SimLipid®

The Bioinformatics Tool for Mass Spectrometry Based Lipidomics Workflows

Below is a list of MS based lipidomics workflows supported by SimLipid. SimLipid can perform lipid identification using exact mass database search, and product ions database search. Subsequent quantitation of the annotated lipids in mass spectra by correcting isotopic overlapping of m/z peaks belonging to different biological species, and mapping of the annotated lipids across biological groups for differential lipidomics analysis is also facilitated.

Abbreviations:
DDA: Data Dependent Acquisition
DIA: Data Independent Acquisition
RP: Reversed Phase
NP: Normal Phase
ESI: Electrospray Ionisation
HPLC: High Performance Liquid Chromatography
UPLC: Ultra-Performance Liquid Chromatography
SFC: Supercritical Fluid Chromatography

Sl. # Method Separation Method MS Instrument MS/MS Data Acquisition Literature
1 Normal Phase or Reverse Phase LC-QTOF MS
  1. RP separations: Agilent Zorbax EclipsePlus RRHD, 2.1 x 100mm, 1.8 µm column with a binary gradient
  2. NP separations: Agilent Zorbax Rx-Sil, 2.1 x 100mm, 1.8 µm column with a binary gradient on an Agilent 1290 UHPLC system
Agilent 6540 Q-TOF with Dual Agilent Jet Stream ESI Source DDA

Authors: Meitei, N.S., Biswas, A., Apte, A., Madden, S., Sartain, M. 

Title: Automatic lipid characterization using SimLipid® from normal phase and reverse phase liquid chromatography -MS, MS/MS data acquired in variable ion modes

Conference: 63rd ASMS Conference on Mass Spectrometry & Allied Topics (2015), St. Louis

Link

2 SFC -QTOF MS Columns 1, and 2 connected in series:
  1. EC-C18
  2. hybrid UPC2 BEH

Agilent 6540 Q-TOF MS DDA

Authors: Mohsin, S.B., Williams, K., Renu, D., Meitei, N.S., Kalakoti, S., Madden, S., Kitagawa, N.

Title: Development of an Integrated Workflow for Profiling and Semi-Quantitative Analysis of Lipids

Conference: 65th ASMS Conference on Mass Spectrometry and Allied Topics (2017), Indianapolis, IN

Link

3 LC-QTOF MS HPLC Instrumentation: Agilent 1290 Infinity Column – ACQUITY UPLC CSH C18 2.1 x 100 mm, 1.7 μm
Bruker Impact II UHR-QqTOF MS DDA

Authors: Meitei, N.S., Gupta, H., Apte, A., Barsch, A., Alving, A., Henao, J.J.A., Stark, K.D.

Title: Automated Lipid Profiling of a Plasma Sample Using Ultra-High Resolution Qq-Time-Of-Flight Impact II™ Mass Spectrometer with SimLipid Software

Conference: 65th ASMS Conference on Mass Spectrometry and Allied Topics (2017), Indianapolis, IN

Link

4 MALDI-FTICR N/A Bruker 15T SolariX FTICR-MS N/A

Boughton, B. and Roessner, U. (2015). Imaging Mass Spectrometry for Spatial Metabolomics. Aus. Biochemist, 46(3): 9-11.

Link

5 Waters® UPLC- QTOF(SONAR) MS CSH 1.7 μm C18 reversed phase (RP) 2.1 x 100 mm LC column
Waters Xevo G2-XS QtoF ( operated in

SONARTM mode) MS

DIA

Authors: Gethings, L. A., Meitei, N.S., Vissers, J.P.C., Heywood, D., Castro-Perez, J., Langridge, J. I.,

Title: Utilization Of SimLipid for the Characterization of Metabolic Syndrome Related Lipids Acquired Uing a Novel Scanning Quadrupole DIA Acquisition Method.

Conferences: 13th Annual Conference of the Metabolomic Society (2017), Brisbane, Australia & 65th ASMS Conference on Mass Spectrometry and Allied Topics (2017), Indianapolis, IN

Link

6 Waters® UPLC-TOF(

HDMSE) MS

LC system: ACQUITY UPLC Column: ACQUITY UPLC CSH C18 2.1 x 100 mm, 1.7 μm
Waters SYNAPT G2 HDMS System
DIA

Authors: Isaac, G., McDonald, S., Astarita, G.

