Proteomics Data Quality Assessment

Proteomics mass spectrometry data is fundamental to proteomics analysis. The quality of mass spectrometry spectra is closely related to the accuracy of the search analysis results. Therefore, the quality assessment of proteomics data is particularly important. To ensure the reliability of bioinformatics analysis, PTM BIO evaluates the quality of identified proteome data from the following four aspects:

1. Peptide Matching Error Distribution
2. Peptide Count Distribution
3. Peptide Length Distribution
4. Protein Molecular Weight Distribution

1. Analysis of Peptide Matching Error Distribution

The distribution of errors between the actual and theoretical relative molecular weights of all matched peptides is shown in the figure below:

Figure 1 Peptide Matching Error Distribution

2. Analysis of Peptide Count Distribution

The distribution of the number of peptides contained in identified proteins is shown in the figure below:

Figure 2 Peptide Count Distribution

Note: The horizontal axis represents the range of peptide counts, and the vertical axis represents the number of proteins.

3. Analysis of Identified Peptide Length Distribution

The distribution of lengths of identified peptides is shown in the figure below:

Figure 3 Peptide Length Distribution

Note: The horizontal axis represents the distribution of peptide lengths, and the vertical axis represents the number of peptides.

4. Analysis of Protein Molecular Weight Distribution

Figure 4 Protein Molecular Weight Distribution

Note: The horizontal axis represents the range of protein molecular weights, and the vertical axis represents the number of proteins.