{
  "experimentMode": {
    "name": "AdvancedDS",
    "title": "ADVANCED DEEP SCAN",
    "description": "Combines up to 5 exclusion and inclusion lists with multiple ID injections to comprehensively fragment relevant precursor ions and submits multiple samples.",
    "details": "Combines up to 5 exclusion references into 1 exclusion list per group.\n Combines up to 5 inclusion references into 1 inclusion list per group. \n Injects ID samples until all inclusion list ions are fragmented or user-defined number of ID samples are reached. \n Submits an experiment with several groups.",
    "imgSrc": "Deep_Scan.png"
  },
  "experimentTemplate": {
    "settings": [
      {
        "name": "experimentHeaderImage"
      },
      {
        "name": "selectPycoTemplate"
      },
      {
        "name": "experimentDetails"
      },
      {
        "name": "instrumentMethods"
      },
      {
        "name": "experimentParameters"
      }
    ],
    "injections": [
      {
        "name": "customInjectionsGridAdvancedDs"
      }
    ]
  },
  "experimentConcepts": [
    {
      "experimentParameters": [
        {
          "header": "Experiment Parameters"
        },
        {
          "name": "overrideFactorParameters"
        },
        {
          "name": "exclusionPeakWindowExtension"
        },
        {
          "name": "inclusionPeakWindowExtension"
        },
        {
          "name": "inclusionIntensityFactor"
        },
        {
          "name": "preferredIonsParameters"
        },
        {
          "name": "exclusionTimeParameter"
        },
        {
          "name": "isotopesExclusionList"
        },
        {
          "name": "exclusionListIntensityThreshold"
        },
        {
          "name": "inclusionListIntensityThreshold"
        },
        {
          "name": "mzTolerance"
        }
      ]
    },

    {
      "customInjectionsGridAdvancedDs": [
        {
          "name": "advancedDsInjectionHeaders"
        },
        {
          "name": "advancedDsColumnHeaders"
        }
      ]
    },
    {
      "advancedDsInjectionHeaders": [
        {
          "header": "AcquireX Template Injections"
        },
        {
          "name": "groupDropdown",
          "displayName": "Group #",
          "type": "string",
          "model": 0,
          "errorStatus": false,
          "id": "groupSelect"
        },
        {
          "name": "groupEditBlock",
          "id": "groupEditControl",
          "type": "button",
          "controls": [
            {
              "name": "edit",
              "displayName": "Edit",
              "type": "button",
              "id": "editButton",
              "icon": "fa fa-pencil fa-lg",
              "mode": "Add"
            },
            {
              "name": "delete",
              "displayName": "Delete",
              "type": "button",
              "id": "deleteButton",
              "icon": "fa fa-trash fa-lg",
              "mode": "Add"
            },
            {
              "name": "update",
              "displayName": "Update",
              "type": "button",
              "id": "updateButton",
              "icon": "fa fa-check fa-lg",
              "mode": "Edit"
            },
            {
              "name": "cancel",
              "displayName": "Cancel",
              "type": "button",
              "id": "cancelButton",
              "icon": "fa fa-remove fa-lg",
              "mode": "Edit"
            }
          ]
        },
        {
          "name": "numberOfBlanks",
          "displayName": "Blanks",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 10,
          "model": 0,
          "errorStatus": false,
          "id": "blankInjections"
        },
        {
          "name": "numberOfExclusionReference",
          "displayName": "Excl. Ref",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 5,
          "model": 0,
          "errorStatus": false,
          "id": "exclusionReferenceInjections",
          "details": [
            {
              "description": [
                "Step 1: Sample injection",
                "Step 2: Background ion detection",
                "Step 3: Exclusion list creation"
              ]
            }
          ]
        },
        {
          "name": "numberOfInclusionReference",
          "displayName": "Incl. Ref",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 5,
          "model": 0,
          "errorStatus": false,
          "id": "inclusionReferenceInjections",
          "details": [
            {
              "description": [
                "Step 1: Sample injection",
                "Step 2: Component ion detection",
                "Step 3: Inclusion list creation"
              ]
            }
          ]
        },
        {
          "name": "numberOfDsInjections",
          "displayName": "Deep Scan Inj.",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 30,
          "model": 0,
          "errorStatus": false,
          "id": "dsInjections",
          "details": [
            {
              "description": [
                "Step 1: New method creation from template method using exclusion and/or inclusion lists",
