Before we can process data, we need data. Here, we describe the different scan modes to acquire data:
Full scan data
data-dependent analysis (DDA)
data-independent analysis (DIA)
and iterative exclusion data-dependent analysis (IE-DDA)
We also talk about ideas for setting up a sequence and which file types are needed for our software platforms.
If your vendor does not support IE-DDA which is our recommended acquisition mode for LC-HRMS, you can find an open-source software here:
https://innovativeomics.com/software/ie-omics/
https://pubmed.ncbi.nlm.nih.gov/28265968/
Also for deconvolution of all ions data (which is now built into FluoroMatch/LipidMatch/PolyMatch see:
https://pubs.acs.org/doi/10.1021/jasms.3c00244
