Shotgun Lipidomics Assistant (SLA)
What is the SLA?
The SLA is Python application that facilitates the DMS Shotgun Lipidomics Workflow. It is an open-source software that is available with established methods for comprehensive lipidomic analysis that is based on the Sciex Lipidyzer™ platform. It is used by numerous labs across the world to generate high quality lipidomics data.
The SLA is Python application that facilitates the DMS Shotgun Lipidomics Workflow. It is an open-source software that is available with established methods for comprehensive lipidomic analysis that is based on the Sciex Lipidyzer™ platform. It is used by numerous labs across the world to generate high quality lipidomics data.
What is required to use this workflow?
- The methods facilitated by the SLA have only been validated on Sciex instruments with the SelexION devices, Sciex 5500 and 6500+.
- The method will also require a set of standards that are commercially available from Avanti Polar Lipids. The current methods use UltimateSPLASH ONE (330820) and SPLASH Booster (330740). The Tuning method uses EquiSPLASH (330731).
- Lastly, the method requires the SLA application which is available on Github.
- The methods facilitated by the SLA have only been validated on Sciex instruments with the SelexION devices, Sciex 5500 and 6500+.
- The method will also require a set of standards that are commercially available from Avanti Polar Lipids. The current methods use UltimateSPLASH ONE (330820) and SPLASH Booster (330740). The Tuning method uses EquiSPLASH (330731).
- Lastly, the method requires the SLA application which is available on Github.
How can I get started?
Below we have provided protocols, papers, videos, and the Github link to the software itself, that will help you get started with the SLA workflow.
Below we have provided protocols, papers, videos, and the Github link to the software itself, that will help you get started with the SLA workflow.
- Download the Application from Github. The most recent version can be found here. https://github.com/syjgino/SLA/releases/tag/v1.5book Note that the “Doc” folder included with the application contains the Analyst methods for two of the most common hardware configurations (Shimadzu LC-30/Sciex 5500 and Shimadzu LC-40/Sciex 6500+). It also includes all the dictionaries the SLA uses for the most recent workflow (v4).
- The most complete instructions for running the SLA can be found in the Readme file on Github or downloaded HERE.
- This methods paper published in JASMS in 2021 describes how the SLA works and validates the method. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8985811/
- This video provides an overview of running the SLA, including tuning, running, and data analysis (18 minutes). While produced some years ago using an older version of the SLA, it gives users a sense of how to perform the workflow. https://www.youtube.com/watch?v=1bBZkzZ6BM0
5. This video describes the data package generated by the SLA (15 min). While intended for clients
of the UCLA Lipidomics Lab, it is useful for all SLA users.
https://www.youtube.com/watch?v=PjUbVt968co
of the UCLA Lipidomics Lab, it is useful for all SLA users.
https://www.youtube.com/watch?v=PjUbVt968co
6. This video will walk you through filling out the sample map (6 min). Again, while intended for
clients of the UCLA Lipidomics Lab, it is useful for all SLA users.
https://www.youtube.com/watch?v=EsL1mgq4C1k
clients of the UCLA Lipidomics Lab, it is useful for all SLA users.
https://www.youtube.com/watch?v=EsL1mgq4C1k
7. If you’d like to know what kind of lipidomics studies have been performed using the SLA, see
the list of publications that sited the JASMS methods paper.
https://pubmed.ncbi.nlm.nih.gov/?linkname=pubmed_pubmed_citedin&from_uid=34637296
the list of publications that sited the JASMS methods paper.
https://pubmed.ncbi.nlm.nih.gov/?linkname=pubmed_pubmed_citedin&from_uid=34637296