Hi Tipos
These are good questions to ask. Understanding every part of your data processing is the key to getting the most out of your data. Regarding your question about Mask Method, Channel, Threshold and Trim, Joe has written a detailed explanation about masks here: https://notes.iolite.xyz/posts/masks/.
To explain what the Index Channel is, you should be aware that iolite can handle data were the same channels are not measured in all files within a session. It does this by using an Index Channel; that is, a channel that is present in all files. The time data associated with this channel will then become Index Time, the time data for all channels created by a Data Reduction Scheme. For most cases, the same channels are measured throughout an entire session, and so the Index Channel can be any channel.
Regarding getting negative values, this does (at first) appear counter-intuitive: how can you have negative concentrations? Or for that matter, negative counts per second? However, the most common reason for this is that your baseline spline is greater than the counts during your analysis (that is, parts of your analysis are less than the baselines). If you think this is in error, you should check that your baseline selections correctly reflect your baselines. This could mean that you may need to adjust them to avoid background anomalies (spikes), or add additional selections so that the baseline spline properly follows the backgrounds. You can also adjust the baseline spline type if the default (Spline_AutoSmooth) is not reflecting how you think your baselines are changing. I quite often use 'StepFoward'. You can change the Spline Type by double-clicking the spline name in the Time Series View.
To describe what the Baseline Subtract DRS is doing, it is simply subtracting the value of the baseline spline for each channel. You can see the baseline spline as a dashed green line when you click on the Baseline group in the Time Series View. The channels calculated usually have the suffix "_CPS" to indicate that that are different from the raw input channels and have been baseline corrected.
I hope that helps. If you have any followup questions, please reply to this post.
Cheers,
Bence