用于糖组学数据解析
，援手分析质谱数据并鉴别糖链结构

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SimGlycan是一款MSⁿ数据分析软件。它预测聚糖结构
，对其进行评分并天生与给定MS谱亲昵匹配的可能聚糖列表。支持糖肽和开释的聚糖谱。

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SimGlycan凭据MS/MS和多级质谱 (MSⁿ ) 数据预测聚糖的结构。此表
，使用LC-MS/MS糖肽数据分析糖肽的支持有助于糖基化钻研。SimGlycan接受尝试性MS/MS数据
，将它们与自己的数据库进行匹配
，了局天生排序的候选结构列表。每个候选者的等级暗示候选结构和尝试聚糖之间的靠近度。排名是凭据稳重的评分机造推算的
，该机造思考了在尝试MS/MS光谱中观察到的结构特异性诊断离子以及观察到的峰的强度。

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SimGlycan还支持异构体分化的多级质谱 (MSⁿ ) 数据分析。

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SimGlycan特点：

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强的聚糖和糖肽数据库

SimGlycan数据库是一个大型关系数据库
，蕴含9,964种聚糖、22,814种糖蛋白*、6,826种已知生物起源的聚糖和5,874种已知类此外聚糖。随着更多聚糖信息的颁布
，该数据库会不休更新。

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支持MALDI MS/MS和LC-MS/MS工作流程

支持H、Li、Na、Mg²⁺、K、HCOO^-和NH4⁺等分歧的加合物以及Na+H、Li+H等加合物组合
，以及基于分歧的可扩大 MS/MS碎片模式仪器设置
，SimGlycan能够分析糖肽和开释聚糖的MALDI和LC-MS/MS数据
，这些聚糖是未衍生化、全甲基化和还原端建饰的
，而不会影响分析了局。

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数据输入文件体式

SimGlycan能够直接自动加载由SCIEX（TripleTOF^TM 5600系统、TOF/TOF 5800、4800 Plus MALDI TOF/TOF^TM分析仪、4000 QTRAP^?和QSTAR^?Elite系统）的质谱仪产生的输入数据文件。Agilent Technologies（Agilent 6200系列TOF LC/MS和Agilent 6500系列Q-TOF LC/MS系统）
，Bruker Corporation（ultrafleXtreme^TM?MALDI TOF/TOF, ultraflex^TM?MALDI TOF/TOF, autoflex^TM TOF和TOF/TOF, maXis^TM?UHR-TOF, micrOTOF^TM, micrOTOF-Q^TM, solariX^TM Qq-FTMS和amaZon^TM 离子阱系列）
，Thermo Scientific^TM（LTQ FT Ultra、LTQ Velos、LTQ XL、LTQ Orbitrap Discovery、LTQ Orbitrap Velos、LTQ Orbitrap XL、MALDI LTQ Orbitrap、Orbitrap Elite, Q Exactive和Thermo Scientific^TM Orbitrap^TM?Fusion^TM Tribrid质谱仪和Thermo Scientific^TM Q Exactive^TM 混合四极杆-Orbitrap质谱仪）和Waters公司（SYNAPT G2 HDMS、SYNAPT G2 MS、Xevo G2 QTof、Xevo QTof MS、Xevo TQ MS和Xevo TQ-S平台）。使用mzData和mzXML体式支吃熹他质谱仪。此表
，SimGlycan也接受手动输入、TXT和XLS文件体式。不论你的仪器是什么的
，都能够用第三方工具将输出了局转换为这些体式。

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TMT定量*

SimGlycan此刻支持基于质谱的定量糖学工作流程
，使用aminoxyTandem Mass Tags (TMT)。aminoxyTMT6试剂可能有效的对聚糖进行相对定量
，提高象征聚糖的电离效能
，从而提高分析通量。通过丈量来自相应MS/MS光谱的汇报离子峰强度来量化聚糖。用户能够指定幼至0.0001的容差。提取峰强度后
，调整氨氧基TMT汇报离子信号以注明每种TMT变体中的同位素杂质。用户能够选择全数聚糖谱匹配中的总和/均匀/中值汇报离子强度作为聚糖的数量。各类图表
，如条形图、点图等。

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多级质谱（MSⁿ）数据分析

SimGlycan蕴含对执行多级/序列质谱 (MSⁿ ) 数据分析的支持。MSⁿ是一种对来自MS/MS（或前级MS）的产品离子进行沉碎裂的技术
，是解决异质性、分支模式和同压寡糖结构的有效技术之一。它允许分辨拥有类似特点片段模式的聚糖
，这些片段模式在MS/MS光谱中无法分辨。随着MS (n)水平的增长
，天生的片段变得拥有结构特异性
，这有助于解析同量异位寡糖或对选定结构进行具体表征。

