https://wiki-ms.microbe-ms.com/index.php?title=Peak_Detection&feed=atom&action=historyPeak Detection - Revision history2024-03-29T07:46:42ZRevision history for this page on the wikiMediaWiki 1.39.2https://wiki-ms.microbe-ms.com/index.php?title=Peak_Detection&diff=87&oldid=prevLaschp: /* Peak picking - basic concepts */2023-03-18T11:50:47Z<p><span dir="auto"><span class="autocomment">Peak picking - basic concepts</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> 1. The first step of peak detection in MicrobeMS involves the generation of </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> 1. The first step of peak detection in MicrobeMS involves the generation of </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> a threshold function represented by a S-shaped curve (see <del style="font-weight: bold; text-decoration: none;">sreenshot </del>below)</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> a threshold function represented by a S-shaped curve (see <ins style="font-weight: bold; text-decoration: none;">screenshot </ins>below)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:Threshold-for-peak-picking.jpg|500px|thumb|right|Threshold function ''Y(m/z)'' for peak picking]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:Threshold-for-peak-picking.jpg|500px|thumb|right|Threshold function ''Y(m/z)'' for peak picking]]</div></td></tr>
</table>Laschphttps://wiki-ms.microbe-ms.com/index.php?title=Peak_Detection&diff=21&oldid=prevLaschp: Created page with "== Introduction == Peak picking is an essential (and the final) step of the spectral pre-processing pipeline. The result of peak picking is a peak table which is attached to the mass spectra. In MicrobeMS peak picking can be started via the ''find peaks'' command of the ''Peak pick'' pulldown menu (shortcut <ctrl>+P), or by pressing the ''peak'' button located in the ''Peak pick'' tab. Screenshot of the peak pick window == Peak picking - b..."2023-03-18T09:26:44Z<p>Created page with "== Introduction == Peak picking is an essential (and the final) step of the spectral pre-processing pipeline. The result of peak picking is a peak table which is attached to the mass spectra. In MicrobeMS peak picking can be started via the ''find peaks'' command of the ''Peak pick'' pulldown menu (shortcut <ctrl>+P), or by pressing the ''peak'' button located in the ''Peak pick'' tab. <a href="/index.php?title=File:Peak-pick.jpg" title="File:Peak-pick.jpg">right|Screenshot of the peak pick window</a> == Peak picking - b..."</p>
<p><b>New page</b></p><div>== Introduction ==<br />
<br />
Peak picking is an essential (and the final) step of the spectral pre-processing pipeline. The result of peak picking is a peak table which is attached to the mass spectra. In MicrobeMS peak picking can be started via the ''find peaks'' command of the ''Peak pick'' pulldown menu (shortcut <ctrl>+P), or by pressing the ''peak'' button located in the ''Peak pick'' tab.<br />
<br />
[[File:Peak-pick.jpg|right|Screenshot of the peak pick window]]<br />
<br />
== Peak picking - basic concepts ==<br />
<br />
Peak picking in MicrobeMS is always carried out on the basis of original, or pre-processed mass spectra, i.e. the content of existing peak table produced by software packages from other vendors will be ignored. The key idea of peak picking in MicrobeMS is based on two observations. Firstly, it is often convenient to limit the number of peaks per mass spectrum to pre-defined values. Secondly, the analytical sensitivity of MALDI-TOF mass spectrometry is different in different m/z regions: The sensitivity is higher in the low m/z region and lower in the high m/z region.<br />
These two observations are addressed with the procedure described next:<br />
<br />
1. The first step of peak detection in MicrobeMS involves the generation of <br />
a threshold function represented by a S-shaped curve (see sreenshot below)<br />
<br />
[[File:Threshold-for-peak-picking.jpg|500px|thumb|right|Threshold function ''Y(m/z)'' for peak picking]]<br />
<br />
2. The threshold function is a special type of a [https://en.wikipedia.org/wiki/Generalised_logistic_function generalized logistic function].<br />
This function is defined by the following equation:<br />
<br />
Y(m/z) = Y(1) + Y(2)/{1+e^(Y(2)*k/(x-x(1)))}<br />
<!-- :<math>Y(t) = A + { K-A \over (C + Q e^{-B t}) ^ {1 / \nu} }</math> --> <br />
<!-- :<math>\sqrt{1-e^2}</math> --><br />
<br />
Y(m/z) - the intensity threshold function<br />
Y(1) - the minimum intensity with a default value of <br />
2% of the maximum peak intensity<br />
Y(2) - the difference between the maximum peak intensity <br />
and the minimum intensity (Y1) scaled by a factor <br />
delta(cts)<br />
k - slope of the curve at the m/z position <br />
masslow + x(1), x(1) = delta(m/z)<br />
x - the m/z vector (in m/z units) ranging from masslow <br />
