I have problem with xcms results. The integration results of selected peak A by online xcms are different from those directly extracted from the raw file. From total 6 samples, 4 out of 6 had the similar peak area as those directly extracted from the raw file and 2 of them were way off the raw file. The retention time of peak A varies from 21.45 min to 22.71 min across the samples. But when I looked at another known peak, the results of all samples all matched those from raw file. The retention time of this peak varies from 30.18 min to 30.9 min across the samples. Is this issue related to peak alignment? I set the retention initial grouping at 90s and bw at 40 in Alignment. I also tried 30s for retention initial grouping and 20 bw in Alignment. I got the same result. If my issue is related to the setting, could you please give me some suggestion? I am using LC-Orbitrap. Thanks very much for any help.