Retention time alignment using a combination of LamaParama and subset-based alignment

[CLUES-Emory]

Hello, We are trying to explore how to improve the processing speed for the retention time alignment step, which often takes 2-5x longer than the peak detection. One option we are exploring is the LamaParama corrections using our internal standards; however, these are not included in our instrument blanks and since these are not detected the retention times for these injections will not be corrected.

To account for this, we are trying to combine LamaParama with a subset that includes our pooled samples, but I do not see an option for subsetting in the LamaParama parameters (as is available for the other correction methods). Is there anyway to implement this?

Also, any suggestions on how to improve processing time for the alignment step (for studies including 1000-5000 samples) would be greatly appreciated.

As always, thanks for your excellent work on XCMS!