feat(chromatogram extraction): fix and update isolation window target…

… extraction

Now able to extract both precursor and product isolation window target m/z, respectively.

fix #3

README.md

@@ -39,30 +39,42 @@ Data extraction and spectrum filtration have been tested on data acquired from t
    <tr>
       <th>Instrument Vendor</th>
       <th>MS Platform</th>
+      <th>Status</th>
+   </tr>
+   <tr>
+      <td rowspan="4">Bruker</td>
+      <td>EVOQ TQ-MS</td>
+      <td>Not Working</td>
    </tr>
    <tr>
-      <td rowspan="3">Bruker</td>
       <td>ImpactII QToF-MS</td>
+      <td>Working</td>
    </tr>
    <tr>
       <td>solariX MRMS</td>
+      <td>Working</td>
    </tr>
-      <tr>
+   <tr>
       <td>timsTOFPro TIMS-ToF-MS</td>
+      <td>Not Working</td>
    </tr>
    <tr>
       <td rowspan="3">Waters</td>
       <td>XEVOTQXS TQ-MS</td>
+      <td>Working</td>
    </tr>
    <tr>
-      <td>XEVOTQXS DESI-MS</td>
+      <td>XEVOG2XSQTOF DESI-MS</td>
+      <td>Working</td>
    </tr>
       <tr>
       <td>XEVOG2XSQTOF REIMS</td>
+      <td>Working</td>
    </tr>
    <tr>
       <td>SCIEX</td>
       <td>QTRAP6500+ TQ-MS</td>
+      <td>Working</td>
    </tr>
 </table>
 

src/__tests__/initChromatogramArray.test.js

@@ -17,9 +17,10 @@ describe('initChromatogramArray', () => {
       chromatogramType: 'total ion current chromatogram',
       polarity: null,
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
       intensityArray: [],
       msLevelArray: [],
@@ -32,9 +33,10 @@ describe('initChromatogramArray', () => {
       chromatogramType: 'base peak chromatogram',
       polarity: null,
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
       intensityArray: [],
       msLevelArray: [],
@@ -68,9 +70,10 @@ describe('initChromatogramArray', () => {
       chromatogramType: 'extracted ion chromatogram',
       polarity: null,
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
       intensityArray: [],
       msLevelArray: [],
@@ -96,15 +99,18 @@ describe('initChromatogramArray', () => {
     expect(chromatogram[0].dwellTime).toStrictEqual(
       testBasicChromatogram[0].dwellTime,
     );
-    expect(chromatogram[0].isolationWindowTarget).toStrictEqual(
-      testBasicChromatogram[0].isolationWindowTarget,
+    expect(chromatogram[0].precursorIsolationWindowTarget).toStrictEqual(
+      testBasicChromatogram[0].precursorIsolationWindowTarget,
     );
     expect(chromatogram[0].collisionType).toStrictEqual(
       testBasicChromatogram[0].collisionType,
     );
     expect(chromatogram[0].collisionEnergy).toStrictEqual(
       testBasicChromatogram[0].collisionEnergy,
     );
+    expect(chromatogram[0].productIsolationWindowTarget).toStrictEqual(
+      testBasicChromatogram[0].productIsolationWindowTarget,
+    );
     expect(chromatogram[0].timeArray).toStrictEqual(
       testBasicChromatogram[0].timeArray,
     );
@@ -139,15 +145,18 @@ describe('initChromatogramArray', () => {
     expect(chromatogram[3].dwellTime).toStrictEqual(
       testTargetedChromatogram[3].dwellTime,
     );
-    expect(chromatogram[3].isolationWindowTarget).toStrictEqual(
-      testTargetedChromatogram[3].isolationWindowTarget,
+    expect(chromatogram[3].precursorIsolationWindowTarget).toStrictEqual(
+      testTargetedChromatogram[3].precursorIsolationWindowTarget,
     );
     expect(chromatogram[3].collisionType).toStrictEqual(
       testTargetedChromatogram[3].collisionType,
     );
     expect(chromatogram[3].collisionEnergy).toStrictEqual(
       testTargetedChromatogram[3].collisionEnergy,
     );
+    expect(chromatogram[3].productIsolationWindowTarget).toStrictEqual(
+      testTargetedChromatogram[3].productIsolationWindowTarget,
+    );
     expect(chromatogram[3].timeArray).toStrictEqual(
       testTargetedChromatogram[3].timeArray,
     );

src/__tests__/parseMZML.test.js

@@ -254,22 +254,19 @@ describe('parseMZML', () => {
     expect(await parseMZML(testConfigParam));
   });
 
-  // ! Uncovered Lines - extractChromatogram.js line 55, 62, 79, 105
-  // Line 55 - Assignation of value (mappedValue || paramValue) works but don't know why it doesn't pick up in test
-  // Line 62 - userParamMap array check with the test data is always false
-  // Line 79 - isolationWindowMap.cvParam array check with the test data is always false
-  // Line 105 - binaryData.cvParam array check with the test data is always true
+  // ! Uncovered Lines - extractChromatogram.js line 91-92, 125-126
+  // Test data only consist of isolationWindowTarget for the mappedKey (Both precursor and product data)
 
