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• ProMass是一種自動生物分子解卷積和報告軟件包，用于處理Thermo Scientific的Xcalibur或Waters MassLynx數據系統上采集的ESI / LC / MS數據或單個ESI質譜圖。ProMass被設計用于高通量應用。
• 當用電噴霧（ESI）離子化時，大的生物分子主要是多電荷的。當以正離子模式分析時，由于堿性氨基酸和氨基末端，肽或蛋白質將在多個位點質子化。另一方面，作為酸性磷酸骨架的結果，以負離子模式分析的寡核苷酸在多個位點被去質子化。這種多次充電通常導致包含一系列電荷狀態的ESI質譜。這些復雜的光譜必須“解卷積”或“轉化”，以便確定生物分子的不帶電荷的質量。 ProMass為執行整個LC / MS數據集的解卷積提供了一個自動化平臺。
• ProMass從一開始就設計用于高通量應用。實際上，運行ProMass的正常方式是通過Xcalibur或MassLynx示例列表。因此，您可以運行樣品列表，讓ProMass在處理它們，或者在您方便的時候批量重新處理列表。 ProMass使用稱為ZNova的新型去卷積算法，可產生無偽像的解卷積質譜圖。 ZNova可用于處理各種生物分子（包括蛋白質，寡核苷酸，肽等）的數據。與其他許多反卷積算法不同，ZNova可以適應低電荷狀態譜和低信噪比的數據。 ProMass自動地以任何網頁瀏覽器的易用和交互式格式報告結果。頂級摘要頁面匯總了多次運行的結果，并將其顯示在單個超鏈接頁面上，以便您快速瀏覽結果。目標質量特征允許您自動從LC / MS數據中搜索多個目標質量數。目標質量特征包括結果顏色編碼，使您可以快速磨合可能需要進一步關注的樣品。
• 特征：
• ProMass不僅僅是解卷積軟件。ProMass是一個工具，允許您以高度協作的基于Web的格式處理和傳達您的結果。
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• 生物分子質譜自動去卷積以確定分子量：適用于蛋白質，多肽，寡核苷酸等。
• 適用于Thermo Xcalibur或Waters MassLynx數據系統的ProMass版本。
• 使用專有ZNova算法的無偽影解卷積，無需手動干預去除偽像峰值。
• 用Xcalibur處理方法靈活處理LC / MS峰。
• 處理Windows剪貼板上的光譜數據。
• 自動化的基于Web的報告，包括總結報告，色譜圖（UV和MS），原始質譜圖和解卷積質譜圖。
• 自動計算目標寡核苷酸和多肽的預期質量。
• 顏色編碼的結果顯示，頂級匯總報告和樣品盤查看器可以快速查看結果。
• 自動搜索多個目標群體，并以顏色編碼的基于Web的摘要報告結果。
• 基于Excel的總結報告選項
• 從寡核苷酸或蛋白質序列自動識別末端或內部片段
• 支持鑒定來自多個寡核苷酸或蛋白質序列的片段（例如雙鏈體）
• 支持指定修飾的寡核苷酸
• 支持“模糊”靶標物質，如PTM或蛋白質藥物綴合物
• 根據反卷積峰強度和色譜圖面積百分比計算目標質量純度估算值
• XML輸出
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• ProMass版本分為標準版和HR版本。ProMass HR版本包含標準版的所有功能，另外，HR版本還具備以下額外功能：
  
• 包括帶有ReSpectTM算法的完整ReView PPL數據處理包
• Deisotoping用于同位素分辨質譜的單同位素質量測定，以獲得更高的質量準確度（例如，Orbitrap數據<3 ppm）。
• 質譜峰形建模，用于提高同位素未分辨質譜的分辨率
• 用于同位素未解析質譜的PPL電荷反褶積算法
  
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• ProMass for Xcalibur系統要求
• 用戶應該遵循安裝計劃使用的Xcalibur版本的一般系統要求。運行ProMass for Xcalibur的系統要求如下：
• 必須安裝Thermo Xcalibur v.2.0.7或更高版本
• 應安裝Thermo XDK（包含在Xcalibur CD中）以啟用自動化功能
• 所需的PC與已安裝的Thermo Xcalibur版本具有相同的要求
• Microsoft Windows XP到Windows 10（受Xcalibur-Windows兼容性限制）
• 安裝程序和幫助文件至少需要110 MB的可用磁盤空間
  
• 注意： ProMass不包含Web服務器軟件。如果要在本地計算機上查看結果，則不需要Web服務器。但是，如果您想通過Internet或Intranet與他人共享數據，則需要Web服務器。
  
