11.1 Spectral Quality Control

To evaluate spectral quality, we recommend users to upload both MS1 and MS2 files to general all graphs (Uploading MS2 files only will generate graphs only for MS2 files). Uploading Thermo experiment log file will help generate additional information. Type in purity window size value (AMU) for precursor purity graph, then click the “Submit” button to run quality check tool. When it is complete, a view button will appear. Click “View” to display quality graphs.

Figure 11.1.1: Quality check submit page

When there are more than MS1/MS2 files, the IP2 combines the data and generates an overall distribution of the graphs. To display graphs for each MS1/MS2 files, users need to click the “Show Each” link on top of each graph.

The IP2 provides three different groups of graphs.

• MS1-based graphs

1. precursor purity within isolation window (m/z)
2. precursor charge state
3. precursor m/z
4. precursor M+H+
5. precursor intensity
6. average precursor intensity by retention time

• MS2-based graphs

1. number of MS2 by retention time
2. MS2 base peak intensity
3. average intensity of peaks with S/N > 3 in MS2 scan

• MS1/MS2-based graphs

1. number of MS1 scans
2. number of MS2 scans
3. MS1 ion injection time
4. MS2 ion injection time
5. average MS1 ion injection time by retention time
6. average MS2 ion injection time by retention time
7. number of peaks in MS1 scan
8. number of peaks in MS2 scan
9. average number of peaks in MS1 scan by retention time
10. average number of peaks in MS2 scan by retention time

Figure 11.1.2: Quality graphs for MS1

Figure 11.1.3: Quality graphs for MS2

Figure 11.1.4: Quality graphs for MS1/MS2

Note: At this time, we are expanding quality control tools throughout the IP2 pipeline, such as protein identification, quantification, etc.