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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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SimLipid®

Upgrades

SimLipid® 4.20 Released

Enhanced speed of loading raw data files and peaklists into project.

The number of MS and MS/MS spectra that can be searched in a batch increased to 5000 for CEF files workflow.

SimLipid® 4.10 Released

SimLipid® now has increased throughput, users can batch search up to 2000 MS or MS/MS spectra (or 2000 compounds in LC-MS workflow).

In-silico fragments of lipids, such as Charge Remote Fragment (CRF) ions in Glycerolipids (TAG and DAG) and Glycerophospholipids, have been updated in the product database in order to identify fragmentation patterns observed in MALDI TOF/TOF spectra.

SimLipid's proprietary ranking mechanism just got better. Fragment pattern matching is much more accurate than ever before.

Support for Carnitine lipids has been added.

Report generation functionality has been enhanced. Users can now export results of up to 50,000 spectra.

For Agilent users, writing to CEF File has now been increased to 100 from the current 25.

Project management is now more user friendly. The scans/spectrum for which lipids are identified are color coded with the name/abbreviation/molecular formula of the identified lipid displayed along side.

SimLipid® 4.00 Released

SimLipid® now 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 *.raw (Thermo Scientific™), mzData and mzXML data files and generate peaklists for 15 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 LOESS techniques. Up to 10 peaklists can be aligned and the results can be exported to HTML, CSV and MS Excel formats.

SimLipid® 3.50 Released

SimLipid® now supports structural elucidation of Fatty Acyls and Sterols using MS/MS data. The in silico fragments of these lipids have been updated in the product database to incorporate fragmentation patterns to bring the MS/ MS database strength to 29,484 lipids. This also includes Glycerophospholipids, Glycerolipids, Prenols, Saccharolipids and Sphingolipids.

SimLipid® structure database now includes 36,224 lipid species containing 8 lipid categories viz. Glycerophospholipids, Sphingolipids, Fatty Acyls, Glycerolipids, Sterols, Prenols, Saccharolipids and Polyketides.

SimLipid® 3.40 Released

Users can now run a high throughput search of 1000 scans, up from 300 scans in the previous versions. After the analysis, the results can be exported to HTML, CSV and MS Excel file formats.

Options are now made available for selecting MS and MS/MS profiles to be included in a batch run based on retention time, precursor m/z and intensity.

Users can now 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.

Users can now apply multiple filter options to peak lists while importing them into a project.

SimLipid® 3.30 Released

The new version offers compatibility with 64-bit Windows OS affording significant enhancements in processing large data.

The processing speed of the SimLipid® database server has been improved significantly to reduce the time required to complete a high throughput search.

SimLipid® can read MS, MS/MS data along with ion species information from Agilent's Compound Exchange File (*.cef) and write results to the file for further downstream processing in MassHunter and Mass Profiler Professional (MPP).

After performing data analysis, users can export results from 1000* MS and MS/ MS profiles, from the previous 300, to HTML, CSV and MS Excel file formats.

*For Agilent's CEF (*.cef).

SimLipid® 3.20 Released

SimLipid® can now import large datasets of up to 20,000 scans, enabling data analysis of complete chromatographic runs.

SimLipid® now provides a comprehensive solution to validate unknown lipid structures. Structures are identified by aligning MS/MS profiles (of the lipids identified) from different ion modes based on retention time.

SimLipid® can import filtered MS and MS/MS scans by loading data from a specified retention time window and/or from a specified precursor m/z range.

SimLipid® fully supports Waters' DDA and direct infusion work flows. Users can import Waters' direct infusion data in MS Excel file format along with Precursor Ion Scan (PIS) and Neutral Loss Scan (NLS) information.

In addition to importing peaklists in MS Excel (.xls), SimLipid® can now average the scans as well.

SimLipid® 3.10 Released

SimLipid® now enables comparative analysis of profiled lipids from multiple biological samples. The analysis results can be exported in HTML/ Excel/ CSV formats.

The averaged spectrum can now be loaded by averaging multiple scans for the specified retention time range.

To facilitate data analysis from Thermo Scientific™ instruments, SimLipid® now imports "label data" acquired by the FTMS analyzer.

SimLipid® 3.00 Released

SimLipid® now enables relative quantification of profiled lipids by normalizing the intensity values based on internal standard. The program facilitates specification of endogenous/exogenous lipids as internal standards. The program corrects the intensities for isotopic overlapping of peaks from low resolution spectra and facilitate accurate quantification of lipids from biological mixtures. The quantified data can be then exported to a spreadsheet compatible .csv file and .xls formats.

High Throughput Lipid Profiling mode now enables users to analyze up to 300 scans in a single batch search.

Annotation of acylium ions for GP and GL lipids is now supported in SimLipid®.