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糖肽定性分析

好多质谱仪允许在化合物从在线分离系统中洗脱时捕获MS/MS 数据。这种LC-MS/MS步骤会天生很大的数据集
，必要复杂的信息学工具在色谱分离过程中分配糖肽结构。这将提高分析效能并提供更深刻的质谱糖蛋白组数据分析。SimGlycan此刻支持鉴别复杂混合物的糖肽
，这些混合物由LC分离并由MS/MS在批处置模式下检测。SimGlycan将使用第三方工具识此外蛋白质ID、蛋白质序列或肽序列作为初始输入。SimGlycan鉴别可能的聚糖-肽组合
，并凭据MS/MS数据中观察到的峰对它们进行排序
，这些峰对应于理论糖肽中的诊断离子Ｄ芄环治鲇涤1到20 ppm和0.1到2000 milli Dalton (mDa) 之间误差容限的高分辨率正确质量数据。

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项目治理

SimGlycan提供项目治理
，将了局与输入配置文件和搜索参数有关联。您能够打开肆意数量的项目。用户能够在一个项目中导入20,000个光谱。项目能够凭据起源、尝试室或钻研指标进行分类。这很关键
，尤其是在进行大规模聚糖分析项目时。您能够通过单击按钮接见聚糖有关信息。与基于Web的利用法式分歧
，SimGlycan将其保留在您自己的推算机上。

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可用信息蕴含：

聚糖结构：显示聚糖的分子结构（碳水化合物序列）。

Glycan Fragments：使用Domon Costello碎片规定显示定名法、结构、m/z值和质量。为每个片段分配一个序列号。

i) 糖苷片段：显示单个糖苷和糖苷/糖苷片段。

ii) 交叉环片段：显示单个交叉环和糖苷/交叉环片段。

糖肽结构：显示肽序列和蛋白质糖基化位点以及聚糖结构。

注解质谱并天生汇报： SimGlycan能够使用cartoons或Domon-Costello定名法对证谱进行注解
；姑枋隽似蔚牡绾勺刺。

导出带注解的峰列表：用户能够将全数搜索了局的带注解的峰列表从20,000个MS/MS光谱导出到单个项目汇报。用户能够在带注解的峰列表中只蕴含匹配的片段或同时蕴含匹配和不匹配的片段。

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绘造聚糖

SimGlycan使用户可能绘造和编纂聚糖和糖肽结构。只需单击按钮
，即可增长或删除单糖、肽链或HSO 3、Etn等取代基
，并可批改分支点和异头衔接。在每一步
，绘造结构的碎片化使用户可能比力尝试数据和理论数据
，使用户可能查看他的批改是否使理论聚糖更靠近尝试数据。此职能很大地有助于解析糖链结构
，尤其是当指标糖链的数据尚不成用时。

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质谱诠释

软件通过凸起显示与理论碎片相匹配的尝试m/z致反援识喙释质谱
，并天生描述陆续单糖单元损失的注解光谱。这有助于钻研人员成立分支模式并验证聚糖的根基单元。每个峰都能够使用cartoons或Domon Costello定名法来暗示。若是碎片是多电荷的
，也会显示碎片的电荷状态。

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SimGlycan可能天生带注解的质谱
，以适合页面或基于感兴致的区域。它还会将其导出以与您的同事分享发现。

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单一的界面使您可能放大特定的画图地位
，指定m/z领域以显示特定的画图部门
，还能够将画图作为图像文件导出到MS PowerPoint
，以便颁布了局并与同事共享信息。

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Cartoons是使用尺度的单糖职能糖组学（CFG）定名法构建的（在CFG注解不成用的情况下使用自界说符号）。您能够同时绘造全数类型的糖苷片段
，同时以符号暗示体式注解光谱。

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*此职能在SimGlycan企业版中可用。

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SimGlycan企业版

SimGlycan企业版现已推出。若是您使用的是个人定造数据库或专罕见据
，企业版是您在寻找的解决新型聚糖的安全工具。您能够从数据库中增长或删除聚糖结构
，或创建您自己的子数据库以缩幼搜索领域
，直接从您的工作站方便。多个聚糖的结构信息能够存储在一个文件中并增长到数据库中
，从而节俭功夫。

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系统要求：

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对于Windows	必要	推荐
CPU	Intel Core i3	i5 / i7
内存	12GB	12GB或更高
硬盘空间	200GB	500GB或更高
屏幕分辨率	1024×786	>1024×768

Windows 支持的平台：Vista/Windows 7/Windows 8/Windows 10/Windows 11

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【英文介绍】

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SimGlycan is an innovative MSn data analysis software. It predicts the glycan structure, scores it & generates a list of probable glycans that closely match the given MS profile.

