SimLipid是一种高通量脂质鉴定和定量软件
。它能够处置来自数百个LC-MS和MS/MS尝试运行的原始数据，用于LC峰检测、峰拾取、分子特点发现和保留功夫校准
。原始数据或峰列表（蕴含已处置的LC-MS数据的数据集）能够进行MS和MS/MS数据库搜索以进行结构解析，即便在批处置的模式下也是如此
。专有的评分机造可分辨每次MS/MS扫描的等压候选结构
。

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SimLipid特点：

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强的脂质结构数据库

SimLipld数据库是一个可扩大的关系数据库，蕴含9种脂质类别，即Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Polyketides, Prenols, Saccharolipids, Sphingolipids和Sterols
。该数据库存储了40,312种脂质和15,08,293种结构特定的MS/MS特点离子
。除此之表，该数据库还存储了5227个前体扫描和肿咴损失扫描三沉四极杆质谱法的转换，别离对应于glycerophospholipids, glycerolipids, 和sphingolipids的1,179、393和221个特有的脂肪
；
。

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用户能够创建自界说数据库*来存储精选脂质以及保留功夫和漂移功夫
。创建自界说数据库后，能够使用保留功夫和漂移功夫容差作为初始搜索谓词来执行用于脂质结构鉴定的MS和MS/MS数据库搜索
。此职能便于用户创建LC-MS或Ion Mobility-MS模板
；从而使他们可能利用LC-MS和IMS技术进行钻研
。

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其他数据库链接蕴含Kyoto Encyclopedia of Genes and Genomes (KEGG)、人类代谢组数据库（HMDB）、生物感兴致的化学实体（CEBI）、PubChem物质数据库、LIPIDBANK和LIPIDAT
。数据库不休更新
。

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图1：SimLipid数据库的示意图

请把稳：* 该职能在法式的企业版中可用

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项目治理和数据可视化

SimLipid提供项目治理，将脂质分析了局与输入配置文件和搜索参数有关联
。您能够创建肆意数量的项目
。您还能够批量导入数百个原始数据文件
。来自尝试性MS运行的原始数据：总离子色谱图、已鉴定的脂质、MS或MS/MS光谱，以及它们相应的数据库信息都显示在一个工作台中
。

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图 2：SimLipid软件的典型图形用户界面：一个单一的工作台，使您可能可视化LC-MS、ESI-MS、MALDI-MS尝试扫描的原始数据、执行数据库搜索后的了局以及已识此皮毛应信息脂质
。

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SimLipid提供以下附加职能：

1. 对应于指定保留功夫窗口和/或前体m/z领域的均匀MS和MS/MS扫描
。

2. 凭据支持的文件体式的前体离子 m/z、电荷状态、保留功夫、强度和漂移功夫对加载的数据集进行排序
。

3.?鉴别脂质的扫描/光谱用色彩编码，旁边显示已鉴别脂质的名称/缩写/分子式
。

4.?查看指标m/z的提取离子色谱图
。

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高通量MS脂质搜索

SimLipid通过针对SimLipid数据库中Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Polyketides, Prenols, Saccharolipids, Sphingolipids和Sterols的已知脂质结构搜索脂质前体离子，从多个MS峰列表数据中实现高通量脂质分析
。用户能够对误差容限幼于或蹬宗50ppm或2000milliDalton(mDa)的高分辨率数据执行MS脂质搜索
。SimLipid支持正离子模式下的[M+H]、[M+NH4]、[M+Na]、[M+C5H12N]、[M+Li]离子和[M-H]、[M+AcO]、[M +Cl]、[M-CH3]、[M+OAcO]和[M+HCOO]在负离子模式下
。用户还能够从MS脂质谱触发产品离子数据分析
Ｄ芄皇褂煤蜓≈手掷嗟牟防胱邮堇囱橹ざ杂τ谇疤錷/z的概括脂质
。用户能够从预约义的m/z值和相应离子种类列表中导入已蕴含在高通量搜索中的前体m/z值的离子种类
。这有助于在可变离子模式和分歧的加合物中进行MS/MS搜索
。有多个选项可用于凭据保留功夫、前体m/z和强度选择要蕴含在批次运行中的MS和MS/MS配置文件
。

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使用MS/MS和MS^E数据进行高通量脂质结构解析

SimLipid支持使用来自Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Polyketides, Prenols, Saccharolipids, Sphingolipids和Sterols的MS/MS和MS^E光谱的前体和产品离子m/z数据对脂质进行结构解析
。已识此外脂质凭据一种排序算法进行评分，该算法批注理论脂质与尝试数据的相对靠近水平
Ｄ芄环治鲇涤0.001-50ppm和0.1到2,000milliDalton?(mDa) 之间误差容限的高分辨率正确质量数据
。