                "Step 2: Sample injection",
                "Step 3: Exclusion and Inclusion list modification from fragmented precursor ions"
              ]
            }
          ]
        },
        {
          "name": "numberOfGroups",
          "displayName": "# Groups to Add",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 25,
          "model": 0,
          "errorStatus": false,
          "id": "numberOfGroups"
        },
        {
          "name": "groupAddBlock",
          "id": "groupAddControl",
          "type": "button",
          "controls": [
            {
              "name": "add",
              "displayName": "Add",
              "type": "button",
              "id": "addButton",
              "icon": "fa fa-plus-circle fa-lg",
              "mode": "Add"
            }
          ]
        },
        {
          "name": "overviewBlock",
          "displayName": "Overview",
          "type": "button",
          "id": "overviewButton",
          "iconOn": "fa fa-pencil-square-o fa-lg",
          "iconOff": "fa fa-th-large fa-lg",
          "iconOnTooltip": "Groups Edit",
          "iconOffTooltip": "Groups Overview",
          "mode": "Overview"
        },
        {
          "name": "numberOfUnknown",
          "type": "array",
          "value": [],
          "id": "unknownInjections"
        },
        {
          "name": "contextMenu",
          "id": "contextMenu",
          "items": [
            {
              "id": "insertAbove",
              "displayName": "Insert Inj Above",
              "icon": "fa fa-arrow-up context-menu-icon",
              "show": true
            },
            {
              "id": "insertBelow",
              "displayName": "Insert Inj Below",
              "icon": "fa fa-arrow-down context-menu-icon",
              "show": true
            },
            {
              "id": "deleteInj",
              "displayName": "Delete Inj",
              "icon": "fa fa-trash-o context-menu-icon",
              "show": false
            },
            {
              "id": "copyDown",
              "displayName": "Copy Down",
              "icon": "fa fa-copy context-menu-icon",
              "show": false
            },
            {
              "id": "fillDown",
              "displayName": "Fill Down",
              "icon": "fa fa-angle-double-down context-menu-icon",
              "show": false
            },
            {
              "id": "undo",
              "displayName": "Undo",
              "icon": "fa fa-undo context-menu-icon",
              "show": false
            }
          ]
        }
      ]
    },
    {
      "advancedDsColumnHeaders": [
        {
          "name": "name",
          "displayName": "Name",
          "type": "String"
        },
        {
          "name": "acquireXSampleType",
          "displayName": "Type",
          "type": "String"
        },
        {
          "name": "groupId",
          "displayName": "Group",
          "type": "String"
        },
        {
          "name": "instMethod",
          "displayName": "Instrument Method",
          "type": "String"
        },
        {
          "name": "vialPosition",
          "displayName": "Vial",
          "type": "String"
        },
        {
          "name": "injVol",
          "displayName": "Inj Vol(ul)",
          "type": "Number"
        },
        {
          "name": "comment",
          "displayName": "Comment",
          "type": "String"
        }
      ]
    },
    {
      "experimentHeaderImage": [
        {
          "src": "Design_Experiment_Deep-Scan.png",
          "type": "image"
        }
      ]
    },
    {
      "experimentDetails": [
        {
          "header": "Experiment Details"
        },
        {
          "name": "storageFolder",
          "id": "storageFolder",
          "model": "",
          "displayName": "Experiment Folder",
          "type": "file",
          "required": true,
          "regex": "experimentFolderRegex",
          "errorMessage": "The Experiment Folder field format is invalid"
        },
        {
          "name": "experimentName",
          "id": "experimentName",
          "model": "",
          "displayName": "Experiment Name",
          "type": "string",
          "required": true,
          "regex": "experimentNameRegex"
        },
        {
          "name": "useNameExtension",
          "id": "useNameExtension",
          "model": false,
          "displayName": "Apply Name Extension",
          "type": "boolean"
        },
        {
          "name": "isDisplayCommentColumn",
          "id": "isDisplayCommentColumn",
          "model": false,
          "displayName": "Display Comment Column",
          "type": "boolean"
        },
        {
          "name": "groupControls",
          "type": "group",
          "controls": [
            {
              "name": "applyToAll",
              "id": "applyToAll",
              "displayName": "Apply To All Groups",
              "type": "button",
              "tooltip": {
                "header": "Apply To All Groups",
                "message": "Applies the below Instrument Methods and Experiment Parameters to all the groups in the experiment."
