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ProMass是一種自動(dòng)生物分子解卷積和報(bào)告軟件包，用于處理Thermo Scientific的Xcalibur或Waters MassLynx數(shù)據(jù)系統(tǒng)上采集的ESI / LC / MS數(shù)據(jù)或單個(gè)ESI質(zhì)譜圖。ProMass被設(shè)計(jì)用于高通量應(yīng)用。
當(dāng)用電噴霧（ESI）離子化時(shí)，大的生物分子主要是多電荷的。當(dāng)以正離子模式分析時(shí)，由于堿性氨基酸和氨基末端，肽或蛋白質(zhì)將在多個(gè)位點(diǎn)質(zhì)子化。另一方面，在負(fù)離子模式下分析的寡核苷酸由于酸性磷酸骨干而在多個(gè)位點(diǎn)去質(zhì)子化。這種多次充電通常導(dǎo)致包含一系列電荷狀態(tài)的ESI質(zhì)譜。這些復(fù)雜的光譜必須“解卷積”或“轉(zhuǎn)化”，以便確定生物分子的不帶電荷的質(zhì)量。 ProMass為執(zhí)行整個(gè)LC / MS數(shù)據(jù)集的解卷積提供了一個(gè)自動(dòng)化平臺(tái)。
ProMass從一開(kāi)始就設(shè)計(jì)用于高通量應(yīng)用。實(shí)際上，運(yùn)行ProMass的正常方式是通過(guò)Xcalibur或MassLynx示例列表。因此，您可以運(yùn)行樣品列表，讓ProMass在處理它們，或者在您方便的時(shí)候批量重新處理列表。
ProMass使用稱(chēng)為ZNova的新型去卷積算法，可產(chǎn)生無(wú)偽像的解卷積質(zhì)譜圖。 ZNova可用于處理各種生物分子（包括蛋白質(zhì)，寡核苷酸，肽等）的數(shù)據(jù)。與其他許多反卷積算法不同，ZNova可以適應(yīng)低電荷狀態(tài)譜和低信噪比的數(shù)據(jù)。 ProMass自動(dòng)地以任何網(wǎng)頁(yè)瀏覽器的易用和交互式格式報(bào)告結(jié)果。摘要頁(yè)面匯總了多次運(yùn)行的結(jié)果，并將其顯示在單個(gè)超鏈接頁(yè)面上，以便您快速瀏覽結(jié)果。目標(biāo)質(zhì)量特征允許您自動(dòng)從LC / MS數(shù)據(jù)中搜索多個(gè)目標(biāo)質(zhì)量數(shù)。目標(biāo)質(zhì)量特征包括結(jié)果顏色編碼，使您可以快速磨合可能需要進(jìn)一步關(guān)注的樣品。
ProMass HR通過(guò)合并來(lái)自Positive Probability Ltd（PPL）的全套算法，包括用于高分辨率數(shù)據(jù)處理的其他功能。Promass HR方法可以利用PPL算法，該算法允許對(duì)同位素分辨的質(zhì)譜進(jìn)行單同位素質(zhì)量測(cè)定或?qū)ν凰匚捶直娴馁|(zhì)譜進(jìn)行更高的分辨率。通過(guò)與Promass標(biāo)準(zhǔn)版本相同的強(qiáng)大機(jī)制，可以自動(dòng)實(shí)現(xiàn)PPL方法。結(jié)果也通過(guò)相同的易于使用和直觀的基于Wed的輸出顯示。
特征：
ProMass不僅僅是解卷積軟件。ProMass是一個(gè)工具，允許您以高度協(xié)作的基于Web的格式處理和傳達(dá)您的結(jié)果。
生物分子質(zhì)譜自動(dòng)去卷積以確定分子量：適用于蛋白質(zhì)，多肽，寡核苷酸等。
適用于Thermo Xcalibur或Waters MassLynx數(shù)據(jù)系統(tǒng)的ProMass版本。
使用專(zhuān)有ZNova算法的無(wú)偽影解卷積，無(wú)需手動(dòng)干預(yù)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(shù)據(jù)。
自動(dòng)化的基于Web的報(bào)告，包括總結(jié)報(bào)告，色譜圖（UV和MS），原始質(zhì)譜圖和解卷積質(zhì)譜圖。
自動(dòng)計(jì)算目標(biāo)寡核苷酸和多肽的預(yù)期質(zhì)量。
顏色編碼的結(jié)果顯示，匯總報(bào)告和樣品盤(pán)查看器可以快速查看結(jié)果。
自動(dòng)搜索多個(gè)目標(biāo)群體，并以顏色編碼的基于Web的摘要報(bào)告結(jié)果。
基于Excel的總結(jié)報(bào)告選項(xiàng)
從寡核苷酸或蛋白質(zhì)序列自動(dòng)識(shí)別末端或內(nèi)部片段
支持鑒定來(lái)自多個(gè)寡核苷酸或蛋白質(zhì)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(biāo)物質(zhì)，如PTM或蛋白質(zhì)藥物綴合物