Title: Automated Lipid Identification Using UPLC/HDMSE in Combination with SimLipid

Waters Application Note No. 720004169EN

Link

7 Waters®

UPLC- TOF (MSE) MS

LC system: ACQUITY UPLC with 2D Technology Column: 1st Dimension Column: UPLC BEH HILIC 2.1 x 100mm, 1.7 μm
2nd Dimension Column: UPLC CSH C18 2.1 x 100mm, 1.7 μm
Trap Column: UPLC VanGuard CSH C18 2.1 x 5mm
Waters SYNAPT G2 HDMS System DIA

Authors: Netto, J.D., Sing, S.F., Ditcham, W., Borowitzka, M., Ritchie, M.

Title: Inter-Strain Comparative Lipidomics of Microalgae Using Multi-Dimensional Separation Techniques

Conference: 19th International Mass Spectrometry Conference (IMSC), 2012, Kyoto.

Link

9 LC-Orbitrap based MS Accela 1250 quaternary pump with Accela Open autosampler Thermo Scientific LTQ Orbitrap Velos Pro Hybrid MS DDA

Authors: Meitei, N.S., Arun Apte, Rahlouni, F., Sullivan, D. J., Shulaev, V.

Title: Automated Lipid Profiling of Malaria Samples Using Orbitrap Velos Pro Mass Spectrometer with LipidSearch and SimLipid Software

Conference: 65th ASMS Conference on Mass Spectrometry and Allied Topics (2017), Indianapolis, IN

Link

10 HPLC- TOF MS

HPLC: Acquity HSS T3 1.8μm, 2.1 x 100mm @ 60oC

SCIEX TripleTOF® 5600 System DDA

Authors: Meitei, N.S., Sreenidhi, A.K., Apte, A., & Ubhi, B.K.

Title: LC-MS and MS/MS based Large Metabolomic Data Processing and Analysis using SimMet®.

Conference: 63rd ASMS Conference on Mass Spectrometry & Allied Topics (2015), St. Louis.

Link

11 MALDI-MS/MS N/A SCIEX TOF/TOF™ 5800 system DDA

Authors: Meitei, N.S., Apte, A., Waidelich, D., Abdi, F., Glueckmann, M.

Title: Automatic Characterization of Lipids Using Charge Remote Fragmentation Ions and Peaks Characteristic of Fatty Acid Fragmentation From MALDI MS/MS Data

Conference: 62nd ASMS Conference on Mass Spectrometry and Allied Topics (2014), Baltimore

Link

12 Shotgun based Precursor Ion/Neutral Loss Scanning experiments
1. N/A



2. HPLC: Phenomenex Kinetex C8 (150 × 2.1 mm, 2.6 μm) @ 45o C

1. Shimadzu LCMS-8040


2. Shimadzu LCMS-8060

1. Authors: Gupta, R., Sadowski, M., Meitei, N. S., Blanksby, S. J.

Title: Shotgun Lipidomics of Prostate Cancer Cells Using ESI-MS Shimadzu 8050 and Simplified Data Analysis by SimLipid Software

Conference: 13th Annual Conference of the Metabolomic Society (2017), Brisbane, Australia

Link 1

2. Authors: Nakanishi, T.

Title: Phospholipid analysis using SimLipid software

Shimadzu Document No. LAAN-A-LM-E120

Link 2





Posters and Presentations

Shotgun Lipidomics of Prostate Cancer Cells Using ESI-MS Shimadzu 8050 and Simplified Data Analysis by SimLipid...

Utilisation of SimLipid for the Characterisation of Metabolic Syndrome Related Lipids Acquired Using a Novel Scanning Quadrupole DIA...
Read More >>

Application Notes

Phospholipid analysis using SimLipid software

- Shimadzu Document No. LAAN-A-LM-E120

Automated Lipid Identification Using UPLC/HDMSE in Combination with SimLipid

- Waters Application Note No. 720004169EN
Read More >>



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