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多沉前体离子扫描（PIS）和肿咴损失扫描（NLS）三沉四极杆质谱法基于脂质分析和定量的步骤

来自多个PIS/NLS的数据能够使用原生文件体式或尺度体式导入SimLipid软件
。用户能够通过凭据生物/技术复造对数据文件进行分类，在SimLipid中对尝试设计进行建模

；趖arget fatty acyls/head group fragment ions或其肿咴损失的脂质鉴定以批处置模式进行
。

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SimLipid可能量化对应于MS光谱上观察到的峰的脂质
。量化是通过凭据所选内标的观察强度对强度值进行归一化来实现的
。该法式有助于将内源性/表源性脂质规范为内部尺度
。为了可能从低分辨率光谱中定量脂质，SimLipid校对了同位素沉叠的强度
。这有助于正确量化生物混合物中的脂质
。量化数据以及其他信息（例如峰m/z、分子式、分歧样品中的校对、未校对和归一化强度）能够导出为与电子表格兼容的.csv和.xls体式
。

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LC MS和LC-MS/MS高通量数据处置

SimLipid处置LC-MS和MS/MS数据以进行峰检测、滑润、色谱解卷积、峰去同位素和分子特点查找
。该法式将检测到的峰值m/z值与相应的MS/MS光谱对齐，从而可能使用来自MS和MS/MS数据的前体和产品离子数据鉴别脂质结构
。

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图 3：使用MPIS/NLS QqQ MS步骤数据的SimLipid软件脂质分析和定量工作流程示意图

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SimLipid还有助于对从分歧生物样品中鉴定的脂质进行比力和定量分析
。使用RANSAC技术，凭据保留功夫、m/z值、观察到的强度和电荷状态的一致性，对从分歧峰列表中检测到的峰进行对齐
。至多能够对齐200个峰值列表，了局能够导出为HTML、CSV和MS Excel体式
。

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SimLipid软件提供LC-MS峰列表的单一工作台视图
；在尝试性LC-MS运行中确定的脂质列表
；在特定保留功夫鉴定的脂质结构
；数据库中已鉴别脂质的有关信息
；和总离子色谱图，在已鉴别脂质的保留功夫处带有垂直条
。

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图 4：SimLipid软件的典型图形用户界面：LC-MS峰列表的单一工作台视图、在保留功夫点识此外脂质列表、在选定保留功夫点的脂质结构以及带有垂直线的样品色谱图暗示显示的脂质结构的保留功夫点
。

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鉴定脂质的质谱注解

SimLipid使用脂质注解质谱，并为MS、MS/MS以及MS^E鉴别碎片离子
。这有助于通过凸起显示与产品数据库中的理论脂质结构相匹配的尝试m/z致反诠释质谱
。

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注解的质谱能够调整/沉新调整大幼以适合页面或基于感兴致的区域
。用户能够使用鼠标光标或通过指定m/z领域来放大/缩幼到特定的画图地位
。此表，用户能够将到注解的光谱导出为可蕴含MS PowerPoint中的图像（PNG和JPEG体式），从而推进钻研幼组之间的信息共享
。

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图 5：SimLipid软件的典型图形用户界面：已鉴别脂质TG(56:3) 的注解MS/MS光谱
。光谱中观察到的两个强峰别离对应于结构的特有脂肪酸链的特点离子18:1和20:1
。

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天生汇报

分析质谱数据后，用户能够从50,000个MS和MS/MS配置文件中天生HTML、csv和MS Excel体式的指标导向汇报
。用户能够将SimLipid设置为在执行分析后自动启动汇报
Ｄ芄惶焐幕惚ㄓ糜冢

• Profiled MS Spectra：可以为生物标志物钻研天生分歧生物样品中存在的异质脂质丰度的比力分析
  。

• MS和MS/MS数据：汇报显示与在MS搜索中通常遇到的前体m/z值相对应的误报，以及在子离子数据分析期间识此外脂质的概率分数
  。这样的汇报是通过结合MS脂质谱及其互补的MS/MS或MS^E脂质谱天生的
  。

