Products >> Upgrades >> SimLipid®

SimLipid version 6.06 Released

The new version includes the following enhancements:

• Improved Loading of Shimadzu (QTOF) Native Data Files: SimLipid now accommodates the latest data reading algorithm offered by Shimadzu Corporation. This has significantly improved the data loading capability and data analysis accuracy of SimLipid for the Shimadzu QTOF instrument series.

• Fixes to reported issues.

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SimLipid version 6.05 Released

The new version includes the following enhancements:

• Improved Peak Picking Algorithm for DDA Data: SimLipid now incorporates a new peak picking algorithm for accurate assignment of precursor m/z values of MS/MS scans while loading tandem MS data (acquired using DDA method). For a precursor m/z value of an MS/MS spectrum, SimLipid identifies the isotope cluster containing the precursor m/z from MS1 data and then assigns the m/z at monoisotopic peak as the precursor m/z of the MS/MS scan, enabling accurate identification of lipid species.

• High Throughput Data Analysis Workflow for LC-MS and (DIA) MS/MS Experiments: SimLipid processes LC-MS and MS/MS raw data acquired using Data Independent Acquisition (DIA) methods, accurately detects peaks and associates product ions to their precursor ions. The software then aligns peaks detected from different peaklists based on agreement of retention time, m/z value, observed intensity and charge state. Peaklists or aligned peaklists can be further subjected to MS/MS database search for accurate identification of lipid structures in batch mode.

• HRMS Based Lipidomics Analysis: Automated experimental design modeling for HRMS based lipidomics analysis workflow that involves MS1 data averaging and alignment of m/z peaks across biological and technical replicates.

• Frequency Tables and Charts: SimLipid now includes an intuitive graphical interpretation of lipid profiles of LC-, MALDI, Shotgun-, MS and MS/MS based experimental runs using pie and bar charts. Easy comparative analysis of lipid profiles across samples is now facilitated using frequency tables.

• Statistical Analysis: Export LC-MS and MS/MS database search results to CSV format files that can be directly imported into MetaboAnalyst# or MetaboScape* software for downstream statistical analysis.

• Export Results: Based on filter criteria such as Score and Matched RI, users can export unique lipid IDs along with retention times, quadrupole position (bin) / drift time and ion species information into MS Excel or CSV file formats.

• Create LC-MS and Shotgun-MS Templates**: SimLipid now facilitates direct import of HTP reports generated from Shotgun-MS and LC-MS workflows in order to create custom database(s) which can be used for MS/MS search for elucidating lipids.

• Import Raw Data Directly from Waters MassLynx UHPLC-MS^E .raw Files: SimLipid can now directly import raw data (centroid and lock mass-corrected) from Waters MassLynx UHPLC-MSE .raw files.

** Functionality available in Enterprise Edition.
# Xia, J. and Wishart, D.S. (2016) Curr. Prot. in Bioinformatics, 55:14.10.1-14.10.91.
* https://www.bruker.com/products/mass-spectrometry-and-separations/ms-software/metaboscape/overview.html

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SimLipid version 6.04 Released

The new version includes the following enhancements:

• Precursor Intensity Correction: A more efficient algorithm for identification of isotopic envelops for precursor m/z value of each MS/MS spectrum from their preceding MS1scan(s) is now incorporated. The new proprietary algorithm corrects the precursor m/z and precursor intensity for Thermo Fisher Scientific native *.raw and Shimadzu's native *.lcd (Q-TOF) raw data before loading the files to SimLipid. Export of corrected precursor intensity to .xls or .csv format files is now supported to help in down-stream analysis.

• Support Bruker's .mgf Files: Bruker's MetaboScape generated *.mgf (mascot generic format) files containing MS and MS/MS data along with ion species information can now be directly imported to SimLipid, enabling lipid profiling and identification using MS and MS/MS database search in SimLipid. Results generated by SimLipid can be directly imported to MetaboScape software for further statistical and pathway analysis.

• High Throughput Data Analysis from DIA Experiments: A comprehensive high-throughput workflow for data-independent acquisition using Agilent's Q-TOF mass spectrometers is now supported. The workflow is based on sequential isolation and fragmentation of precursor masses centered on the mass defect of lipid masses enabling high confidence lipid species identification and relative quantitation.

• Reduced Analysis Time: Time required for file loading, high throughput search and loading of identified lipid species has been significantly reduced enabling you to complete your analysis faster.

• New characteristic ions observed in positive ion mode MS/MS spectra of Steryl Esters and Cholesterol and Derivatives are now included in the database enabling accurate identification of lipid species from these classes using MS/MS database search.

• Enhanced portable reports for LC-MS workflows that can directly be imported into MetaboAnalyst software for further downstream statistical analysis.

• Faster loading of Thermo Fisher Scientific native *.raw files using the recently released RawDataReader from the company.