• 英文簡介
• Introduction:
• Large biomolecules when ionized by electrospray (ESI) are predominantly multiply charged. When analyzed in the positive ion mode, peptides or proteins will be protonated at multiple sites as a result of the basic amino acids and amino terminus. On the other hand, oligonucleotides analyzed in the negative ion mode are de-protonated at multiple sites as a result of the acidic phosphate backbone. This multiple charging usually results in ESI mass spectra that contain a range of charge states. These complex spectra must be “deconvoluted” or “transformed” in order to order to determine the uncharged mass of the biomolecule. ProMass provides an automated platform for performing deconvolution of entire LC/MS data sets.
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• Overview:
• ProMass is an automated biomolecule deconvolution and reporting software package that is used to process ESI/LC/MS data or single ESI mass spectra acquired on Thermo Scientific’s Xcalibur or Waters MassLynx data systems. ProMass was designed from the start for high-throughput applications. In fact, the normal way to run ProMass is through the Xcalibur or MassLynx sample list. Therefore, you can run a list of samples and have ProMass process them at the end or batch reprocess the list at your convenience.
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• ProMass uses a novel deconvolution algorithm known as ZNova that produces artifact-free deconvoluted mass spectra. ZNova can be used to process data from a wide variety of biomolecules including proteins, oligonucleotides, peptides, etc. Unlike many other deconvolution algorithms, ZNova can accommodate low charge state spectra and data of low signal-to-noise ratio. ProMass reports the results automatically in an easy-to-use and interactive format viewable from any web browser. A top-level summary page summarizes the results from multiple runs and displays them on a single hyperlinked page allowing you to navigate your results quickly. Target mass features allow you to search for multiple target masses from LC/MS data automatically. The target mass features include results color coding, allowing you to quickly hone in on the samples that may require further attention.
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• ProMass HR includes additional features for high-resolution data processing by incorporating the full suite of algorithms from Positive Probability Ltd (PPL). ProMass HR methods can utilize the PPL algorithms that allow for monoisotopic mass determination of isotopically resolved mass spectra or enhanced resolution of isotopically unresolved mass spectra. The PPL methods may be automated thru the same powerful mechanism as the standard version of ProMass. Results are displayed through the same easy-to-use and intuitive web-based output as well.
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• Key Features of ProMass:
• ProMass is more than just deconvolution software. ProMass is a tool that allows you to process and communicate your results in a highly collaborative web-based format.
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• Automated deconvolution of biomolecule mass spectra to determine molecular mass: applicable to proteins, peptides, oligonucleotides, etc.
• ProMass versions for either Thermo Xcalibur or Waters MassLynx data systems
• Artifact-free deconvolution using proprietary ZNova algorithm, no manual intervention required to remove artifact peaks
• Flexible processing of LC/MS peaks directed by Xcalibur processing method
• Process data from a spectrum on the Windows clipboard
• Automated web-based reporting, including summary report, chromatograms (UV and MS), raw, and deconvoluted mass spectra
• Automatically calculate expected masses of target oligonucleotides and polypeptides
• Color-coded results display, top-level summary report, and sample plate viewer allow for rapid visualization of your results
• Automatically search for multiple target masses and report results in color-coded web-based summary
• Excel-based summary report option
• Automatic identification of terminal or internal fragments from oligonucleotide or protein sequences
• Support for identifying fragments from multiple oligo or protein sequences (e.g., duplexes)
• Support for specifying modified oligonucleotides
• Support for “fuzzy” target masses such as PTM’s or protein drug conjugates
• Dynamic sorting of columns in web-based reports
• Target mass purity estimation computed from deconvolution peak intensities and chromatogram area percents
• XML output
• Additional Features of ProMass HR:
• ProMass HR includes all of the features of the standard version of ProMass, plus the following:
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• Includes the full ReView PPL data processing package with ReSpect? algorithms
• Deisotoping for monoisotopic mass determination of isotopically resolved mass spectra for superior mass accuracy (e.g., <3 ppm on Orbitrap data).
• Mass spectral peak shape modeling for enhanced resolution of isotopically unresolved mass spectra
• PPL charge deconvolution algorithm for isotopically unresolved mass spectra
• For more information, access our ProMass HR applications guide.
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• ProMass for Xcalibur System Requirements
• You should follow the general system requirements for installing the version of Xcalibur that you plan to use. The system requirements for running ProMass for Xcalibur are listed below:
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• Thermo Xcalibur v. 2.0.7 or later must be installed
• The Thermo XDK (included on the Xcalibur CD) should be installed to enable the automation features
• The required PC has the same requirements of the installed version of Thermo Xcalibur
• Microsoft Windows XP through Windows 10 (limited by Xcalibur-Windows compatibility)
• At least 110 MB of free disk space is required to install the program and help files
  
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• Spectral deconvolution is a processor-intense operation. Therefore, a fast microprocessor is best if you want fast execution times or if you are processing complex spectra.
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• Note:ProMass does not include web server software. A web server is not required if you want to view your results on a local machine. However, if you want to share your data with others over the internet or intranet you will need a web server.