• 多个数据集：一份汇报，其中蕴含对从分歧离子模式和加合物中获得的分歧MS或MS/MS光谱分析的脂质进行比力分析
  。

• Retention Time：该汇报使用户可能通过凭据保留功夫对齐MS/MS曲线来钻研在可变离子模式下采集的MS/MS光谱中观察到的碎片离子
  。这提供了一个工作流程解决规划，用于鉴别属于GP、SP、GL等类此外未知脂质的结构，其中对应于脂肪酸链的诊断离子在阴性光谱中被观察到，而对应于head group的诊断离子在阳性离子光谱中被观察到
  。

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图 6：使用导出到MS excel文件的MS/MS数据识此外脂质
。

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数据库搜索

您还能够通过脂质缩写/通用名称、质量、化学成分或脂质ID搜索感兴致的脂质结构
。

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系统要求：

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对于Windows	必要	推荐
CPU	Core i3	更高
内存	8GB	16GB
硬盘空间	25GB可用硬盘	更高
屏幕分辨率	1024×786	>1024×768

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

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【英文介绍】

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SimLipid is a high throughput lipid identification and quantification software. It can process raw data from hundreds of LC-MS and MS/MS experimental runs for LC-peak detection, peak-picking, molecular feature finding and retention time alignment. The raw data or peaklists – dataset containing processed LC-MS data – can be subjected to MS and MS/MS database search for structural elucidation, even in batch mode. A proprietary scoring mechanism distinguishes isobaric candidate structures for each MS/MS scan.

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SimLipid Features

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Robust Lipid Structure Database

SimLipid database is a scalable relational database containing 9 lipid categories namely, Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Polyketides, Prenols, Saccharolipids, Sphingolipids and Sterols. The database stores 40,312 lipids, and 1,508,293 structure-specific in-silico MS/MS characteristic ions. Besides this, the database also stores 5227 transitions of precursor ion scan and neutral loss scan triple quadrupole mass spectrometry methods corresponding to 1,179, 393, and 221 unique fatty acyls from glycerophospholipids, glycerolipids, and sphingolipids respectively.

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User can create custom databases* to store curated lipids along with retention times, and drift time. Once a custom database is created, MS, and MS/MS database search for structural identification of lipids can be performed using retention time, and drift time tolerances as initial search predicates. This functionality facilitates users to create LC-MS or LC-Ion Mobility-MS templates; thereby enabling them to exploit the state of the art LC-MS and IMS technologies for their research.

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Other database links include Kyoto Encyclopedia of Genes and Genomes (KEGG), Human Metabolome Database (HMDB), Chemical Entities of Biological Interest (CEBI), PubChem Substance database, LIPIDBANK, and LIPIDAT. The database is continuously being updated.

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Project Management and Data Visualization

SimLipid provides a comprehensive project management, associating lipid analysis results with input profiles and search parameters. You can create any number of projects. You can also import hundreds of raw data files in batch mode. The complete raw data from an experimental MS run: total ion chromatogram, identified lipids, MS or MS/MS spectrum, and their corresponding database information are displayed in a single workbench.

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SimLipid provide following additional features:

1.?Average MS and MS/MS scans corresponding to a specified retention time window and/or a precursor m/z range.

2.?Sort the loaded datasets on the basis of Precursor Ion m/z, Charge State, Retention Time, Intensity and Drift Time for the file formats supported.

3.?The scans/spectrum for which lipids are identified are color coded with the?name/abbreviation/molecular formula of the identified lipid displayed along side.

4.?View extracted ion chromatogram of a target m/z.

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High Throughput MS Lipid Search

SimLipid enables high throughput lipid profiling from multiple MS peak list data by searching lipid precursor ion against the known lipid structures available in the SimLipid database for Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Polyketides, Prenols, Saccharolipids, Sphingolipids and Sterols. Users can perform MS Lipid Search for high resolution data with an error tolerance less than or equal to 50 ppm or 2000 milliDalton (mDa). SimLipid supports [M+H], [M+NH4], [M+Na], [M+C5H12N], [M+Li] ions in the positive ion mode and [M-H], [M+AcO], [M+Cl], [M-CH3], [M+OAcO] and [M+HCOO] in the negative ion mode. Users can also trigger product ion data analysis from an MS lipid profile. The profiled lipids corresponding to a precursor m/z can be verified using product ion data for candidate lipid species.

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Users can import the ion species for precursor m/z values that have been included in a high throughput search, from a predefined list of m/z values and corresponding ion species. This facilitates MS/MS search in variable ion modes and for different adducts. Multiple options are available for selecting MS and MS/MS profiles to be included in a batch run based on retention time, precursor m/z and intensity.

