Description

This track shows peptide to spectra maps (PSMs) from mass spectrometry data.

The Id of each track can be interpreted by splitting the string on each pipe symbol "|". The fields are:

1. Annotation type
2. Search data base
3. Conitg/ Plasmid Id
4. Experiment name
5. Scan number _ match number

Display Conventions and Configuration

The colours of the mass spectrometry data corresponds with the reading frame of the PSM:

•  Red  + strand 1 frame
•  Blue  + strand 2 frame
•  Green  + strand 3 frame
•  Purple  - strand 4 frame
•  Orange  - strand 5 frame
•  Turquoise  - strand 6 frame

Methods

The samples derive from a mixed culture of 8 bacteria (SIHUMIx) Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Clostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655) and Lactobacillus plantarum (DSMZ 20174). The data set comprise 166 independent measurements, of which 90 used a standard protein preparation protocol and the remaining 76 cover different enrichment protocols to elevate the level of small proteins in solution.

Comet (2019.01 rev. 4) was used to generated PSMs. The search algorithm ran against a 6frame data base of the whole genome which was generated by getorf of the EMBOSS suite. To generate bed files from the resulting output a script was used which is available under github.

Credits

Data were processed at the Bioinformatic Institute of Leipzig. For inquiries, please contact us at the following address: john (at) bioinf.uni-leipzig.de

References

The full details of the sample preparation can be found in Petruschke et al. and Schäpe et al..

The full data set is publicly available via ProteomeXchange with identifier PXD023243.