Interactive Visualization Views

Target View

• 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 start a web server for user to review each target. (example)

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.

Select Target

View MS Acquisition

Select PSM

View PSM

View XIC of Fragment Ions and Precursor Ion

Target View 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 start a web server for user to review each target. (example)

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.

Select Target

View MS Acquisition

Select PSM

View PSM

View XIC of Fragment Ions and Precursor Ion

Comparative Target View 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.
• optional: two sets of precursor list detected by PepPre
• optional: candidate crosslink list

Once finished, TargetWizard will start a web server for user to review each target. (example)

Max. MS1 Mass Error

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

FDR Threshold

used to filter PSM list.

Select Target

View MS Acquisition

Select PSM

View PSM

Crosslink Site View

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

Once finished, TargetWizard will start a web server for user to review each target. (example)

Additional detailed csv reports are also saved to output directory.

Max. Mass Error

mass error used to match PSMs, and MS scans.

Intensity Thres.

threshold used to split XIC curves.

Smooth Width

used to smooth XIC curves.

Select Crosslink Pair

View MS Acquisition

View PSM

View Fragment Ion

Exhaustive Search View for Crosslink

• candidate crosslink pair list
• (multiple) 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 start a web server for user to review each target. (example)

Max. MS1 Mass Error

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

Select Crosslink Pair

Select MS File

View MS Acquisition

View Candidate MS List

View Candidate PSM