Analysis Reports

Basic Data Acquisition Report

• traditional or targeted mass spectrometry data, e.g., TMS.raw.
  • The raw data should be converted into an open-source format such as MS1/MS2. ThermoRawRead is recommended.

Once finished, TargetWizard will save a report to Output Directroy, and open the report automatically in a web browser.

• html report, e.g., BasicAcquisitionReport.html (example).

The report will show statistics plots of the MS data, including:

• Acquisition Speed
• Activation Center
• Ion Injection Time
• Total Ion Current (TIC), Base Peak Intensity (BPI), Base Peak Mass (BPM)
• …

For many plots, you can change the settings including RT range, barplot bin size, etc. The plot will be updated automatically.

You can also click the legend of a plot to hide or display some items.

Target Selection Report

• target list (multiple formats supported), e.g., TargetWizard.all.TW.target.csv.

Once finished, TargetWizard will save a report to Output Directroy, and open the report automatically in a web browser.

• html report, e.g., TargetSelectionReport.html (example).

The report will show statistics plots of the MS data, including:

• Acquisition Load
• Charge State Distribution
• Mass Distribution
• …

For many plots, you can change the settings including RT range, barplot bin size, etc. The plot will be updated automatically.

You can also click the legend of a plot to hide or display some items.

Target Acquisition Report

• target list (multiple formats supported), e.g., TargetWizard.all.TW.target.csv.
• traditional and targeted mass spectrometry data, e.g., DDA.raw and TMS.raw.
  • The raw data should be converted into an open-source format such as MS1/MS2. ThermoRawRead is recommended.
• (filtered) identification results of targeted mass spectrometry data, e.g., TMS_fdr.pfind.csv.
• optional: precursor list detected by PepPre

Once finished, TargetWizard will save two reports to Output Directroy.

• csv report of all targets, e.g., TMS.target.TargetAcquisitionReport.csv.
• csv report of all PSMs, e.g., TMS.psm.TargetAcquisitionReport.csv.

Max. MS1 Mass Error

mass error used to match targets, PSMs, and MS scans.

FDR Threshold

used to filter PSM list.

MS Sim. Thres.

used to match traditional and targeted MS scans.

Peptide Fragment Ion Coverage Report

• (filtered) identification results of targeted mass spectrometry data, e.g., TMS_fdr.pfind.csv.
• traditional or targeted mass spectrometry data, e.g., TMS.raw.
  • The raw data should be converted into an open-source format such as MS1/MS2. ThermoRawRead is recommended.

Once finished, TargetWizard will save reports to Output Directroy, and open a html report automatically in a web browser.

• html report, e.g., PeptideCoverageReport.html (example).
• csv report including detailed fragment information.

The report will show statistics plots of fragment ion coverage of peptides, including:

• Overall Peptide Coverage Distribution
• Peptide Coverage Distribution of Specific Ion Types
• …

For many plots, you can change the settings including barplot bin size, FDR, etc. The plot will be updated automatically.

You can also click the legend of a plot to hide or display some items.

Target Acquisition Report for Crosslink

• target list (multiple formats supported), e.g., TargetWizard.all.TW.target.csv.
• traditional and targeted mass spectrometry data, e.g., DDA.raw and TMS.raw.
  • The raw data should be converted into an open-source format such as MS1/MS2. ThermoRawRead is recommended.
• (filtered) crosslink identification results of targeted mass spectrometry data, e.g., TMS.plink.csv.
• optional: (filtered) linear peptide identification results of targeted mass spectrometry data, e.g., TMS_fdr.pfind.csv.
• optional: precursor list detected by PepPre
• optional: candidate crosslink list

Once finished, TargetWizard will save two reports to Output Directroy.

• csv report of all targets, e.g., TMS.target.TargetAcquisitionXLReport.csv.
• csv report of all crosslink PSMs, e.g., TMS.crosslink.TargetAcquisitionXLReport.csv.
• csv report of all linear peptide PSMs, e.g., TMS.linear.TargetAcquisitionXLReport.csv.
• csv report of all monolink PSMs, e.g., TMS.monolink.TargetAcquisitionXLReport.csv.
• csv report of all looplink PSMs, e.g., TMS.looplink.TargetAcquisitionXLReport.csv.

Max. MS1 Mass Error

mass error used to match targets, PSMs, and MS scans.

FDR Threshold

used to filter PSM list.

MS Sim. Thres.

used to match traditional and targeted MS scans.

Peptide Fragment Ion Coverage Report for Crosslink

• (filtered) identification results of targeted mass spectrometry data, e.g., TMS_fdr.pfind.csv.
• traditional or targeted mass spectrometry data, e.g., TMS.raw.
  • The raw data should be converted into an open-source format such as MS1/MS2. ThermoRawRead is recommended.

Once finished, TargetWizard will save reports to Output Directroy, and open a html report automatically in a web browser.

• html report for linear peptides, e.g., PeptideCoverageReport.html (example).
• html report for crosslinks, e.g., PeptideCoverageXLReport.html (example).
• csv report including detailed fragment information for linear, monolink, looplink, and crosslink peptides.

The report will show statistics plots of fragment ion coverage of peptide pairs or α/β peptides, including:

• Overall Peptide Coverage Distribution
• Peptide Coverage Distribution of Specific Ion Types
• …

For many plots, you can change the settings including barplot bin size, FDR, etc. The plot will be updated automatically.

You can also click the legend of a plot to hide or display some items.

Comparative Signal-to-Noise Ratio Report for Crosslink

• target list (multiple formats supported), e.g., TargetWizard.all.TW.target.csv.
• two sets of traditional or targeted mass spectrometry data, e.g., DDA.raw and TMS.raw.
  • The raw data should be converted into an open-source format such as MS1/MS2. ThermoRawRead is recommended.
• two sets of (filtered) crosslink identification results of targeted mass spectrometry data, e.g., DDA.plink.csv and TMS.plink.csv.

Once finished, TargetWizard will save two reports to Output Directroy.

• csv report of all targets, e.g., TargetWizard.all.TW.target.NoiseRatioDualXLReport.csv.
• csv reports for each set of crosslink identifications, e.g., DDA.plink.NoiseRatioDualXLReport.csv and TMS.plink.NoiseRatioDualXLReport.csv.