0.12817.1]

- Added top N selection for regulation analysis

- Added line for percentile qvalue filtering in data completeness plot

- Added identification numbers for percentile qvalue filtering in Experiment overview

大版本更新[Release Notes]What is new in Spectronaut 10

- One-click peak integration

- Support for generic search engine format

- Better scalability for library generation

- Modifications filter for library generation

- Amino acid filter for library generation

- New precision iRT reference sets

- Support for labelled workflows from Protein Pilot and Proteome Discoverer

- External library import in prepare perspective

- Improved kernel density model

- Improved numerical resolution for Q-value calculation

- Improved scalability for DIA analysis

- Improved flexibility for quantification definition

- Improved performance for direct loading from vendor formats

- Gene annotation and ontology support

- GO annotation in candidates list and report

- Sample correlation matrix in post analysis perspective

- New multi vendor HTRMS Converter

[Bug Fixes 9.0.11240.14]

- Improved flexibility for external modified sequence parsing

[Bug Fixes 9.0.11240.13]

- Improved performance for speclib generation from ProteomeDiscoverer data

[Bug Fixes 9.0.11240.12]

- Improved loadup speed for spectral library selection in analysis setup

- Full PAP refresh on removing runs

[Bug Fixes 9.0.11240.11]

- Added "EG.UsedForProteinGroupQuantity" field for report

- Added "F.Iontrace" export option into report

[Bug Fixes 9.0.11240.10]

- Added support for labeled modifications in Proteome Discoverer

[Bug Fixes 9.0.11240.8]

- Improved mass tolerance estimate for centroid data

- Added static mass tolerance selection option

- Enabled dynamic calibration set size

[Bug Fixes 9.0.11240.5]

- Improved interference correction for labeled workflows

[Bug Fixes 9.0.11240.3]

- Added gradient statistics for precision iRT calibration (dpp, peak capacity, median fwhm)

[Bug Fixes 9.0.11240.1]

- Modification synonyms were not remembered

- Added "User Manual" link to about page

- User generated enzymes were not working

大版本更新[Release Notes]What is new in Spectronaut 9.0

- Improved scalability and memory efficiency

- Improved performance

- iRT Kit support for DIA/HRM/SWATH

- Added Bruker impact II™ support

- Improved quantification flexibility

- Hierarchical clustering and heatmap

- Labeled DIA/HRM/SWATH support

- Generate labeled library from label-free

- Library generation from protein pilot

- Protein coverage plot

- Improved modification handling

- Experiment overview in post analysis perspective

- Library plots in prepare perspective

- Extensive iRT set for library generation

[Bug Fixes 8.0.9600.9]

- Added speclib support for multiple search engine searches in Proteome Discoverer 2.0

[Bug Fixes 8.0.9600.4]

- Improved memory footprint of speclib generation pipeline

- Improved Proteome Discoverer speclib generation when using raw data acquired in centroid mode

[Bug Fixes 8.0.9600.3]

- Added protein meta to pivot report

[Bug Fixes 8.0.9600.2]

- Improved protein annotation for PAP using Stripped or Modified Sequences

[Update]

- Changed default columns for PAP

- Added %Change column

- Added Ratio Column

[Sprint #39 Release]

- Loading bar in protein database panel

- Improved memory efficiency

- Icon for "enhanced" spectral libraries

- Improved Full XIC mode for plots

- Added meta to merged libraries

- Protein quantity bar plot on protein group node level

- Added import/export of settings schemas

大版本更新[Release Notes]What is new in Spectronaut 8.0

- Spectrum library refinement (e.g. for PTMs)

- Protein inference (IDPicker)

- Proteotypicity annotation

- Interference correction on MS1

- Improved support for WiSIM (Fusion instrument family)

- Improved quantitation for SWATH data

- Empirical resolution estimate in run summary

- Lower memory requirements

- Improved profiling algorithm

- Improved user interface for setting up experiments

- Native support for fractionation

- More flexibility for library generation

- Built in spectral libraries for a number of organisms and tissues

- Improved fragment ion selection for spectral library generation

- Protein quantities in report

- Show normalized profiles in PAP

- Analysis details (CVs, Reproducibility)

- MS1 calibration in QC

[Bug Fixes 7.0.8065.17]

- Improved fragment selection for libraries from PD2.0

- Improved support for Thermo Fusion WiSIM-DIA methods

- Improved auto-update message

- Added ShapeQualityScore to report

- Added ShapeQualityScore filter to review

[Sprint #36 Release]

- Improved performance

- Improved memory efficience

- Method developement analysis in PAP

- CV analysis in PAP

- ML Stratification

- SVM support for machine learning

- Improved MS1 Only support

- Compressed kit-files

- Manual fragment selection

- New update message window

- Experimental drift-time support

- BGSMS file support

[Bug Fixes 7.0.8065.16]

- Improved robustness for mass calibration

[Bug Fixes 7.0.8065.15]

- Support for MaxQuant 1.5.3.8

[Bug Fixes 7.0.8065.13]

- Removed minimum datapoint threshold -> now all comparisons are shown in post analysis

[Bug Fixes 7.0.8065.12]

- Added "NotCTerm" modification support for MaxQuant search results

[Bug Fixes 7.0.8065.10]

- Added support for Accepted/Rejected peaks in reporting and post analysis

[Bug Fixes 7.0.8065.9]

- Improved pipeline performance and memory consumption

[Bug Fixes 7.0.8065.8]

- Support for PD 2.0 .pdResult files

[Bug Fixes 7.0.8065.1]

- Improved background subtraction for TripleTOF instruments

大版本更新[Release Notes]What is new in Spectronaut 7.0

- Post analysis perspective

- Regulation analysis using t-test

- Support for non-linear gradients

- Gradient fine structure correction

- Improved performance

- Improved memory efficiency

- Improved calibration

- Merging of GPF raw files

- Decreased HDD consumption

- Protein grouping support for Proteome Discoverer 1.4

- Support for Proteome Discoverer 2.0

- Pivot report

[Bug Fixes 6.0.6846.0]

- Added support for Proteome Discoverer

大版本更新[Release Notes]What is new in Spectronaut 6.0?

- Monitoring QC for user libraries

- Improved normalization

- Normalization report

- Library merging

- Improved library generation

- Improved peak picking

- Improved machine learning

- Up to 40% speed improvement

- Increased memory efficiency

- SNE Files without iontraces

- SNE generation during pipeline mode

- Normalization option in XIC plots