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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 version 5.60 Released

The new version includes the following enhancements:

  • An updated database with 40,298 lipid structures and 1,509,305 structure-specific in-silico MS/MS characteristic ions.

  • 32,208 structure specific characteristic ions of wax mono esters have been added enabling accurate identification of lipid species from wax mono ester class using MS/MS database search.

  • New criteria for filtering lipids based on lipid ontology has been introduced to limit the MS, and MS/MS database search to specific lipids. Users can instruct the program to report lipids based on even/odd numbers of carbon (C) atoms in their fatty acid chains' compositions. Ontology filter is applicable only to Glycerolipids (GL), Glycerophospholipids (GP) and Sphingolipids (SP) categories.

  • MS/MS Score filter has been introduced to screen the candidate lipids during MS, and MS/MS database search, based on the attributes of the observed characteristic ions, namely, (i) types of the characteristic ions – head group, fatty acyls; (ii) threshold value of the relative intensity of characteristic ions – 50% of the base peak for at least 3 structure-specific characteristic ions.

  • HTP search filter to automatically select only those MS/MS scans that did not return any match in previous searches and re-perform MS/MS database search using a different set of search parameters. This enables users to identify lipid species quickly using the MS/MS data where precursor ion species are unknown.

  • For PIS/NLS based shotgun lipidomics workflows, a heatmap showing color coded percentage composition of all the lipid species identified for a target mass in a sample can now be generated with a click of a button.

  • Sub-class filter is now added to restrict the MS and MS/MS database search to only a group of specified lipid sub-classes.

SimLipid version 5.51 Released

The upgrade accommodates fixes to reported issues.

SimLipid version 5.50 Released

The new version includes the following enhancements:

  • The database now contains 40,234 lipid structures

  • The database now contains 1,487,728 structure-specific in-silico MS/MS characteristic ions. The following new characteristic ions in negative ion mode MS/MS spectra of lipids are observed from:
  1. Plasmalogen glycerophosphocholine
    - Loss of the Sn1 chain with 1-(1Z-alkenyl) bond
    - Loss of the Sn2 chain with 2-(1Z-alkenyl) bond

  2. Glycerophosphoglycerols
    - Loss of Sn2 chain along with Glycerol (C3O2H6)
    - Loss of Sn2 chain along with Glycerol (C3O2H6) and H2O

  3. Glycerophosphates class
    - Loss of Sn2 chain- CO2

  4. Glycerophosphoinositol
    - C3H6O5P (characteristic ion of PI class)
  • Support for Waters' native data file (.raw). You can now directly load raw data generated by Waters's triple quadrupole mass spectrometers, namely Xevo TQ-XS, Xevo TQ-S, Xevo TQD, etc.; and Quadrupole Time-of-Flight Mass Spectrometers, namely Xevo G2-XS QTof, and SYNAPT G2-Si, without having to use a third party data conversion tool

  • Support for Shimadzu's native data file (.lcd). You can now import raw data directly from Shimadzu's triple quadrupole mass spectrometers namely LCMS-8050 instrument and other LCMS – triple quadrupole mass spectrometers

  • Compatibility with Bruker Daltonic's latest CompassXtract version (v. 3.2.3)

  • Automated data analysis protocol for Multiplexed Precursor Ion Scan (MPIS) and Neutral Loss Scan (NLS) based Shotgun Lipidomics QqQ workflow. Profiled lipids can be aligned across multiple scans and biological samples within an experiment based on short name (i.e., #C:#DB), similar fatty acyls (disregarding the position of Sn1, Sn2, Sn3 chains and position of double bonds) or common name/abbreviation

  • Multiple samples can now be compared at a click of a button and the comparative reports generated can be exported for further downstream analysis

  • Custom target masses for precursor ion scan (PIS) and neutral loss scan (NLS) based QqQ mass spectrometry lipidomics experiments can now be added or edited to target a specific lipid class or subclass