-  // ! Uncovered Lines - extractSpectrum.js line 69, 107, 147, 161
+  // ! Uncovered Lines - extractSpectrum.js line 69, 107, 150, 165
   // Line 69 - spectrumData.cvParam array check with test data is always true
   // Line 107 - scanWindowMap.cvParam array check with test data is always true
-  // Line 147 - activationMap.cvParam array check with test data is always true
-  // Line 161 - binaryData.cvParam array check with the test data is always true
+  // Line 150 - activationMap.cvParam array check with test data is always true
+  // Line 165 - binaryData.cvParam array check with the test data is always true
 
   // ! Uncovered Lines - filterSpectra.js line 97-108, 115-117, 127-136
-  // Line 95-106 - Calculation of mass accuracy if m/z falls within range works, but don't know why it doesn't pick up in test
-  // Line 112-114 - Assignation of new basePeakIntensity and basePeakMZ works, but don't know why it doesn't pick up in test
-  // Line 124-133 - Pushing chromatogram data based on spectrum data filtering works, but don't know why it doesn't pick up in test
+  // Line 95-108 - Calculation of mass accuracy if m/z falls within range works, but don't know why it doesn't pick up in test
+  // Line 115-117 - Assignation of new basePeakIntensity and basePeakMZ works, but don't know why it doesn't pick up in test
+  // Line 127-136 - Pushing chromatogram data based on spectrum data filtering works, but don't know why it doesn't pick up in test
 
   // ! Fail to catch decoder() input type error - Code won't reach: decoder.js line 15, 17, 19, 21, 23-24
   // If decoder() throws an error - it is caught and handled within parseMZML()

src/__tests__/typedef.test.js

@@ -194,9 +194,10 @@ describe('typedef', () => {
         chromatogramType: 'total ion current chromatogram',
         polarity: null,
         dwellTime: null,
-        isolationWindowTarget: null,
+        precursorIsolationWindowTarget: null,
         collisionType: null,
         collisionEnergy: null,
+        productIsolationWindowTarget: null,
         timeArray: [0.0031, 0.0052, 0.0074],
         intensityArray: [996, 1346, 50390],
         msLevelArray: [1, 1, 2],
@@ -209,9 +210,10 @@ describe('typedef', () => {
         chromatogramType: 'base peak chromatogram',
         polarity: null,
         dwellTime: null,
-        isolationWindowTarget: null,
+        precursorIsolationWindowTarget: null,
         collisionType: null,
         collisionEnergy: null,
+        productIsolationWindowTarget: null,
         timeArray: [0.0031, 0.0052, 0.0074],
         intensityArray: [370, 390, 38150],
         msLevelArray: [1, 1, 2],
@@ -281,9 +283,14 @@ describe('typedef', () => {
     expect(testData.chromatogram[0]).toHaveProperty('chromatogramType');
     expect(testData.chromatogram[0]).toHaveProperty('polarity');
     expect(testData.chromatogram[0]).toHaveProperty('dwellTime');
-    expect(testData.chromatogram[0]).toHaveProperty('isolationWindowTarget');
+    expect(testData.chromatogram[0]).toHaveProperty(
+      'precursorIsolationWindowTarget',
+    );
     expect(testData.chromatogram[0]).toHaveProperty('collisionType');
     expect(testData.chromatogram[0]).toHaveProperty('collisionEnergy');
+    expect(testData.chromatogram[0]).toHaveProperty(
+      'productIsolationWindowTarget',
+    );
     expect(testData.chromatogram[0]).toHaveProperty('timeArray');
     expect(testData.chromatogram[0]).toHaveProperty('intensityArray');
     expect(testData.chromatogram[0]).toHaveProperty('msLevelArray');

src/typedef/index.mjs

@@ -61,9 +61,10 @@
  * @property {?string} chromatogramType Chromatogram type
  * @property {?string} polarity Polarity
  * @property {?number} dwellTime Dwell time
- * @property {?number} isolationWindowTarget Isolation window target
+ * @property {?number} precursorIsolationWindowTarget Precursor isolation window target
  * @property {?string} collisionType Collision type
  * @property {?number} collisionEnergy Collision energy
+ * @property {?number} productIsolationWindowTarget Product isolation window target
  * @property {[]|number[]} timeArray Retention time array
  * @property {[]|number[]} intensityArray Intensity array
  * @property {[]|number[]} msLevelArray MS level array

src/utils/extractChromatogram.js

@@ -23,6 +23,7 @@ export async function extractChromatogram(configParam, chromatogramArray) {
     const cvParamMap = chromatogramData.cvParam;
     const userParamMap = chromatogramData.userParam;
     const precursorMap = chromatogramData.precursor;
+    const productMap = chromatogramData.product;
     const binaryDataArrayMap =
       chromatogramData.binaryDataArrayList.binaryDataArray;
 