根據(jù)反卷積峰強(qiáng)度和色譜圖面積百分比計(jì)算目標(biāo)質(zhì)量純度估算值
XML輸出
ProMass當(dāng)前可用于Thermo Xcalibur，Waters MassLynx和SCIEX數(shù)據(jù)系統(tǒng)。其他數(shù)據(jù)系統(tǒng)正在開(kāi)發(fā)中。
ProMass版本分為標(biāo)準(zhǔn)版和HR版本。ProMass HR版本包含標(biāo)準(zhǔn)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(shù)據(jù)處理包
Deisotoping用于同位素分辨質(zhì)譜的單同位素質(zhì)量測(cè)定，以獲得更高的質(zhì)量準(zhǔn)確度（例如，Orbitrap數(shù)據(jù)<3 ppm）。
質(zhì)譜峰形建模，用于提高同位素未分辨質(zhì)譜的分辨率
用于同位素未解析質(zhì)譜的PPL電荷反褶積算法
ProMass HR功能
ProMass HR包括用于高分辨率數(shù)據(jù)處理的特性
ProMass HR包括標(biāo)準(zhǔn)的ProMass反褶積算法和Positive Probability Ltd（PPL）數(shù)據(jù)處理包
PPL算法包括：去同位素（用于同位素分辨率質(zhì)譜的單同位素質(zhì)量測(cè)定）、峰值建模和形狀反褶積，以及PPL電荷反褶積算法。
PPL峰形反褶積可與質(zhì)子電荷反褶積相結(jié)合，以提高電荷反褶積前生物分子（如Mab）質(zhì)譜的分辨率。這可以做到與低分辨率的數(shù)據(jù)。
ProMass HR可以引用ProMass參數(shù)文件，該文件嵌入了一個(gè)PPL方法來(lái)自動(dòng)處理Xcalibur樣本列表中的整個(gè)LCMS數(shù)據(jù)集。
ProMass HR使用與標(biāo)準(zhǔn)的ProMass反褶積包相同的易于使用的基于web的界面輸出結(jié)果。
ProMass for Xcalibur系統(tǒng)要求
用戶(hù)應(yīng)該遵循安裝計(jì)劃使用的Xcalibur版本的一般系統(tǒng)要求。運(yùn)行ProMass for Xcalibur的系統(tǒng)要求如下：
必須安裝Thermo Xcalibur v.2.0.7或更高版本
應(yīng)安裝Thermo XDK（包含在Xcalibur CD中）以啟用自動(dòng)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(pán)空間
注意： ProMass不包含Web服務(wù)器軟件。如果要在本地計(jì)算機(jī)上查看結(jié)果，則不需要Web服務(wù)器。但是，如果您想通過(guò)Internet或Intranet與他人共享數(shù)據(jù)，則需要Web服務(wù)器。
適用于Sciex系統(tǒng)要求的ProMass
您應(yīng)該遵循Sciex OS的一般系統(tǒng)要求以實(shí)現(xiàn)Windows兼容性。下面列出了運(yùn)行ProMass for Sciex的系統(tǒng)要求：
支持Windows 7或Windows 10
必須從Sciex獲得ProMass Processor應(yīng)用程序，以允許自動(dòng)處理Sciex數(shù)據(jù)文件。
英文簡(jiǎn)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.
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.
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.
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.
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.
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:
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.
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:
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
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.
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.
