Data quality is a concern in proteomics experiments. In this report, we assess the intrinsic features of the data set at multiple levels.
Table 1. The Design of Experiment
| sample | bioRep | techRep | No. of fraction |
|---|---|---|---|
| 55 | 1 | 1 | 1 |
X!Tandem was used for analyzing the data. Parameters used in the X!Tandem search are shown in Table 2. Protein identifications were inferred from peptide identifications, and each identified protein had at least one associated unique peptide sequence identified at q-value equal or less than 0.01 (equivalent to a 1% FDR). The Occam's razor approach (Nesvizhskii, et al., 2003) was applied to deal with degenerate peptides by finding a minimum subset of proteins that covered all of the identified peptides.
Table 2. The database search parameters
| Item | Value |
|---|---|
| Search engine | X!Tandem |
| Enzyme | NA |
| Fixed modifications | Carbamidomethyl (C) |
| Variable modifications | Oxidation (M) |
| Database | target_decoy.fasta |
| Missed cleavages | 1 |
| Precursor mass error | 10 ppm |
| Fragment mass error | 0.6 Daltons |
This part contains the basic statistics of MS/MS data.
Table 3. Protein identification results for each fraction
| sample | bioRep | techRep | fraction | spectrum_total | spectrum | peptide | protein |
|---|---|---|---|---|---|---|---|
| 55 | 1 | 1 | 5 | 87707 | 208(0.237%) | 105 | 22 |
Summary plot for each technical replicate experiment.
Summary charts for sample: 55, biological: 1, technical: 1.
Figure 1. Missed cleavages chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 2. Precursor ion charge chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 3. Peptide length chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 4. Precursor mass delta (Da) chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 5. Precursor mass delta (ppm) chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 6. Fragment ion mass delta (Da) chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 7. Unique spectrum per protein chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 8. Unique peptide per protein chart for sample: 55, biological replicate: 1, technical replicate: 1.
Figure 9. Protein mass chart for sample: 55, biological replicate: 1, technical replicate: 1.
The common Repository of Adventitious Proteins, cRAP (pronounced "cee-RAP"), is an attempt to create a list of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. The types of proteins included fall into three general classes:
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common laboratory proteins;
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proteins added by accident through dust or physical contact; and
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proteins used as molecular weight or mass spectrometry quantitation standards.
We added the cRAP database in database searching.
Table 4. Identification of contaminant proteins
| Accession | Peptides | Spectrum | Sample | ID | Reason | Class | Description |
|---|---|---|---|---|---|---|---|
| ALBU_BOVIN | 14 | 22 | 55_1_1 | 1 | Reagent and lab contaminant | Laboratory proteins | (P02769) Serum albumin precursor (Allergen Bos d 6) (BSA) |
Reproducibility of total spectra for each fraction
Figure 10. The distribution of the total spectra number
Figure 11. Error bar plot of the total spectra number for each fraction
Reproducibility of identified spectra for each fraction
Figure 12. The distribution of the identified spectra number
Figure 13. Error bar plot of the identified spectra for each fraction
Reproducibility of identified peptides for each fraction
Figure 14. The distribution of identified peptides number
Figure 15. Error bar plot of the identified peptides for each fraction
Reproducibility of identified proteins for each fraction
Figure 16. The distribution of the identified proteins number
Figure 17. Error bar plot of the identified proteins for each fraction
Figure 18. The mass error (Da) of the fragment ions
Figure 19. The mass error (ppm) of the precusor
Figure 20. The mass error (Da) of the precusor
Figure 21. TIC of MS1 distribution
Figure 22. MS1 peak count distribution
Figure 23. MS1 ion count distribution
Figure 24. MS2 peak density distribution
Figure 25. MS2 peak boxplot
Figure 26. MS1 peak count distribution
Figure 27. MS1 peak count distribution
Figure 28. MS1 peak boxplot
