Re: Too few features? Synapt G2S UPLC HILIC
Reply #6 –
Some thoughts:
- ppm at 8-10 might be too low. This accuracy is needed for the whole mass peak. Not just the apex. ~30 ppm might be a better starting point.
- I have had data where centwave didn't do well. I think generally it needs pretty good data to work well (many scans per peak, clear peaks). You can try matched.filter which is better at picking up peaks but you will get more noise. But this should be more similar to markerlynx.
- obiwarp is slow and never worked well for me personally. Perhaps try the loess method.
- It sounds like your main problem is the grouping step since you get few peaks after that.
- The bw parameter seems low. Try setting it it higher at least to try to see if it improves grouping.
- The bw setting is usually the most important, while a sensible mzwid should not affect the grouping that much.
- You have not set your minfrac, minsamp parameters in group. Sensible settings depends on if you defined the groups (by putting them in different folders) and how homogeneous you think each group should be.
- profparam might be causing some bad data but first try to understand if your grouping works. This is much more critical. I don't think 0.1 makes much sense for a QTOF instrument. If it does anything bad or not depends if you have compounds with similar mass closely eluting or not. Again this should be relatively rare so should not completely scramble your data.
- My approach would be this: Find a peak/fragment that should be in all samples but is lost after grouping. I would then use a function I wrote, analyze.xcms.group (viewtopic.php?f=8&t=577&p=1789&hilit=analyze.xcms.group#p1789), to visualize what happened during grouping. --> too few dots --> peak picking issue. --> did it not group them? Did it do it wrong? Can you understand why when you compare the plot to your grouping parameters (m/z or RT dimension is the problem)?