              }
            },
            {
              "name": "groupsList",
              "id": "groupsList",
              "displayName": "Group #",
              "type": "select"
            }
          ] 
        }
      ]
    },
    {
      "instrumentMethods": [
        {
          "header": "Instrument Methods"
        },
        {
          "name": "groupHeader",
          "id": "groupHeader",
          "displayName": "Group Parameters",
          "type": "header"
        },
        {
          "name": "fullScanMethod",
          "id": "blankMethod",
          "displayName": "Full Scan Method",
          "type": "string",
          "isFullScan": true,
          "needInclusion": false,
          "needExclusion": false,
          "isFragmentType": false,
          "instrumentMethodError": false,
          "model": "",
          "associatedSampleTypeList": [ 1, 2, 4, 7 ],
          "tooltip": {
            "header": "Full Scan Method",
            "message": "The instrument method that the Xcalibur data system uses to generate data for detecting peaks, component-like features, and constant background ions; and to assemble precursor ion exclusion and inclusion lists. Make sure to use an AcquireX template method or that your MS instrument method meets the following criteria:",
            "list": [ "Uses the MS1 Full Scan with a single continuous scan range.", "Turns polarity switching off." ]
          },
          "errorMessage": "The Full Scan Method is not present in the specified path."
        },
        {
          "name": "msnTemplateMethod",
          "id": "mS2Method",
          "displayName": "MSn Template Method",
          "type": "string",
          "isFullScan": false,
          "needInclusion": true,
          "needExclusion": true,
          "isFragmentType": false,
          "instrumentMethodError": false,
          "model": "",
          "associatedSampleTypeList": [ 3, 7 ],
          "tooltip": {
            "header": "MSn Template Method",
            "message": "The instrument method to be combined with precursor exclusion or inclusion lists that an Xcalibur analysis generated using the Full Scan Method. Make sure to use an AcquireX template method or that your MS instrument method meets the following criteria:",
            "list": [
              "(If applicable) Adds the Targeted Mass filter between the MS and ddMS2 scan nodes.",
              "(If applicable) Adds the Targeted Mass Exclusion filter between the MS and ddMS2 scan nodes.",
              "Selects the AcquireX check boxes for the appropriate filters."
            ]
          },
          "errorMessage": "The MSn Template Method is not present in the specified path."
        }
      ]
    }
  ],


  "modeInfo": {
    "method": [
      {
        "name": "0",
        "format": "{blankMethod}"
      },
      {
        "name": "3",
        "format": "{msnMethod}_Excl_Incl_{idString}"
      }
    ],
    "append": [
      {
        "name": "0",
        "boolValue": true
      },
      {
        "name": "3",
        "idNumber": "min:2",
        "boolValue": false
      }
    ],
    "block": [
      {
        "name": "0",
        "idValue": "1"
      },
      {
        "name": "3",
        "idValue": "{idNumber}+1"
      }
    ],
    "sampleId": [
      {
        "name": "0",
        "idValue": "1"
      },
      {
        "name": "3",
        "idValue": "ID {idNumber}"
      }
    ],
    "actions": [
      {
        "name": "0",
        "preValue": "",
        "postValue": ""
      },
      {
        "name": "1",
        "isMatrix": true,
        "preValue": "",
        "postValue": "PostAcquisitionLpeExcAction"
      },
      {
        "name": "2",
        "preValue": "",
        "postValue": "PostAcquisitionLpeIncAction"
      },
      {
        "name": "3",
        "preValue": "DefaultPreAcquisitionAction",
        "postValue": "PostAcquisitionReduceAction"
      },
      {
        "name": "7",
        "preValue": "",
        "postValue": "PostAcquisitionWaitProcessingAction"
      }	  
    ],
    "massListName": [
      {
        "name": "0",
        "ApiValue": ""
      },
      {
        "name": "1",
        "isMatrix": true,
        "ApiValue": "GetName"
      },
      {
        "name": "2",
        "ApiValue": "GetName"
      },
      {
        "name": "3",
        "ApiValue": "GetName,SampleId"
      }
    ],
    "massListNextName": [
      {
        "name": "0",
        "ApiValue": ""
      },
      {
        "name": "3",
        "ApiValue": "GetNextName,SampleId"
      }
    ],
    "name": "AdvancedDs"
  },
  "version": "1.0"
}