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A comprehensive high throughput informatics tool for characterizing lipids using precursors and product ions data from MS and MS/MS data
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Robust Lipid Structure Database

SimLipid® database is a large relational database containing 9 lipid categories viz. Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Polyketides, Prenols, Saccharolipids, Sphingolipids and Sterols having 36,299 lipid species. 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. Theoretical fragments of lipids from the categories viz. Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Prenols, Saccharolipids, Sphingolipids and Sterols. are available along with their theoretical masses and corresponding fragment structures.

Project Management

SimLipid® provides a comprehensive project management, associating lipid analysis results with input profiles and search parameters. You can create any number of projects. SimLipid® can import large datasets of up to 500,000 scans in a project, enabling analysis of a complete chromatogram. SimLipid® can import/average filtered MS and MS/MS scans corresponding to a specified retention time window and/or a precursor m/z range. The projects can be classified on the basis of a source, lab or research goal. SimLipid® enables sorting of the peak list data on the basis of Precursor Ion m/z, Charge State, Retention Time, Intensity and Drift Time for the file formats supported. For mzXML and mzData files, sorting can, in addition, be done on Scan No, Parent Scan No and MS Level. This facilitates convenient investigation of data scattered across different scans or profiles by allowing triggering of MS/MS analysis from a peak of interest. The scans/spectrum for which lipids are identified are color coded with the name/abbreviation/molecular formula of the identified lipid displayed along side.

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. SimLipid® supports structural identification with probabilistic score using MS/MS data for 29,484 lipids including Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Prenols, Saccharolipids, Sphingolipids and Sterols.

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.

MS lipid search results include:

  1. Experimental m/z: m/z value obtained from experimental data.

  2. Theoretical m/z: m/z value obtained from SimLipid® database.

  3. Delta Mass: The difference between experimental m/z value and theoretical m/z value of a matched lipid from SimLipid® database.

  4. Intensity: Intensity value corresponding to an m/z value.

  5. Lipid Category: User can select Lipid Categories, Lipid Class and Sub Class to filter the search results.

  6. Abbreviations: It contains lipid structure information in the following format: 'Head group (sn1/sn2)'. For Example PC (16:0/12:0), PS (16:0/18:1(9Z)). Z indicates the number of double bonds at the 9th position.

  7. Ion Type: Ions supported in positive and negative ion mode.

  8. Lipid Structure: Displays the molecular structure of the lipid. Along with the structure, the abbreviation is also displayed.

  9. Lipid Information: When a user selects a particular lipid, additional lipid information such as the Lipid ID, Lipid Abbreviation, Systematic Name, Lipid Category, Main Class, Sub Class, Lipid Mass, Lipid Composition and Other Database Links for every probable lipid structure is displayed.

High Throughput Lipid Structural Elucidation using MS/MS and MSE Data

SimLipid® supports structural elucidation of lipids using MS/MS and MSE data for Carnitines, Fatty acyls, Glycerolipids, Glycerophospholipids, Prenols, Saccharolipids, Sphingolipids and Sterols for 10,000 scans in batch mode. For CEF files, 5000 spectra can be analyzed in batch mode. Identified lipids are sorted 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 1-50 parts per million (ppm) and 0.1 to 2000 milliDaltons (mDa) can be analyzed. Two dimensional structures of the lipids identified are also displayed. Results for HTP search can be fetched by Search ID and exported in Excel/CSV/HTML formats.

High Throughput Lipid Profiling and Quantitation

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.

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

SimLipid® supports LC-MS and LC-MS/ MS high throughput data processing methods such as peak detection, smoothing, chromatogram deconvolution, peak alignment, peak deisotoping and adduct identification corresponding to the peaks detected. SimLipid® can read LC-MS raw data from *baf and *yep (Bruker Corporation), *.wiff (SCIEX), *.raw (Thermo Scientific™), mzData and mzXML data files and generate peaklists for 200 raw data files (LC-MS runs) in a single run. SimLipid® 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.

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 and Gale-Shapely (SMP) techniques. Up to 200 peaklists can be aligned and the results can be exported to HTML, CSV and MS Excel formats.

Mass Spectra Annotation with Identified Lipids

SimLipid® can annotate mass spectra with the lipids 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. For better lipid characterization, each matched peak can be annotated with either the lipid fragment name or its corresponding lipid chemical formula.

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.

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:

  • 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 an 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.

Database Search

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

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