[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