@@ -34,9 +35,10 @@ export async function extractChromatogram(configParam, chromatogramArray) {
       chromatogramType: null,
       polarity: null,
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
       intensityArray: [],
       msLevelArray: [],
@@ -49,8 +51,8 @@ export async function extractChromatogram(configParam, chromatogramArray) {
       : [cvParamMap];
     for (const cvParam of chromatogramCvParam) {
       const mappedKey = keyMap[cvParam.$name];
-      let paramValue = cvParam.$value;
       const mappedValue = valueMap[cvParam.$name];
+      const paramValue = cvParam.$value;
       if (mappedKey) {
         data[mappedKey] = mappedValue || paramValue;
       }
@@ -63,8 +65,9 @@ export async function extractChromatogram(configParam, chromatogramArray) {
         : [userParamMap];
       for (const cvParam of userCvParam) {
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          data[mappedKey] = paramValue;
         }
       }
     }
@@ -80,8 +83,13 @@ export async function extractChromatogram(configParam, chromatogramArray) {
         : [isolationWindowMap.cvParam];
       for (const cvParam of isolationWindowCvParam) {
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          if (mappedKey === 'isolationWindowTarget') {
+            data.precursorIsolationWindowTarget = paramValue;
+          } else {
+            data[mappedKey] = paramValue;
+          }
         }
       }
 
@@ -92,8 +100,30 @@ export async function extractChromatogram(configParam, chromatogramArray) {
       for (const cvParam of activationCvParam) {
         const mappedKey = keyMap[cvParam.$name];
         const mappedValue = valueMap[cvParam.$name];
+        const paramValue = cvParam.$value;
+        if (mappedKey) {
+          data[mappedKey] = mappedValue || paramValue;
+        }
+      }
+    }
+
+    // Product data
+    if (productMap) {
+      const isolationWindowMap = productMap.isolationWindow;
+
+      // Isolation window parameters
+      const isolationWindowCvParam = Array.isArray(isolationWindowMap.cvParam)
+        ? isolationWindowMap.cvParam
+        : [isolationWindowMap.cvParam];
+      for (const cvParam of isolationWindowCvParam) {
+        const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = mappedValue || cvParam.$value;
+          if (mappedKey === 'isolationWindowTarget') {
+            data.productIsolationWindowTarget = paramValue;
+          } else {
+            data[mappedKey] = paramValue;
+          }
         }
       }
     }

src/utils/extractSpectrum.js

@@ -69,8 +69,8 @@ export async function extractSpectrum(
       : [spectrumData.cvParam];
     for (const cvParam of spectrumCvParam) {
       const mappedKey = keyMap[cvParam.$name];
-      let paramValue = cvParam.$value;
       const mappedValue = valueMap[cvParam.$name];
+      let paramValue = cvParam.$value;
 
       if (mappedKey) {
         if (mappedKey === 'basePeakMZ') {
@@ -107,8 +107,9 @@ export async function extractSpectrum(
       : [scanWindowMap.cvParam];
     for (const cvParam of scanWindowCvParam) {
       const mappedKey = keyMap[cvParam.$name];
+      const paramValue = cvParam.$value;
       if (mappedKey) {
-        data[mappedKey] = cvParam.$value;
+        data[mappedKey] = paramValue;
       }
     }
 
@@ -125,8 +126,9 @@ export async function extractSpectrum(
         : [isolationWindowMap.cvParam];
       for (const cvParam of isolationWindowCvParam) {
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          data[mappedKey] = paramValue;
         }
       }
 
@@ -136,8 +138,9 @@ export async function extractSpectrum(
         : [selectedIonMap.cvParam];
       for (const cvParam of selectedIonCvParam) {
         const mappedKey = keyMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = cvParam.$value;
+          data[mappedKey] = paramValue;
         }
       }
 
@@ -148,8 +151,9 @@ export async function extractSpectrum(
       for (const cvParam of activationCvParam) {
         const mappedKey = keyMap[cvParam.$name];
         const mappedValue = valueMap[cvParam.$name];
+        const paramValue = cvParam.$value;
         if (mappedKey) {
-          data[mappedKey] = mappedValue || cvParam.$value;
+          data[mappedKey] = mappedValue || paramValue;
         }
       }
     }

src/utils/initChromatogramArray.js

@@ -19,9 +19,10 @@ export async function initChromatogramArray(configParam) {
       chromatogramType: 'total ion current chromatogram',
       polarity: null,
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
       intensityArray: [],
       msLevelArray: [],
@@ -34,9 +35,10 @@ export async function initChromatogramArray(configParam) {
       chromatogramType: 'base peak chromatogram',
       polarity: null,
       dwellTime: null,
-      isolationWindowTarget: null,
+      precursorIsolationWindowTarget: null,
       collisionType: null,
       collisionEnergy: null,
+      productIsolationWindowTarget: null,
       timeArray: [],
       intensityArray: [],
       msLevelArray: [],
@@ -55,9 +57,10 @@ export async function initChromatogramArray(configParam) {
         chromatogramType: 'extracted ion chromatogram',
         polarity: null,
         dwellTime: null,
-        isolationWindowTarget: null,
+        precursorIsolationWindowTarget: null,
         collisionType: null,
         collisionEnergy: null,
+        productIsolationWindowTarget: null,
         timeArray: [],
         intensityArray: [],
         msLevelArray: [],