In targeted proteomics, such as SRM / MRM / PRM / DIA applications, groups ofchromatograms need to be analyzed frequently. OpenMS provides several powerfultools for analysis of chromatograms. Most of them are part of the OpenSWATHsuite of tools and are also discussed in the OpenSwath documentation.

Peak Detection¶

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Here, we will focus on a simple example where 2 peptides are analyzed. We willneed 2 input files: the chromatogram files that contains the chromatographicraw data (raw SRM traces or extracted ion chromatograms from PRM/DIA data) aswell as the library file used to generated the data which contains informationabout the targeted peptides:

Here we see that for the first group of transitions (tr_gr1), a single peakat retention time 3119 seconds was found. However, for the second group oftransitions, two peaks are found at retention times 3119 seconds and at3055 seconds.

Visualization¶

We can confirm the above analysis by visual inspection of the chrom.mzMLfile produced above in the TOPPView software:

However, our output above contains more information than only retention time:

Based on the output above, we can infer that the peak at 3055 seconds islikely the correct peak for tr_gr2 since it has a high library dot product(0.95) while the peak at 3119 seconds is likely incorrect for tr_gr2 sinceits dot product is low (0.75). We also see that a peak at 3119 seconds islikely correct for tr_gr1 since it matches well with the expected libraryintensities and has a high dot product (0.99).

Note: to get an overview over all available scores for a particular MRM feature f, you can use

Smoothing¶

Now you may want to show the chromatograms to your collaborator, but you noticethat most software solutions smooth the chromatograms before display. In orderto provide smooth chromatograms, you can apply a filter using pyOpenMS:

Which leads to the following smoothed chromatographic traces:

Chromagraphy is 'the art to compose a drawing by means of lines and geometrical figures and to imitate it with colored materials,' according to Rouget de Lisle.

Technique[edit]

This technique described in 1839 in France, in Paris, exposes a set of methods and of processes to produce tapestries and tissues. It includes the following techniques:

• The printing in black and in color on paper, pattern and tissues,
• The preparation of colors and materials necessary for the draftsmen, for the colourers and the manufacturers of carpet and tapestries, classified according to a chromatic table,
• A manufacturing process of point, innovative in 1839,
• The art to make industrially tapestries comparable to the best tapestries in that time.

Definitions[edit]

Chromagraphie: art to compose a model by means of lines and of geometrical figures, and to imitate it with colored materials. Rouget de Lisle described its process of composition and printing of works in color on paper, pattern and tissues as allowing to save 50% of time with regard to a manual realization.

Chromagraphic Pencil Nc15 Nw20

Etymology[edit]

The word chromagraphy comes from ancient Greek Khrôma which means 'color' and Graphein who means 'writing'. This etymology is comparable to that of the scientific term 'chromatography', appeared only in 1908 and which must not be confused with the chromagraphy of Rouget de Lisle.

History[edit]

The intention of Rouget de Lisle was to create 'a funny and lucrative activity to the ladies and to the artists colourers “by developing the work of the color” by the composition of tasteful models which make them love and look for' and by propagating 'the feeling and the love of the beautiful.'He began to gather and to classify the knowledge of the painters and the manufacturers of tapestries to realize their works of a 'pleasant, economic and complete' way. These works ending in the chromagraphy benefited from the support of big names of the domain in the time, among which the administrator of the royal factory of Tapestries (Manufacture des Gobelins), Mr Lavocat, the director of the dyes of the royal factories, Mr Chevreul, the foreman of the royal factory of tapestries, Mr Deyrolles, with his son, painter of the models of carpet. Rouget de Lisle was himself a pupil of Mr Chevreul.

Principle[edit]

The general principle is to simplify the complete chain leading from a work to its reproduction on another support, as the carpet or the tissue. Rouget de Lisle attempts to refocus the work of the various workers on tasks with values added, as well for the persons as for their productions. He brings a particular attention to the quality throughout the process, in particular on the management of colors and their exact reproductions. He exposes ' the law of the simultaneous contrast ' and the 'chromatic Table' allowing to end in quality printings. He so obtains 200 tints all in all. These 200 tones are codified by a language allowing their fast reproductions during the preparation of tapestries. The drawing of the work to be reproduced completed by the symbols of tints of every points constitutes the chromagraphy. This system reminds the modern description of a computer file of Bitmap type or GIF 8 bits. Rouget de Lisle also integrates signs for the various types of points to be realized.

Example[edit]

Example of Chromagraphy by Rouget de Lisle : (to be done)

One of the tables of signs symbolizing tints: (to be done)

One of the tables of tones according to the rules of the simultaneous constrate exposed(explained) by Rouget de Lisle in his work on the chromagraphie: (to be done)

Notes and references[edit]

Chromagraphics

All the extracts and examples of Rouget de Lisle result from a reproduction of its work published in 1839, on Chromagraphy (see the external references). The chromagraphy in its spirit and its principle gets closer to digital arts appeared since the end of 20th century computer paintings, prints, drawings, etc.). The chain of digital printing from a file of digital image recall the mechanical production line described by Rouget de Lisle, but in a computer and a modern industrial machine, such as a printer, a weaver, etc.

See also[edit]

References[edit]

External links[edit]

Chromagraphics Santa Rosa