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SimGlycan predicts structure of glycans from the MS/MS and multi-stage mass spectrometry (MSn) data. Furthermore, comprehensive support for resolving glycopeptides using LC-MS/MS glycopeptide data facilitates glycosylation studies. SimGlycan accepts experimental MS/MS data, matches them with its own database and finally generate a list of ranked candidate structures. Rank of each candidate indicates the proximity between the candidate structure and the experimental glycan. The rank is calculated based on a robust scoring mechanism that considers structure specific diagnostic ions observed in the experimental MS/MS spectra as well as the intensity of those observed peaks.

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SimGlycan also supports multistage mass spectrometry (MSn) data analysis for isomers differentiation.

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SimGlycan Features

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Robust Glycan and Glycopeptide Database

SimGlycan database is a large relational database containing 9,964 glycans, 22,814 glycoproteins*, 6,826 glycans with known biological sources and 5,874 glycans with known classes. The database is continuously updated as information on additional glycans is published.

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Support for MALDI MS/MS and LC-MS/MS Workflows

With comprehensive support for different adducts such as H, Li, Na, Mg²⁺, K, HCOO^- and NH4⁺ and adduct combinations such as Na + H, Li + H etc. along with scalable MS/MS fragmentation patterns based on different instrument settings, SimGlycan can analyze MALDI – and LC- MS/MS data for glycopeptides and released glycans that are underivatized, permethylated and reducing end modified with no compromise on the results of the analysis.

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Data Input File Formats

SimGlycan allows direct automatic loading of input data files generated by mass spectrometers from SCIEX (TripleTOF^TM?5600 System, TOF/TOF 5800, 4800 Plus MALDI TOF/TOF^TM?Analyzer, 4000 QTRAP^??and QSTAR^??Elite Systems),?Agilent Technologies (Agilent 6200 Series TOF LC/MS and Agilent 6500 Series Q-TOF LC/MS systems), Bruker Corporation (ultrafleXtreme^TM?MALDI TOF/TOF, ultraflex^TM?MALDI TOF/TOF, autoflex^TM?TOF and TOF/TOF, maXis^TM?UHR-TOF, micrOTOF^TM, micrOTOF-Q^TM,?solariX^TM?Qq-FTMS, and amaZon^TM?ion trap series), Thermo Scientific^TM?(LTQ FT Ultra, LTQ Velos, LTQ XL, LTQ Orbitrap Discovery, LTQ Orbitrap Velos, LTQ Orbitrap XL, MALDI LTQ Orbitrap, Orbitrap Elite, Q Exactive and Thermo Scientific^TM?Orbitrap^TM?Fusion^TM?Tribrid mass spectrometer and Thermo Scientific^TM?Q Exactive^TM?hybrid quadrupole-Orbitrap mass spectrometer) and Waters Corporation (SYNAPT G2 HDMS, SYNAPT G2 MS, Xevo G2 QTof, Xevo QTof MS, Xevo TQ MS and Xevo TQ-S platforms).?Other mass spectrometers are supported using mzData and mzXML formats. Besides, manual entry, TXT and XLS file formats are also accepted by SimGlycan. No matter what make your instrument is, the output can be converted to these formats using third party tools.

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TMT Quantitation*

SimGlycan now supports the Mass Spectrometry-based quantitative glycomics workflow using aminoxyTandem Mass Tags (TMT). aminoxyTMT6 reagents enable efficient relative quantitation of glycans, improving labeled-glycan ionization efficiency thereby increasing analytical throughput. Glycans are quantified by measuring reporter ion peak intensities from the corresponding MS/MS spectra. User can specify a tolerance as small as 0.0001. Following extraction of peak intensities, the aminoxyTMT reporter ion signals are adjusted to account for isotopic impurities in each TMT variant. Users can select the sum/average/median reporter ion intensities across all glycan-spectral matches as the quantity of a glycan. Various charts such as bar chart, dot-plot etc. are plotted to facilitate visualization of the quantity of each glycan in different TMT channels and across biological samples.

