[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