Matrix data output
The output of a scan matrix file is trigged by the -p flag in RawTools.
Windows
>RawTools.exe parse -f [path to raw file to be analyzed] -p
Linux
$mono RawTools.exe parse -f [path to raw file to be analyzed] -p
MacOS
$mono RawTools.exe parse -f [path to raw file to be analyzed] -p
The output file should resemble the image below when opened in Excel. The image is truncated due to size.
The data can be interpreted as described below. By default, RawTools outputs scan data for all triggered MS2 scans.
| Name | Description |
|---|---|
| MS3ScanNumber | The index number of the MS3 scan associated with the listed MS2 scan (if an MS3 method was used). |
| MS2ScanNumber | The index number of the MS2 scan. |
| MS1ScanNumber | The index number of the MS1 scan that the MS2 scan was triggered from. |
| QuantScanRetTime | The retention time in minutes of the current MS2 or MS3 scan (if an MS3 method was used). |
| ParentScanRetTime | The retention time in minutes of the MS1 scan that triggered the current MS2 scan. |
| Duty Cycle | The amount of time in seconds required to complete the duty cycle where the current MS2 scan was acquired. |
| MS2ScansPerCycle | The number of MS2 scans triggered by the MS1 scan where the current MS2 was triggered from. |
| ParentIonMass | The m/z of the parent mass for the current MS2 scan. |
| MonoisotopicMass | The monoisotopic mass of the parent ion for the current MS2 scan. |
| PrecursorCharge | The charge state of the parent ion for the current MS2 scan. |
| ParentPeakFound | A TRUE or FALSE indicator of whether a peak for the parent mass was found by RawTools when looking in prior and following MS1 scans. |
| PeakFirstScan | The first MS1 scan index where the parent mass for the current MS2 scan is observed. |
| PeakMaxScan | The MS1 scan index where the maximum parent ion peak intensity for the current MS2 scan was observed. |
| PeakLastScan | The last MS1 scan index where the parent mass for the current MS2 scan is observed. |
| BaseLinePeakWidth(s) | The peak width in seconds at baseline for the parent mass corresponding to the current MS2 scan. |
| PeakParentScanIntensity | The intensity of the parent ion in the MS1 scan where it triggered the MS2 event. |
| PeakMaxIntensity | The max intensity of the parent ion across the MS1 scans where it is observed. |
| MS1IonInjectionTime | The time in milliseconds used for ion injection for the MS1 scan corresponding to triggering the current MS2 scan. |
| MS2IonInjectionTime | The time in milliseconds used for ion injection for the MS2 scan. |
| MS3IonInjectionTime | The time in milliseconds used for ion injection for the MS3 scan corresponding to the current MS2 scan. |
| HCDEnergy | If HCD was used, this value corresponds to the NCE setting used for the current MS2 scan. |
| MS1MedianIntensity | Median intensity of all ions observed in the MS1 scan that triggered the current MS2 event. |
| MS2MedianIntensity | Median intensity of all ions observed in the current MS2 scan. |
The parse command can also be used in combination with the '-u' flag to add precursor area quantification to the output.
Windows
>RawTools.exe parse -f [path to raw file to be analyzed] -pu
Linux
$mono RawTools.exe parse -f [path to raw file to be analyzed] -pu
MacOS
$mono RawTools.exe parse -f [path to raw file to be analyzed] -pu
Using the -u flag will trigger the addition of a new column in addition to those above.
| Name | Description |
|---|---|
| ParentPeakArea | The calculated area-under-the-curve of the parent peak. |