PEAKS Studio 13 更新 最新授权

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PEAKS Studio 13 提供完整的自下而上的蛋白质组学解决方案，具有更高的准确性、灵敏度和速度。PEAKS为各种应用更新了工作流程，例如深入的经典和非经典肽和蛋白质鉴定，使PEAKS成为独特的解决方案。从 DDA 到 DIA 数据支持，PEAKS Studio 13 提供了一个全面的解决方案，将您的研究提升到新的高度！®® ®

专为发现而构建。
针对准确性进行了优化。

PEAKS Studio 以无与伦比的深度、机器学习支持的算法以及对所有主要供应商的无缝支持重新定义了蛋白质组学分析。PEAKS 具有详细且易于使用的图形用户界面 （GUI）。

增加 10%

使用深度学习的
ID

无与伦比

DDA & DIA
性能

支持 8

主要
供应商

DDA 和 DIA 做得好：多引擎强国

In PEAKS 13, the DDA and DIA workflows have been streamlined into two powerful options: Proteome and Peptidome.

The Proteome workflows support traditional protein identification and quantification, with results focused at the protein level. Meanwhile, the Peptidome workflows leverage DeepNovo’s deep learning-based de novo sequencing, combined with peptide database searches and sequence variant analysis, to deliver insights at the peptide level.

Users can customise their analysis workflows, selecting which steps to run and adding or modifying steps at any point. Results are organised into intuitive result nodes, making it easier to interpret, explore, and validate your data.

Key Features

PEAKS 13 uses the latest PEAKS algorithm for all analyses, including data loading/refinement, identification and quantification. Deep learning-boosted identification workflows are available for both DDA and DIA analysis for increased identification rates of over 10%.​

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Streamlined Workflow with Direct Database search for DIA

PEAKS Studio 13 offers a unique DIA workflow to maximise identification of peptides by integrating four methods: spectral library search, direct database search, de novo sequencing, and sequence variant analysis with up to 20% increase in identification and quantification, and faster processing times for CPU and GPU resources.

• A library search is performed against a predefined spectral library. Peptide spectra without a library match can be directly searched against a protein database.
• A protein sequence database is directly searched with DIA data. Advanced machine learning algorithms allow improved accuracy and sensitivity of peptide identification. During this step of the pipeline, PEAKS 13 DIA workflow now supports the identification of any PTMs specified by the user. This will enable an increase in identification of modified peptides without requiring their entries in a spectral library.
• Unmatched spectra from the database search are de novo sequenced.
• High-scoring de novo peptides are mapped against the database to find sequence variants using the SPIDER algorithm.
• Identified peptides from both the spectrum library search and protein sequence database search can be used in a quantification analysis.
  

The library search and the database search methods are optional. Users can conduct only a library search, a library-free direct database search, or both steps in sequence.

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LC/MS 数据精炼视图

用户现在可以轻松地在 LC/MS 图上可视化母离子、有和没有相关母离子的鉴定以及从头标签，以改进结果验证。

此外，肽选项卡和 LC/MS 图的集成更加无缝。单击一个或多个鉴定结果，显示和比较支持的碎片离子。这使得验证重叠的肽鉴定变得容易。

支持的碎片离子也显示在肽选项卡的 LC/MS 快照中。用户还可以单击以在完整的 LC/MS 图上显示鉴定结果。

基于特征的识别

• MS1 基于特征的鉴定提高了灵敏度和肽鉴定效率。
• 专为 DDA 技术设计，可提高重现性。
• 集成数据库搜索和从头测序，以扩展深入分析。
• 在 PEAKS DDA 工作流程中激活深度学习增强，以最大限度地提高肽鉴定效率。
  