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SimLipid version 6.03 Released

The new version includes the following enhancements:

1. Increased Throughput:

• Import raw data or peaklists from 2,000,000 scans at a click of a button.
• Database search for 100,000 MS or MS/MS scans in batch mode.
• Export search results of 100,000 MS or MS/MS scans to MS excel and CSV format files for further analysis.
• Filter results based on Score and Matched RI for high confidence results.

2. Significantly Faster Data Processing:

• Averaging of data from MS or MS/MS scans is now 30x faster.
• MS/MS Database Search is now 3x faster.
• MS Database Search is now 12x faster.
• LC-MS peaklists MS/MS Database Search is now 12x faster.

Refer Performance Testing Report.

3. Multiple Report Layouts:

• Export each identified lipid species for an MS/MS scan based on user specified filter criteria to an MS Excel file, with each IDed lipid taking up a row. This layout is recommended for exporting lipid IDs from DIA tandem MS data analysis when there is high likelihood of multiple lipids identified for an MS/MS spectrum.
• Export all the identified lipid species for an MS/MS scan based on user specified filter criteria to an MS excel file, with each IDed lipid taking up a column with headers: Rank 1, Rank 2, …, Rank n. This layout is recommended for exporting lipid IDs from DDA tandem MS data analysis when there is low likelihood of multiple lipids identified for an MS/MS spectrum.
• Export unique lipid IDs for an MS/MS scan based on user specified filter criteria into MS excel or CSV that can directly be imported to the SimLipid database* or for further downstream analysis.

4. An Automated Lipidomics Analysis Workflow using Both the MS/MS and MS Data*:

• Identify lipids with high confidence using MS/MS database search.
• Create a custom database of identified lipids.
• Process the MS data and model experimental design of experiments for facilitating comparative and quantitative analysis.
• Annotate peaks in the MS data using lipid IDs from curated database.
• Compare annotated lipids and their isotopic corrected abundances across biological samples.

* Functionality available in Enterprise Edition.

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SimLipid version 6.02 Released

The upgrade accommodates fixes to reported issues and has much faster performance.

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SimLipid version 6.01 Released

The new version includes the following enhancements:

• SimLipid master database now contains additional 14 Deuterated lipid standards from "SPLASH™ Lipidomix^® Mass Spec Standard" to facilitate validation of the identified lipids from the samples, and subsequent relative quantitation of the IDed lipid species.
  
  
• Faster loading of Waters^® UPLC^® SONAR™ and Waters^® UPLC^® HDMS^E raw data.
  
  
• Faster processing of Waters^® UPLC^® SONAR™ and Waters^® UPLC^® HDMS^E raw data is achieved for peak detection, and peak picking using SimLipid.
  
  
• Matched Ion Intensity (Sum) – sum of observed intensity of product ions corresponding to characteristic fragment ions – of identified lipids can be exported to multiple report file formats such as MS Excel, CSV, and HTML.
  
  
• Several usability enhancements such as directly performing MS and MS/MS Search from the raw data tabular view.

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SimLipid version 6.00 Released

The new version includes the following enhancements:

• DIA Data Processing: The program can process raw data acquired through Data Independent Acquisition (DIA) methods namely, Waters SONAR/HDMS^E methods for peak detection, peak picking, and association of product ions to their precursor ions acquired.
  
  
• View SONAR/HDMS^E Raw and Processed Data: The program facilitates visualization of (a) Raw data - Total Ion Chromatogram (TIC), and Spectra, (b) Processed data – peaklists showing all the detected LC-detected compounds, each compound features:
  
  
  • Extracted ion chromatogram (XIC) of the detected compound (in retention time axis)
  • XIC of the compound in either drift time or quadrupole positions (bin axis)
  • Overlay of XICs of precursor ion m/z and its fragment ions (in either drift time or quadrupole positions (bin) axis).
  
  
• High Throughput MS/MS Data Analysis from DIA Experiments: The program can perform MS/MS database search for over 20,000 potential compounds for accurate identification of lipid structures in batch mode.
  
  
• Support Waters .raw Files: SimLipid can now import raw data directly from Waters native MassLynx® UPLC® SONAR/HDMS^E files.
  
  
• MS/MS Database Search with Multiple Adducts: The program now facilitates users to select multiple probable ion species for the precursor ions. This functionality enables the program not only to reduce the false assignment of lipid species while analyzing LC-MS data due to lack of adequate adduct ions signals in the raw data, but also improves the accuracy of the identified lipids, and reduces the time to complete the data analysis in case of direct infusion ESI-MS/MS lipidomics experiments.
  
  
• Increased Coverage for the MPIS/NLS Experiments*: Users can now add lipid class specific target masses for precursor scan, neutral loss scan based lipidomics experiments. This functionality facilitates users to perform targeted lipidomics analysis covering multiple lipid classes by storing custom set masses in the database.
  
  
• Normalize peak intensity of analytes in samples with respect to internal standards and export results into Agilent’s CEF files, MS excel files.
  
  
• Display summed relative intensity of the matched characteristic ions (Matched RI) of the identified lipids.

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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.

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SimLipid version 5.51 Released

The upgrade accommodates fixes to reported issues.

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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
  

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