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find_peaks: every separate peak in an XIC; n_signal counts scans with the ion - #18
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… the ion peak_boundary measures one peak. A glycopeptide XIC often holds several (an isomer, a second elution), and the reader of one boundary cannot see the peak a minute away. find_peaks takes the trace's local maxima tallest first, bounds each with the same valley walk, and clips boundaries so peaks never overlap; a local maximum inside an earlier peak is a shoulder, not a peak. bridge_dropouts=k fills runs of at most k zero scans with signal on both sides before peak finding. On NGlycoM012 F21 MS1 traces a single empty scan split one elution in two in 914 of 1,878 "second peak" cases without it. PeakMetrics.n_signal and TracePeak.n_signal count the scans in the boundaries above baseline. n_points also counts the two boundary scans, which on a zero-filled trace are empty, so a one-scan blip read as a three-point peak. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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find_peaks: every separate peak in an XIC; n_signal counts scans with the ion