to masshigh<br />
x(1) - delta(m/z)<br />
<br />
3. To obtain the peak tables the intensity threshold function <br />
Y(m/z) is automatically obtained on the basis of parameters <br />
indicated in the window ''peak pick parameters''. If the checkbox <br />
''define number of peaks'' is not checked peak tables will <br />
contain only peaks with intensities larger than the threshold <br />
function. Otherwise the threshold function will be iteratively <br />
scaled until the desired number of peaks has been reached.<br />
<br />
When peak picking has been finished a peak table array containing ''npeaks'' rows and ''four'' columns is created (npeaks denotes the number of peaks in the table, see below for a description of the peak table content). Peak tables are automatically added to the respective MS spectra and are displayed at the left side of the main window of MicrobeMS in a listbox below the listbox denoted with ''MicrobeMS spectra ID`s''. Note that existing peak tables may be overwritten without warning when creating new peak tables. Computational details of peak picking routine are available from the command line window if the checkbox ''peak pick verbose mode'' has been activated.<br />
<br />
== Peak picking - the procedure ==<br />
<br />
To produce peak tables from raw mass spectra the following sequence of steps needs to be taken:<br />
<br />
1. Load the mass spectral data files via the [[Load spectra (Bruker format)|load spectra]] (Bruker data file format), <br />
[[Import Mass Spectra in a mzXML Data Format|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.<br />
<br />
2. Perform [[Spectral Pre-processing|spectral pre-processing]]<br />
<br />
3. Select the respective mass spectra in the listbox at the top left corner (the listbox is <br />
labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.<br />
<br />
4. Choose ''Peak pick parms'' (shortcut: <ctrl>+M) from the ''Peak pick'' pulldown menu, or <br />
alternatively, press the button ''more'' in the ''Pick pick'' panel located at the central <br />
bottom of the main figure of MicrobeMS. A window entitled ''peak pick parameters'' comes up.<br />
Modify parameters of peak pick if necessary. When pressing the button ''display'' the intensity<br />
theshold function will be displayed. ''Hide'' removes this function from display. Press ''done'' <br />
to close this window, the values of modified parameters are not lost by this operation.<br />
<br />
5. To start peak picking press the button ''peak'' (''Peak pick'' panel) or select ''find peaks''<br />
(shortcut: <ctrl>+P) from the ''Peak pick'' pulldown menu. In cases where more than one spectrum <br />
has been selected a progress indicator will inform on the status of peak picking.<br />
<br />
== Format of the peak tables ==<br />
<br />
When peak picking has been finished, a peak table array containing ''npeaks'' rows and ''four'' columns is created (npeaks denotes the number of peaks in the table). The peak tables are attached to the spectral data files and contain the following columns:<br />
<br />
* column #1: the m/z positions of the peaks<br />
* column #2: the respective intensity values (intensity units). Note that the intensity values may represent intensities after baseline correction and normalization in cases where peak tables were obtained from pre-processed spectra. <br />
* column #3: weighting factors (''weights''): these factors are obtained by scaling the values of column #2 (in a 1-norm manner) such that the sum of weighting factors contained in a given peak list equals 100. Note that the ratios between the peak intensities are preserved.<br />
* column #4: contains the intensity values of the threshold function (see above) at the m/z positions given by column #1<br />
<br />
See also [[Data_Format_of_Peak_List_Files|Description of the format of peak list files (*.pkf)]]<br />
<br />
== View peak list ==<br />
<br />
This function allows to view and copy peak list data. Press the ''view'' button in the ''Peak pick'' panel tab to view peak list data (see screenshot below). <br />
<br />
{|<br />
|- style="vertical-align:top;"<br />
|[[File:View-peak-list.jpg|350px|thumb|right|View & copy peak list data]]<br />
| style="width:400px;" | &nbsp; <br>To copy the content of the columns ''copy positions [m/z]'' (peak position), ''intensity [AU]'' (peak intensities from original, or pre-processed spectra), and ''weightings [AU]'' (peak weighting factors) check the appropriate checkboxes at the bottom of the window and press ''copy''.<br />
Checkbox ''transpose lists'': Columns are rotated by 90 degrees if checked (i.e. columns are transposed to lines). <br> <br><br />
Checkbox ''copy ANN formatted weightings'': Activate this checkbox to convert weightings into five different intensity values (bins) which can take values of 1 to 5.<br />
|}</div>Laschp