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High Throughput Lipid Structural Elucidation using MS/MS and MS^E Data

SimLipid supports structural elucidation of lipids using precursor and product ion m/z data from MS/MS and MSE spectra of Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Prenols, Saccharolipids, Sphingolipids and Sterols. Identified lipids are scored based on an innovative ranking algorithm that indicates the relative degree of proximity of theoretical lipids with the experimental data. High resolution accurate mass data with error tolerance between 0.001-50 parts per million (ppm) and 0.1 to 2,000 milliDaltons (mDa) can be analyzed.

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Multiplexed Precursor Ion Scan (PIS) and Neutral Loss Scan (NLS) Triple Quadrupole Mass Spectrometry Methods Based Lipid Profiling and Quantitation

Data from multiple PIS/NLS can be imported into SimLipid software using either native file formats or standard formats. Users can model experimental designs in SimLipid by classifying data files according to biological/technical replicates. Identification of lipids based on target fatty acyls/head group fragment ions or their neutral losses is processed in batch mode.

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SimLipid enables quantifying lipids corresponding to the peaks observed on the MS spectra. Quantification is done by normalizing the intensity values based on the observed intensity of a chosen internal standard. The program facilitates specification of endogenous/exogenous lipids as internal standards. To enable quantification of lipids from low resolution spectra, SimLipid corrects the intensities for isotopic overlaps. This facilitates accurate quantification of lipids from biological mixtures. The quantified data along with other information such as peak m/z, molecular formula, corrected, uncorrected and normalized intensities in different samples can be exported to a spreadsheet compatible .csv and .xls formats.

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LC MS and LC- MS/ MS High Throughput Data Processing

SimLipid processes the LC-MS and MS/MS data for peak detection, smoothing, chromatogram deconvolution, peak deisotoping, and molecular feature finding. The program aligns detected peak m/z values to corresponding MS/MS spectra enabling seamless identification of lipid structures using precursors and product ions data from MS and MS/MS data.

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SimLipid also facilitates comparative and quantitative analysis of lipids identified from different biological samples. The peaks detected from different peaklists are aligned based on the agreement of retention time, m/z value, observed intensity and charge state using the RANSAC techniques. Up to 200 peaklists can be aligned and the results can be exported to HTML, CSV and MS Excel formats.

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SimLipid software provides a single workbench view of the LC-MS peaklist; list of identified lipids in the experimental LC-MS run; Structure of the identified lipid at a particular retention time; associated information of the identified lipid in the database; and total ion chromatogram with a vertical bar at the retention time of the identified lipid.

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Mass Spectra Annotation with Identified Lipids

SimLipid annotates mass spectra with the lipids, and fragment ions identified for MS, MS/MS as well as MSE data. This helps in interpreting mass spectra by highlighting the experimental m/z values that match those of theoretical lipid structures from the product database.

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The annotated mass spectra can be adjudged/re-sized either to fit on a page or based on the area of interest. A user can zoom in/out into a specific plot location using the mouse cursor or by specifying the m/z range. Further, users can export the annotated spectra as images (in PNG and JPEG formats) that can be included in MS PowerPoint, facilitating information sharing amongst research groups.

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Generate Report

After analyzing mass spectrometric data, users can generate goal-oriented reports in HTML, csv and MS Excel formats from 50,000 MS and MS/MS profiles. Users can set SimLipid to launch the report automatically after performing the analysis. The reports that can be generated are for:

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• Profiled MS Spectra: A comparative analysis of the abundance of profiled lipids present in different biological samples can be generated for biomarker studies.

• MS and MS/MS Data: The report displays the false positives corresponding to a precursor m/z value that are usually encountered in an MS search and the probabilistic score of lipids identified during a product ion data analysis. Such a report is generated by combining an MS lipid profile and its complementary MS/MS or MSE lipid profiles.

• Multiple Data Sets: A report containing a comparative analysis of the lipids profiled from different MS or MS/MS spectra acquired in different ion modes and adducts.

• Retention Time: This report enables users to investigate the fragment ions observed in MS/MS spectra acquired in variable ion modes by aligning the MS/MS profiles based on retention time. This provides a complete work flow solution to identify the structure of unknown lipids that belong to categories such as GP, SP, GL etc. where diagnostic ions corresponding to fatty acid chains are observed in negative spectra while those corresponding to head group are observed in positive ion spectra.

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Database Search

You can also search for a lipid structure of interest by lipid abbreviation/common name, mass, chemical composition or lipid ID.