Shotgun Lipidomics Assistant (SLA)
What is the SLA?
The SLA is Python application that facilitates the DMS Shotgun Lipidomics Workflow. It’s an open-source software that is being made available with established methods for comprehensive lipidomic analysis that is based on the Sciex Lipidyzer™ platform. It is being 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’s an open-source software that is being made available with established methods for comprehensive lipidomic analysis that is based on the Sciex Lipidyzer™ platform. It is being used by numerous labs across the world to generate high quality lipidomics data.
What is required to use this workflow?
Currently the methods facilitated by the SLA have only been validated on Sciex instruments with the SelexION device; the Sciex 5500 and 6500+. The method will also require a set of standards that are commercially available from Avanti Polar Lipids. Lastly, it requires the SLA application which is available on Github.
Currently the methods facilitated by the SLA have only been validated on Sciex instruments with the SelexION device; the Sciex 5500 and 6500+. The method will also require a set of standards that are commercially available from Avanti Polar Lipids. Lastly, it requires the SLA application which is available on Github.
How can I get started?
Below we have provided protocols, papers and videos, as well as the Github link to software itself, that will help you get started with the SLA workflow.
Below we have provided protocols, papers and videos, as well as the Github link to software itself, that will help you get started with the SLA workflow.
- Start by downloading the Application itself 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 contains 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 produces 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
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
7. If you’d like to see what kind of lipidomics studies have been performed using the SLA, check the list of publications that have sited the JASMS methods paper. https://pubmed.ncbi.nlm.nih.gov/?linkname=pubmed_pubmed_citedin&from_uid=34637296