详细了解从头测序为您的研究带来的优势。

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混合 DIA 和 PRM

Thermo 的 Hybrid-DIA 技术仅在 PEAKS Studio 中提供，结合了靶向和发现驱动的方法，使其成为临床蛋白质组学应用的理想选择。

Hybrid-PRM/DIA 是一种新的直观数据采集策略，通过智能触发多重平行反应监测 （PRM） 以及使用 DIA 对临床生物样本进行发现驱动的数字化，从而提高特定分析集的灵敏度。重标记的参考肽用作 PRM 和内源性肽监测的触发器。

峰值 PRM

PEAKS 13 采用全新的 PRM 靶向定量工作流程，可精确可靠地定量复杂生物样品中的特定肽。

这种靶向方法使研究人员能够专注于预定义的目标肽，即使在存在干扰物质的情况下也能确保准确且可重现的定量。新的 PRM 靶向定量功能显著提高了工作流程的灵敏度和特异性，使其成为详细蛋白质组学研究和生物标志物验证不可或缺的工具。通过集成这一高级功能，PRM 工作流程为靶向蛋白质组学中的高可信度绝对定量提供了可靠的解决方案。

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PEAKS DeepNovo 肽组学：先进的免疫肽组学解决方案

这种新开发的解决方案是肽组学数据的专业工作流程，结合了数据库搜索、从头测序和突变肽的鉴定。了解更多信息

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质量控制 （QC） 功能，用于从原始数据到结果的深入分析

借助 PEAKS® Studio 13 中的质量控制 （QC） 分析，用户可以评估原始数据和/或结果的统计信息，并获得对 LC-MS 采集属性的有益见解。该自动化工具专为 DDA 和 DIA 数据而设计，将提供用于确定数据质量并评估实验设置的元素。

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The DIA Feature View

DIA Feature View stems from PEAKS dedication to provide a full result transparency allowing the user to investigate, validate, and confirm the precursor. All features, with ID and without ID, are displayed with all fragment assignments, mirror plots to show correlation of empirical and predicted fragments, MS1 and MS2 feature views.

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Quantification 视图

借助 PEAKS Q 的附加模块，PEAKS Studio 还可以同时测定一组样品的相对蛋白质丰度变化，而无需事先了解所涉及的蛋白质。在 PEAKS 13 中，通过 PEAKS PTM 或 SPIDER 搜索找到的肽将包含在定量步骤中。

通过统计分析工具 （倍数变化 >2，FDR <0.01） 鉴定两组之间高度差异表达的蛋白质，并以热图格式显示。

如果选择了“基于特征”的定量，则 LFQ 结果将包含一个新的“仅从头”选项卡，其中包含与数据库不匹配的肽段的定量结果。

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蛋白质观点

Protein View 可在 DDA 和 DIA 工作流程中展示复杂生物样品的蛋白质分析。对于每种蛋白质，序列覆盖度视图显示带有光谱注释的肽图以供验证。使用 PEAKS 传统的从头辅助数据库搜索，用户可以轻松地以蓝色查看已识别的肽序列，而灰色条表示仅从头标签匹配。

使用 PEAKS DB Search 分析的 Bruker timsTOF diaPASEF 数据
肽视图

肽视图提供了从 MS1 中鉴定出的丰度肽的列表。对于每个修饰的肽，修饰位点的置信度 （Ascore） 是相关的。

Bruker timsTOF diaPASEF data analysed with PEAKS DirectDB Search

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Next level confidence: confident PTM/mutation sites identification based on amino acid level evidence

The Post-Translational Modification (PTM) and Mutations Analysis workflow offers next-level confidence by enabling the identification of PTM and mutation sites with high precision, grounded on amino acid level evidence.

This advanced capability allows researchers to pinpoint specific modifications and mutations within proteins, providing a detailed and accurate understanding of protein function and regulation. By leveraging robust algorithms and comprehensive data analysis, this workflow ensures that PTM and mutation sites are identified with exceptional confidence, facilitating deeper insights into protein dynamics and disease mechanisms. This enhanced analytical power is crucial for advancing our understanding of biological processes and developing targeted therapeutic strategies.

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