Click image to enlargeThe workflow editor is driven by templates that can be assembled into a workflow using drag-and-drop functionality. Your custom workflow then enables comprehensive data processing and visualization based upon your experimental needs.
研究管理者
Click image to enlargeStudy manager uses a wizard to guide you through the process of setting up a study, including defining sample types and other variables such as multiple time points or sample variants, such as different yeast strains.
結果分析
Click image to enlargeThe Results analysis interactively links your data and allows you to choose how to visualize it. When selecting samples or components, each view is automatically updated based upon your selection(s).
註釋和生物學闡釋
Click image to enlargeWhether it is for unknown identification and spectral annotation or flux analysis and interpretation and mapping of biological information, Compound Discoverer software allows you to easily report your results, store your data and share your insights.
Click image to enlargeThe consistent mass accuracy and high-resolution spectral data from Orbitrap-based MS systems enables fine isotopic information to be obtained, as shown above for the compound davunavir. The resolution and accuracy provide confidence in elemental composition assignments and subsequent library matching, which can be further confirmed using MS/MS fragmentation information.
無論研究樣本大小為何,每個樣品都包含大量的原始數據點。這些數據點部分相互關聯,而許多則無。要理解此複雜但高品質的 MS 和 MS/MS 資訊,就需要進行數據縮減以獲得有意義的深入洞察。
Click image to enlargeWithin each data file there can be many millions of individual data points depending upon the relative complexity of the sample. To confidently obtain results for each sample, and across samples, each data file must have its array of data points aligned with features detected, e.g., a single compound with multiple isotopic peaks may also have numerous adducts. Once the data has been reduced from raw data into features, components can be assembled and identified.
工作流程可設定為使用拖放功能、使用多重特定應用範本的其中之一或編輯其中一個範本來讓數據處理變得快速而輕鬆。每個處理步驟皆是由給定工作流程樹中的「節點」所決定,它可根據您的研究需求連結來驅動數據處理和解讀;可使用軟體開發人員套件或自訂指令碼,如 R 或 Python 中的指令碼,建立新的節點,然後與指令碼節點一起使用,從而根據您的需求制定工作流程。
Click image to enlargeAn example of a pre-defined workflow template for untargeted metabolomics. This template is designed to find and identify differences between samples. Each node is linked and performs a specific task. Here, retention time alignment is performed before unknown compounds are detected and grouped across all samples within the study. Elemental compositions are predicted using the accurate mass data, with compounds identified using the mzCloud mass spectral library and MS/MS information. Where there is no match from mzCloud, ChemSpider is used. For results with a ChemSpider match, mzLogic is used to rank results by likelihood of a match. Resulting compounds are then mapped to biological pathways using Metabolika. If QC samples are present, then normalization is performed, and subsequent differential analysis calculated (t-test or ANOVA).
Click image to enlargeThe compound results table default layout where the chromatographic overlay (top left) shows the extracted ion chromatograms for each related adduct, as shown in the selected compound spectra (top right). The results table can be tailored to display the information relevant to your study, such as compound annotation, retention time, peak areas, statistical information, MS2 spectral match, and more.
Click image to enlargeCompound Discoverer software allows you to open related tables to quickly access the information used to generate annotations. This figure shows the information related to searching the mzCloud mass spectral library (bottom) along with the related experimental and library fragmentation spectra displayed as a mirror plot (top right).
Click image to enlargeFrom volcano plots from differential analysis (left), S-Plots from partial least squares discriminant analysis (middle), and hierarchical clustering analysis (right), it is easy to visualize complex data sets and determine what is statistically different using Compound Discoverer software. Each plot is active, so data points selected in the plot can be marked in the results tables and vice versa, helping determine the cause of observed differences or similarities and tracking compounds in complex data sets.
Click image to enlargeAcquireX generates an exclusion list from a blank run (matrix matched). Then, an injection of the sample, followed by feature detection and component assembly, populates the inclusion list with compounds detected in the samples. A series of iterative DDA injections follow. Each injection is informed from the previous one, minimizing redundant fragmentation spectra and maximizing relevant spectra and metabolite annotations.
Click image to enlargeUsing DDA with AcquireX significantly increases the number of unique compounds with high-quality fragmentation spectra, so you obtain a more comprehensive picture of what is in your samples, as well as increasing the depth of decision-making MS/MS information available.
Click image to enlargeUsing DDA with AcquireX improves data quality and creates a significant increase in the number of compounds with MS/MS spectra, resulting in improved mzLogic ranking and higher mzCloud similarity scores, ultimately providing higher overall confidence in compound identification and putative unknown identification.
Click image to enlargeStable isotope labelling uses the high-resolution mass spectral data from Orbitrap-based MS, where isotopologues can easily be detected and the respective elemental compositions determined. Compound Discoverer software makes it easy to visualize the amount of label incorporation and resulting isotopic distribution with the ability to map powerful qualitative and quantitative flux analysis information directly onto biological pathways in Metabolika.