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Multi Stage Mass Spectrometry (MSⁿ) Data Analysis

SimGlycan includes comprehensive support to perform Multi Stage/Sequential Mass Spectrometry (MSn) data analysis. MSn, a technique wherein the product ions from MS/MS (or previous stage MS) are subjected to refragmentation, is one of the most effective techniques in resolving heterogeneity, branching pattern and isobaric oligosaccharide structures. It allows discrimination of glycans having similar characteristic fragment patterns which are otherwise indistinguishable in MS/MS spectra. As the level of MS (n) increases, generated fragments become structure specific which assists in resolving isobaric oligosaccharides or detailed characterization of selected structures.

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Glycopeptide Qualitative Analysis

Many of the mass spectrometers allows the capture of MS/MS data as compounds elute from in line separation systems. Such LC-MS/MS approaches generate extremely large datasets, requiring sophisticated informatics tool to assign glycopeptide structures over a complete chromatographic separation. This would enhance analytic productivity and provide greater depth of analysis of mass spectrometric glycoproteomic data. SimGlycan now includes comprehensive support for identifying glycopeptides of complex mixtures separated by LC and detected by MS/MS in batch processing mode. The Protein ID, Protein sequence or Peptide sequences identified by using a third party tool will be used by SimGlycan as initial input. SimGlycan identifies probable glycan-peptide combinations and ranks them on the basis of observed peaks in the MS/MS data corresponding to diagnostic ions from theoretical glycopeptide. High resolution accurate mass data with an error tolerance between 1 to 20 parts per million (ppm) and 0.1 to 2000 milli Dalton (mDa) can be analyzed.

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Project Management

SimGlycan provides a comprehensive project management, associating results with input profile and search parameters. You can open any number of projects. Users can import 20,000 spectra in a project. The projects can be classified on the basis of the source, the lab or the research goal. This is important, especially when conducting large-scale glycan analysis projects. You can access glycan related information at the click of a button. Unlike web based applications, SimGlycan saves it on your own computer.

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The available information consists of:

Glycan Structure: Displays the molecular structure (carbohydrate sequence) of the glycan.

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Glycan Fragments: Displays the nomenclature, structure, m/z value and mass using Domon Costello rules of fragmentation. A serial number is assigned to each fragment.

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i) Glycosidic Fragments: Single glycosidic and glycosidic/glycosidic fragments are displayed.

ii) Cross Ring Fragments: Single cross ring and glycosidic/cross ring fragments are displayed.

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Glycopeptide Structure: Displays the peptide sequence and the sites of protein glycosylation along with the glycan structures.

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Annotate Mass Spectra and Generate Reports: SimGlycan can annotate mass spectra using cartoons or Domon-Costello nomenclature. The charge state of the fragment is also depicted.?

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Export Annotated Peaklist Table: Users can export annotated peaklist for all search results from 20,000 MS/MS spectra to single project report. Users can include either only the matched fragments or both matched and unmatched fragments in the annotated peaklist table.

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Draw Glycans

SimGlycan enables users to draw and edit glycan and glycopeptide structures. A monosaccharide, peptide chain or a substituent such as HSO3, Etn can be added or deleted and branching points and anomeric linkages can be modified at the click of a button. At each step, the fragmentation of the drawn structure enables a user to compare the experimental and theoretical data, enabling the user to see whether his modification brings the theoretical glycan closer to the experimental data. This feature greatly assists in resolving glycan structures, especially when data for glycans of interest is not yet available.

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Mass Spectra Interpretation

Software helps in interpreting a mass spectra by highlighting the experimental m/z values that match those of theoretical fragments and generates an annotated spectrum depicting the loss of consecutive monosaccharide units. This helps researcher to establish the branching pattern and verifying the basic unit of glycan. Each peak can be represented using cartoons or Domon Costello nomenclature. Charge states of fragments are also displayed if the fragments are multiply charged.

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SimGlycan enables generating an annotated mass spectra either to fit on a page or based on the area of interest. It also exports it for sharing the findings with your colleagues.

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The simple interface enables you to zoom into specific plot locations, specify m/z range to display specific plot sections and also to export plots as image files to MS PowerPoint, for publishing results and sharing information with colleagues.

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Cartoons are constructed using standard Consortium for Functional Glycomics (CFG) nomenclature for monosaccharides (custom symbols are used where CFG annotations are not available). You can simultaneously plot all types of glycosidic fragments while annotating the spectra in symbolic representation format.

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*This feature is available in the SimGlycan Enterprise Edition.