How do I avoid batch effects and what sample run order should I use for PTMScan® experiments?

To avoid intra-sample batch effects during liquid chromatography with tandem mass spectrometry (LC-MS/MS), we recommend a run order that involves running one technical replicate of each enrichment, then the remaining replicates in reverse order. For example, samples 1-4 have two replicate injections each: 1A/1B, 2A/2B…, etc. Therefore, the run order would be: 1A, 2A, 3A, 4A, 4B, 4A, 3B, 2B, 2C, 1C.
 

Last updated: October 6, 2025