Matrix data with quant output
The output of a scan matrix file is trigged by the -q flag in RawTools.
Windows
>RawTools.exe -f [path to raw file to be analyzed] -q -r TMT10
Linux
$mono RawTools.exe -f [path to raw file to be analyzed] -q -r TMT10
MacOS
$mono RawTools.exe -f [path to raw file to be analyzed] -q -r TMT10
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 scan. |
| 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. |
| 126Intensity | The intensity of the mass 126 reporter ion. |
| 126Mass | The observed mass of the mass 126 reporter ion. |
| 126Noise | The noise from the Orbitrap pre-amplifier for the mass 126 reporter ion. |
| 126Resolution | The resolution of the mass 126 reporter ion. |
| 126Baseline | The baseline signal in the quantification scan in the mass 126 repoter ion region. |
The data above are when isobaric tags are present in MS2 scans. If you have used SPS-MS3 for quantification, then the output from -q will be modified slightly. The MS3ScanNumber and MS3IonInjectionTime columns will now be filled with values, and the QuantScanRetTime column will now be based on the SPS-MS3 scan rather than the MS2. As above, when the -u flag is specified, the ParentPeakArea column will be added.