Update a help file
<h2>Description</h2>
<p>
- This method aligns detected compounds in different samples through matching their mass fragmentation spectra and retention times.
+ This method aligns detected compounds in different samples through matching their mass fragmentation spectra and
+ retention times.
</p>
<p>
- First, all compounds within a retention time range are collected from all samples. Then, pair-wise scores between those compounds are calculated as follows:
+ First, all compounds within a retention time range are collected from all samples. Then, pair-wise scores between
+ those compounds are calculated as follows:
+</p>
<div align="center" style="margin: 10pt">
S(C<sub>1</sub>, C<sub>2</sub>) = w S<sub>time</sub> + (1 - w) S<sub>spec</sub>
</div>
+<p>
where S<sub>time</sub> is the relative retention time difference between two compounds and S<sub>spec</sub> is the
spectrum similarity between two compounds. Finally, a two-phase procedure is used to determine the best matching
compound in each sample. For more details, see the paper
<br/><br/>
- Jiang, W.; Qiu, Y.; Ni, Y.; Su, M.; Jia, W.; Du, X.: <b>An automated data analysis pipeline for GC-TOF-MS metabonomics studies.</b> <i>Journal of proteome research</i> 2010, 9 (11), 5974-81
+ Jiang, W.; Qiu, Y.; Ni, Y.; Su, M.; Jia, W.; Du, X.: <b>An automated data analysis pipeline for GC-TOF-MS
+ metabonomics studies.</b> <i>Journal of proteome research</i> 2010, 9 (11), 5974-81
</p>
<h2>Parameters</h2>
@@ -51,17 +56,22 @@ compound in each sample. For more details, see the paper
<ul>
<li><b>Min confidence:</b> smallest fraction of samples where a compound should be detected. If the fraction of
samples where a compound is detected is larger then <b>Min confidence</b>, then that compound is included in the
- list of aligned compounds. Otherwise, that compound is discarded. This parameter should be between 0 and 1.</li>
+ list of aligned compounds. Otherwise, that compound is discarded. This parameter should be between 0 and 1.
+ </li>
<li><b>Retention time range:</b> maximum allowed retention time gap between aligned compounds</li>
<li><b>Score tolerance:</b> the minimum matching score required for compounds to be included in the list of
- aligned compounds. This parameter should be between 0 and 1</li>
+ aligned compounds. This parameter should be between 0 and 1
+ </li>
<li><b> Score weight:</b> the weight w that is used in the scoring formula. If w = 0, then only the spectrum
- similarity is used for scoring. If w = 1, then only the retention time proximity is used for scoring.</li>
+ similarity is used for scoring. If w = 1, then only the retention time proximity is used for scoring.
+ </li>
- <li><b>EIC score:</b> method used for calculating the retention time proximity. The <b>retention time difference (fast)</b> is preferred method.</li>
+ <li><b>EIC score:</b> method used for calculating the retention time proximity. The <b>retention time difference
+ (fast)</b> is preferred method.
+ </li>
</ul>
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