Biochemistry 2DGel-based workflow

This use case is based on the workflow at the dep. of Biochemistry http://www.biokem.lu.se/, where part of the work is done by the Lund Proteomics Resource Centre http://www.proteomics.swegene.lu.se/

Requirements

1. Gel-image (tiff-file)
2. pick-list (text-file)
3. xml-file(s) from picking robot
4. Spectrum files (t2d, ASCII)
5. Peak list files (pkl, ?)
6. Mascot /X!tandem result files

Workflow

1. Analysis of gel and production of pick-list. The pick-list is a tab-delimited file with spot-id, x- and y-coordinates. It would be nice to be able to import volume and if it is up or down regulated. This information is available in another file from the analysis software, usually in matrix-format (redwhite3500with manual master-utan gel7.txt and Volume_Grid_truncated.csv).
2. Robot-picking, digestion and spotting. The robot picks the spots from the gel and after digestion spots the results on a metal target plate. In our case we have a different format of the plate, compared to Proteome center. The file from the robot is a XML-file containing the information about which gel-spot is spotted where on the target plates. This step is also explained in Biochemistry 2DGel-based workflow.
3. Mass spectrometry. The spotted target plate is thereafter taken to our mass-spec. at the dep. of Biochemistry and analyzed using MALDI MS and MALDI-MS/MS. This results in one or many spectrum from each spot on the target plate. Usually one MS-spectra and several MSMS-spectra. The machine vendor format is t2d, which is a binary format, but we have possibility to export these files as ASCII-files also. These are the only raw-files of the spectra. Both MS and MSMS spectra can also be exported in an analyzed form, as peak-lists. But it must also be possible to analyze the spectra with an external program as Piums.
4. Treatment of spectra. Spectra can be processed in many ways to improve quality. Baseline correction, smoothing to mention some. A treated spectra is not a raw-file! Peak-lists can also be treated in many ways to improve quality, filters, clustering to mention some.
5. Protein identification. The spectra, usually peak-lists (Piums takes MS ASCII-raw files), are analyzed with for example Mascot or VEMS. The results are thereafter presented in a report. The report should be a list of gel-spots with related protein identifications. The gel-spots should also be marked on a gel-image. This can often be done by the analysis software used in step 1.