Click image to enlargeThe FISh scoring node enables fragment structure annotation and uses the Thermo Scientific HighChem Fragmentation Library for real data from more than 52,000 fragmentation schemes to help localize (bio)transformation. Exact matches are shown in green, with transformation-shifted matches highlighted in blue (above), showing how the site of transformation is identified.
Click image to enlargePattern scoring allows you to flag compounds that match user-specified natural or artificial isotopic patterns. Including and using additional traces such as UV, PDA, CAD and analog, such as radio label traces, as shown above, ensures that minimal potential metabolites, impurities or degradants are missed.
Compound Class Scoring 節點提供了另一項工具,以確保不遺漏任何內容。它使用一組代表性片段,是由某一化合物類別中的一個或多個已知分子所建立出來的,可鑑定相關或來自同一化合物類別的其他成分。
Click image to enlargeThe Compound Class scoring node allows you to identify compounds that are structurally related, ensuring that nothing is missed, from metabolites to potentially toxic or harmful extractables, leachables or degradants.
Click image to enlargeUpper left shows the Total Ion Chromatogram (TIC) for a sample in bile matrix, illustrating the potential complexity and matrix interferences present; bottom left shows the resulting trace following the use of Multiple Mass Defect Filtering (MMDF) and how it can be used to effectively simplify complex matrix samples such as bile, feces, blood, and plasma. The plot on the right demonstrates how the mass defect plot can be used to visualize data and mine using Kendrick formulas, for example unknown polymer identification. All data is interactively linked between plots and data tables within Compound Discoverer software to streamline data review.
Click image to enlargeYou can direct creation or expansion of mzVault spectral libraries or TraceFinder software format lists using text lists, mass lists, inclusion and exclusion lists, enabling you to streamline your analyses and subsequent targeted screening and/or quantitative analysis with minimal effort.
Click image to enlargeCombining stable isotope labelling with the visualization capabilities of Metabolika, allows you to overlay exchange rate information to provide a highly visual way of reviewing and reporting qualitative flux analyses.
Click image to enlargeUsing pooled QC samples, which are analyzed throughout data acquisition, allows for the correction of batch-effects over time. Correction for each sample is performed individually, the upper plot shows a curve fitted to the QC samples, with the bottom plot showing the resulting data set after correction. This capability is based upon a peer-reviewed methodology published by Dunn et. al. in Nature Protocols. Compound Discoverer software provides the capability to also view the impact of any changes to the data pre- and post- normalization according to this protocol.
Click image to enlargeDemonstrating the connectivity of data within Compound Discoverer software, the data points highlighted by blue circles in the Volcano Plot (bottom right) are selected within the Compound Table (bottom left). Selecting any compound in any plot automatically updates all plots to show the relevant data. The interconnected tools enable you to rapidly identify differences and the compounds or groups of compounds responsible for those differences. Additionally, it streamlines follow-on confirmation by giving you the ability to filter and review the relevant data.
Click image to enlargeFrom Principal Components Analysis (PCA) for unbiased review of data to supervised techniques like Partial Least Squares – Discriminant Analysis (PLS-DA) and the use of S Plots (left) identify compounds that give rise to any observed grouping of samples. Hierarchical Clustering (center) not only shows the clustering of samples along the x-axis, and clustering of compounds on the y-axis, it provides user-configurable heat mapping to visualize any clustering. Box Whisker Charts (right) allow visualization by groupings, time points, and more, with dynamic.
探索化合物之間的關係,可為您的數據組揭露其他訊息和深入解析。藉由 Molecular Networks,您可以根據轉化和光譜相似性 (例如,一系列的 Phase I 和 Phase II 轉化) 來互動式地探索您分析之中化合物之間的關係。
Click image to enlargeThe fully interactive Molecular Networks visualization browser allows you to view your data in a different way. Identified compounds are shown by nodes (circles) and when a relationship is identified, the nodes are connected. Selecting a node (compound) or connection (transformation) displays pertinent information (right) about the identified compound and the relevant transformation(s). All of the visualized data can be interactively filtered using thresholds, data quality information or text search for specific compounds or transformations.
片段離子搜索 (FISh) 是根據由理論式片段預測或實驗 MSn 數據所擷取的母化合物之片段模式,提供結構相似化合物的快速篩檢。母化合物結構及其潛在代謝物會被用於過濾掉絕大多數的基質相關背景離子,從而使相關化合物之鑑定變得快速輕鬆。FISh 提供了 Phase l 和 Phase II 生物轉化的詳盡列表,並提供建立自訂列表的功能。
Click image to enlargeIn addition to filtering the structurally similar compounds, FISh automatically localizes transformation sites, labels, and applies color-coding to fragments common to the parent and filtered results. In the Mirror Plot example shown here, exact matches to proposed metabolite fragments are shown in green and transformation shifted matches are blue.