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Add SequenceWindow description
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hsiaoyi0504 authored and fcyu committed Oct 25, 2024
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Expand Up @@ -717,6 +717,8 @@ Quantification results from MS1-based isotopic labeling experiments are generate

**Peptide** stripped peptide sequence containing the modification sites, residues with localized modifications are shown in lower case

**SequenceWindow** peptide sequence around the localized modified site.

**MaxPepProb** highest PeptideProphet probability of the PSMs with the sequence that are used in quantification

**ReferenceIntensity** Real reference channel abundance is used if one has been provided, otherwise these values are virtual reference abundances from the average abundance across the channels in a plex, more usage information [here](https://fragpipe.nesvilab.org/docs/tutorial_tmt.html#quantification-settings). If the experiment contains multiple plexes, average reference intensity across all plexes is used. Values are log2 scaled, with global minimum reference intensity used to impute missing values.
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