Looking at your data

All 4 blue channel spectra: SX target (SXT); SX sky/FPE (SXS), DX target (DXT), DX sky/FPE (DXS); are recorded on the blue CCD and all 4 red channel spectra on the red CCD. The spectral formats on the blue and red channel images are flipped about the X-axis with respect to one another because of the field lens which transmits one and reflects the other. On the blue CCD, the DX spectra are on top of the SX spectra but on the red CCD, the SX spectra are on top of the DX ones. 

From Strassmeier et al 2015, the spectral formats on the CCD’s for each of the cross dispersers can be depicted as follows, where the CD is indicated with a roman numeral in the lower right of each:

This diagram only depicts a single slice, and the square box outlines the CCD.

In the screenshots below, a few notable features are pointed out to help orient observers to the data:

1. 1. For example, when observing with the Red channel CD5, Halpha is visible in the 6th order from the bottom.  The atmospheric O2 ‘B’ band is located near the middle. Note that in the red channel, the bluer to redder wavelengths appear from bottom to top.
      
   2. With the red channel CD6 (right image below), the O2 ‘A’ band is located in the 3rd order from the bottom. The Ca triplet is in the 4th, 5th, and 6th orders from the top.
      
   3. When observing with CD3 (left image above) in the blue channel, the blue to red wavelengths appear from top to bottom.

 

PEPSI uses a MOSAIC CCD with 16 amplifiers. The fiber’s different core diameters and their respective image slicers set the three different nominal resolutions of the spectrograph (50,000, 130,000 and 250,000). Each fiber head is actually a pair of fibers. A fiber pair consists of an off-axis sky fiber or FPE (SXS and DXS) and an on-axis target fiber (SXT and DXT).  The target fiber is positioned on-axis, the other one is off-axis and receives light by a sky position 6 arcsec away from the target.
Below is an example of a ThAr with the D200 with the 4 fibers labeled zoomed in.  The D200 fiber corresponds to 5 slice image slicer:

When observing with the D100, the fiber cross-section would be broken into 7 slices instead of 5:

On-sky images do suffer from Amplifier glow/artifacts.  These have been found to calibrate out.

The Fits Image Browser GUI and Viewer can be used during observing for quick data quality assessments. As images are read out they are listed in the FITS Image Browser.  The latest PEPSI RED and BLUE images are automatically displayed in the Viewer.  This Viewer contains a number of tools for basic data quality assessment.  Images can be added and analyzed from the “FITS Images Browser”.

Select the spectrum (highlighted with teal colour) you want to look at from ‘FITS Image Browser‘ with Enter or click the arrow icon to send it to ‘Spectrum viewer‘. One can also look at multiple spectra by selecting them and clicking the double arrow icon.

Note that when adding images, they will appear in the active window in the Spectrum Viewer (not necessarily in the red and blue orientation.  The active window in ‘Spectrum Viewer ‘ has a cyan frame. Select the area you want to look at closer by drawing a red box with, for example, a mouse. To see a summed spectrum from a selected area Press ‘Enter‘, or Click the normal ‘Sigma‘ icon (one-dimensional cross-cut in the horizontal direction) on top of the viewer (the other sigma makes it in the vertical direction)

Additional details about the functions and use of the Fits Image Browser can be found here.