  • Lipid structures can be exported from the SimLipid database and novel lipid structures can be imported to the database for further analysis

  • Data from multiple scans within specified m/z and retention time tolerances can now be auto-averaged while loading the data itself. The process not only considerably reduces the time taken for data processing before a search but also improves the quality of the data

  • A quality peak picking process is now introduced in which average data from MS scans having relative TIC and BPC greater than a user specified threshold is picked up

SimLipid version 5.10 Released

The new version includes the following enhancements:

SimLipid has now incorporated an improved peak picking and peak detection algorithm allowing faster processing of LC-MS and MS/MS data. The new proprietary algorithm enables the program to perform peak detection and molecular feature finding for any raw data file at least 3 times faster than the previous versions of the program while ensuring important compounds and their molecular features are not missed out.

SimLipid® 5.00 Released

The new version includes the following enhancements:

  • Model experimental designs by grouping LC-MS runs into different biological/technical replicates.

  • Statistical analysis such as ANOVA, t-test and fold change to assist lipid differential analysis across multiple samples.

  • Visualize raw data, peaklists, identified lipids, statistical analysis results and annotated spectra together in a newly integrated workspace.

  • Additional diagnostic ions for Glycerophospholipids (GP) based on experimental spectra reported in Library of Glycerophospholipids Standards are now included in the database.

  • Improved algorithm for noise data reduction and filters to remove redundant peaks from aligned peaklist.

  • Improved peak picking algorithm to support direct infusion MS data analysis workflows.

  • Enhanced report format to export fragment names along with their corresponding m/z values and peak intensity for matched ions in MS/MS spectra.

  • LC-MS and -MS/MS support has been extended for Bruker (baf, yep & fid) and SCIEX (wiff) native data files formats along with Thermo (raw), mzXML and mzData.

  • With this release, we have changed the licensing and Annual Maintenance Policy. For details, please visit the Annual Maintance Policy.

SimLipid® 4.50 Released

The new version includes the following enhancements:

  • A new and improved algorithm for isotope peak correction enabling accurate lipid identification and quantitation, as the intensities of overlapping isotopic peaks are corrected and reported.

  • An even more accurate algorithm for averaging scans enabling more accurate identification.

  • Total abundance of a lipid is now reported. It is calculated after taking into account the intensity of its lower isotopes, enabling accurate quantitation.

SimLipid® 4.40 Released

The new version includes the following enhancements:

SimLipid now offers comprehensive raw data visualization. The chromatogram along with a dynamic view of the mass spectrum and the search results is now available.

The TIC (Total Ion Chromatogram), XIC (Extracted Ion Chromatogram) and BPC (Base Peak Chromatogram) can also be plotted for both MS and MS/MS levels at a click of a button. Both, the chromatogram plots and the mass spectrum plots can be zoomed into, so as to investigate and highlight important peaks. Export of the mass spectrum data is available as well.

MS1 data can now be averaged on the chromatogram itself for a specified retention time range, enabling faster analysis.

SimLipid® 4.30 Released

The new version includes the following enhancements:

SimLipid now enables exporting data analysis results including lipid structures to Microsoft Excel file making it easier for users to present their lipid characterization findings. Results can be sorted based on lipid score to present a ranked list. Additional information such as number of carbon-carbon double bonds, number of triple bonds, number of carbon double bonds in fatty acyl chain is also made available for comprehensive reporting.

SimLipid now allows input of up to 200 files at a click of a button for mzXML, mzData, BRUKER, AB SCIEX and Thermo Fisher Scientific native data files.

SimLipid® now has an even more increased throughput, users can batch search 10,000 MS or MS/MS spectra.

AB SCIEX's WIFF file loading is now much more easier and faster. SimLipid 4.30 has a redesigned WIFF import mechanism which eliminates the need to install Analyst®.

For Agilent users, results from MS/MS database search can be exported to the proprietary CEF format using filters based on score thresholds, retention time range, precursor m/z range etc. for futher downstream processing by MassHunter and MPP.

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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