Quality Control

This operation performs Quality Control on Peak Lists.

Usage

You can execute this operation by clicking the button or following the menu Analysis/Peak List Quality Control.

A dialog will appear allowing you to select the following options:

• Peak Lists: previously loaded Peak Lists. You can choose between Labeled or Unlabeled Peak Lists.
• Intra-sample alignment method: Forward algorithm or MALDIquant.
  If you choose the Forward algorithm, you also have to set:
  • Tolerance type: PPM (Points per million), Absolute or Relative. Default is PPM.
  • Tolerance value: tolerance used together with the tolerance type to consider two peaks the same. Default is 300.
  • Reference type: First, Median, Last, Average, Average up or Average down. Default is Average (AVG).
  If you choose MALDIquant, you also have to set:
  • Tolerance value: tolerance used to consider two peaks the same. Default is 0.002.



Peak List Quality Control dialog

 

Output and visualization

As a result of this operation, a new Quality Control Result is added to the clipboard. Every time a new Quality Control Result is accessible, it can be inspected with the Quality Control View.

This view presents to tabs: the samples tab, with information relative to the samples, and the replicates tab, with information relative to the replicates.

The samples tab has one data table and two chart tabs: the global analysis and the sample analysis. If the Peak Lists used are Labeled, there will be a third chart tab called Labels analysis.
The data table has as many rows as samples. For each sample row, it presents the following columns:

• Sample: the name of the sample.
• Class: if available, the label of the sample.
• Spectra: number of spectra (replicates) contained in the sample.
• Min. Mass: minimun m/z value present in the sample.
• Max. Mass: maximum m/z value present in the sample.
• Min. Masses: minimum number of peaks of the spectrum with less peaks in the sample.
• Max. Masses: maximum number of peaks of the spectrum with less peaks in the sample.
• Avg. Masses: average number of peaks of the spectra in the sample.
• Std. Dev.: standard deviation of the number of peaks of the spectra in the sample.
• POPXX: where XX is a percentage of the number of spectra. Count of the number of peaks with Percentage of Presence (POP) XX.
• Align. Masses: count of masses that have been matched across the spectra in the sample.
• Split >= XX: percentage of masses that have a POP higher or equal to XX.
• Count >= XX: count of masses that have a POP higher or equal to XX.

The global analysis chart tab presents a box plot where the Count >= XX columns are the categories.




Global analysis chart


The labels analysis chart tab presents a box plot where the Count >= XX columns are the categories and moreover, there is one serie per label in the data set.




Labels analysis chart


The sample analysis chart tab presents a box plot where each sample is a serie. For a given sample, its vector of values is constructed from the POPXX columns. Let a Sample A have POP20 = 2, POP40 = 1, POP60 = 3, POP80 = 2 and POP100 = 1, its serie data will be {20, 20, 40, 60, 60, 60, 80, 80, 100}.



Samples analysis chart

The replicates tab has one data table and chart two tabs: the global analysis and the replicates analysis. If the Peak Lists used are Labeled, there will be a third chart tab called Labels analysis.
The data table has as many rows as replicates in the data set. For each replicate row, it presentes the following columns:

• Spectra: the name of the spectra.
• Sample: sample which the spectra belongs to.
• Class: if available, the label of the spectra.
• Masses count: number of peaks of the spectra.
• Min. Mass: minimum m/z value present in the spectra.
• Max. Mass: maximum m/z value present in the spectra.
• Min. Int.: minimum intensity value present in the spectra.
• Max. Int.: maximum intensity value present in the spectra.
The global analysis chart tab presents two box plots. The former has the Masses count as a single category and the second one has the Min. Mass and Max. Mass columns as categories.




Global analysis chart


The labels analysis chart tab is equal to the global analysis chart with one addition: it has one serie per label in the data set.




Labels analysis chart


The replicates analysis chart tab is the same as the sample analysis chart with the difference that here there is one serie per replicate instead of one serie per sample.



Replicates analysis chart

Export results

You can export the data tables by clicking the right-corner button of the tables () and choosing the "Export to CSV" option. You can find more information about this at section Export results.

You can also select the entire table (by pressing keys CTRL+A) or a specific range of cells and copy its contents by pressing keys CTRL+C. Then, you can paste this information in any other programs such as calc sheets or text editors, either pressing keys CTRL+V or the software specific options.

You can export charts by right-clicking on them and then selecting the "Save as.." option. A dialog will appear allowing you to select the file to save the chart.