SimLipid® 2.40 Released

Seamless integration withThermo Scientific™ and AB SCIEX mass spectrometers will now enable SimLipid® to load native files, without the use of third party conversion tools. SimLipid® is compatible with the following Thermo Scientific™ mass spectrometers: LTQ FT Ultra, LTQ Velos Dual-Pressure Ion Trap, LTQ XL* Linear Ion Trap, LTQ Orbitrap Discovery, LTQ Orbitrap Velos, LTQ Orbitrap XL, LTQ Orbitrap XL ETD, MALDI LTQ Orbitrap.

SimLipid® is compatible with the following AB SCIEX mass spectrometers:
TripleTOF™ 5600 System, TOF/TOF 5800, 4800 Plus MALDI TOF/TOF™ Analyzer, 4000 QTRAP® and QSTAR® Elite Systems

The High Throughput search report is re-organized to present the results that are more meaningful for analyzing data..

SimLipid® 2.30 Released

SimLipid® now supports structural elucidation of sphingolipids using MS/MS data.

In silico fragments for lipids have been updated in the product database to incorporate fragmentation patterns observed on MALDI TOF/TOF spectra.

SimLipid® database now includes 29,892 lipid species along with additional biological information such as lipid abbreviation, systematic name, mass, composition and links to other databases.

SimLipid's proprietary ranking mechanism just got better. The streamlining of branching and composition parameters now results in a more accurate analysis.

SimLipid® automatically assigns sphingomyelins and glycerophosphocholines during Isotopic Peak Correction.

SimLipid® can now import native file formats (*.fid, *.baf and *.yep) generated by Bruker Corporation mass spectrometers.

SimLipid® 2.20 Released

SimLipid® can now generate a comprehensive report of MS and complementary MS/MS or MSE data in Excel/CSV/HTML formats.

SimLipid® also generates a comparative report to validate lipids identified in different ion mode/adducts. Lipid species identified from MS or MS/MS data in variable ion modes and adducts are aligned and exported in Excel/CSV/HTML formats.

SimLipid® 2.10 Released

SimLipid® can now perform high throughput MS and MS/MS data analysis. Users can load up to 4000 scans containing MS and MS/MS or MSE in batch mode and analyze 200 scans in a batch. This functionality facilitates high-throughput lipid profiling using mass spectrometry for lipid identification and quantification studies.

Uses can now trigger product ion data analysis from an MS lipid profile by simply selecting a peak of interest and triggering product ions data analysis using MS/MS or MSE data. This facilitates convenient investigation of MS and MS/MS data.

SimLipid® now support [M+K] ions to perform precursor and product ion data analysis.

SimLipid® 2.00 Released

SimLipid® now supports sorting of the peak lists in a project on the basis of Precursor Ion m/z, Charge State, Retention Time, Intensity, Drift Time, Scan No, Parent Scan and MS Level for Text, Excel, mzXML, mzData and Waters MSE files. This facilitates convenient investigation of data scattered across different scans or profiles by allowing triggering of MS/MS analysis from a peak of interest.

SimLipid® 1.20 released

SimLipid® now supports the following:
Search Templates- Create a template using the search parameters used frequently to analyze MS and MS/ MS data. This will enable you to save the time and the effort of entering the same parameters for repetitious analysis.

Formate Adduct- Analyze your data using the formate adduct (HCOO), used most commonly during electrospray.

Retention Time and Drift Time- Export Retention Time and Drift Time from MS and MS/MS search to help identify if the lipids are from the same or different species.

Error Tolerance in mDa- An additional unit for specifying the MS Search, MS/MS Search and Isotopic Peak Correction error tolerance is now available. The error tolerance range in mDa is 0.1 to 2000.

SimLipid® 1.10 Released

SimLipid® now supports the following:

Lipid Structural Elucidation- Structural elucidation of lipids using MS/MS data for Glycerophospholipids, Glycerolipids, Prenols and Saccharolipids.

Ranking- An innovative ranking algorithm that indicates the relative degree of proximity of theoretical lipids with the experimental data and sorts the results based on the score derived.

MS Lipid Search- Lipid profiling by searching lipid precursor ion against the known lipid structures available in the SimLipid® database for Sphingolipids, Fatty Acyls, Glycerolipids, Sterols, Prenols, Saccharolipids, Polyketides and Glycerophospholipids.

Isotopic Peak Correction- Correction of Peak intensity values on the basis of the calculated isotope percentage of lipids either on parent molecular formula or molecular formula after subtracting neutral loss fragment, providing a platform for further quantitative data analysis.

Updated Database- Large relational database containing 8 lipid categories viz. Glycerophospholipids, Sphingolipids, Fatty Acyls, Glycerolipids, Sterols, Prenols, Saccharolipids and Polyketides with 21,905 lipid species.

High Resolution Data Support- MS and MS/MS data analysis for high resolution data with an error tolerance of up to 20 ppm or between 0.0001 and 2 Da can now be performed.

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