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Importing a sample list

Importing a Sample List

Import a sample list
  • My Work > double-click an analysis > Acquire tab
You can import a sample list from a Microsoft Excel document.
To ensure an imported list maps correctly, columns must assume the same column names as the Sample list. Only then can Excel files transfer to the UNIFI software.
Rules:
  • The column names in the Excel spreadsheet must match the column names that you specified when you configured the Sample list in the Analysis Method.
  • Column names are case-insensitive.
  • If the Excel spreadsheet does not include all the columns in the Sample list, the UNIFI software populates the columns with the default values specified in the Analysis Method.
  • If the Excel spreadsheet includes extra columns that do not exist in the Sample list, the UNIFI software prompts you to continue.
  • The first line of the Excel spreadsheet is a header row.
  • You can import an unlimited number of rows.
  • Some values that you add in the sample list are restricted and flagged if they fall outside the allowed parameters.
To import a sample list from an Excel file:
  1. Click File > Import sample list.
  2. Select an Excel sample list with the file extension .xls or .xlsx, and then click OK.
Result: The sample list includes the imported information.

Import files for reuse

Import Files for Reuse

Import files for reuse

  • UNIFI Main Menu > View my work

You can import files from other applications for reuse. After importing, if you delete the files from your computer, you can restore them from UNIFI software when you want to work with them again.

You can import files from a variety of applications. For most files you import, the import process creates two copies of the file: a copy of the file in its original format for storage, and a second copy of the file in a UNIFI format that is suitable for reuse. To help you differentiate between these copies, UNIFI software classifies each copy as a specific data type, and then lists the type in the Item Type field in the Explorer Folder Contents table.

Types of files you can import:

Application File type Import results in Explorer
Adobe Acrobat

4.0-9.0

 .pdf A single PDF copy of the file for storage, restoration, and viewing as a report. UNIFI software classifies the file as an Adobe Acrobat File Data data type.

Rule: Although you can view the file as a report in the Report Viewer, you cannot use the file to create a report extraction method. For imported PDF files, UNIFI software classifies the file item type as Adobe Acrobat File Data. In a report extraction method, you can only use files that are assigned the Report item type. To determine the item type of a file, in the Explorer Folder Contents table, see the value in the Item Type column.
Microsoft Word

2003, 2007, 2010

 

 .doc.docx

.docm

.dot

.dotx

.dotm

 

 Two copies of the file in these formats:

Microsoft Word file, for storage and restoration. UNIFI software classifies the file as a File Data data type.

PDF file, for viewing as a report. UNIFI software classifies the file as a Report data type.

Requirement: To create the report copy, Microsoft Word must be installed on the computer; otherwise, one copy of the file is imported for storage and restoration.
Microsoft Excel

2003, 2007, 2010

 .xls.xlsx

.xlsm

.xlt

 

 Two copies of the file in these formats:

Microsoft Excel file, for storage and restoration. UNIFI software classifies the file as a File Data data type.

PDF file, for viewing as a report. UNIFI software classifies the file as a Report data type.

Tip: If the file contains multiple spreadsheets, each spreadsheet appears as a separate page in the report.

Requirement: To create the report copy, Microsoft Excel must be installed on the computer; otherwise, one copy of the file is imported for storage and restoration.
Waters MassLynx 4.1 .raw folder containing raw data files For each set of folders you import, copies of the folders in these formats:

A file data group containing all of the folders for storage and restoration. UNIFI software classifies the group as a File Data Group data type.

A sample set containing all of the files in the folders as injection data for analysis and processing. UNIFI software classifies the set as a Sample Set data type.

Tip: To reduce the amount of file storage, you can choose to create the sample set only.
Waters MassLynx 4.1 .spl sample list file For each set of folders you import, copies of the folders in these formats:

A file data group containing all of the folders for storage and restoration. UNIFI software classifies the group as a File Data Group data type.

A sample set containing all of the files in the folders as injection data for analysis and processing. UNIFI software classifies the set as a Sample Set data type.

Tip: To reduce the amount of file storage, you can choose to create the sample set only.

During the import process, some application file properties are also imported for viewing in Explorer. Before you import files, in the file applications, modify these file properties, or ensure that information is contained in the properties, so that you can more easily find the files after you import them into UNIFI software. For example, in Microsoft Office files, you can modify properties such as the author and title of a document. For instructions on how to modify file properties, consult the file’s source application documentation.

The following table lists the application file properties that get imported into UNIFI software, the UNIFI fields that you must add to display the imported properties, and the UNIFI field categories where you can find the fields to add them to the Folder Contents table. To view the file properties in UNIFI software, you must add the UNIFI field columns that display imported file properties to the view that is applied to the table.

Application file properties imported into UNIFI fields:

Application Imported file property UNIFI field that displays the file property UNIFI category under which to find the field to add to the table
Adobe Acrobat File

Author

PDF Producer

Subject

 Name (application)

User (application)

Producer (application)

Description

 File Data

File Data

File Data

Common Fields
Microsoft Word* Author

Comments

Subject

 User (application)

Remark

Description

 File Data

Common Fields

Common Fields
Microsoft Excel* Author

Comments

Subject

 User (application)

Remark

Description

 File Data

Common Fields

Common Fields
Waters MassLynx Acquired Name**

Acquired Data**

Injection Volume**, ***

Job Code

Sample Description

Sample ID**

Sample Type**

User Name**

Bottle Number**

 Item Name

Acquired Date (application)

Injection volume

Remark

Description

Sample ID

Sample type

User (application)

Well position

 Common Fields

File Data

Sample Data

Common Fields

Common Fields

File Data

Sample Data

File Data

Sample Data
* Imported file properties are displayed only when viewing the File Data item type copies that were created for storage and restoration.

** Property is displayed only when viewing the data set content for the selected File Data Group or Sample Set item types.

*** Injection volume from the experimental record.

Before you import files, keep this information in mind:

  • To import a file into a folder, you must have access to the folder. During the import process, if a problem occurs accessing the folder (for example, another user deletes the folder or revokes your access to the folder), UNIFI software imports the file into the Review Required folder, where it remains until you move it to a different folder.
  • If you import password-protected files, you must enter the file passwords so that UNIFI software can create report copies of the files. When you restore the files to your computer, the files are restored with their original settings, and will be password-protected again in their source applications. Depending on the type of file you import, these are how the files are treated in UNIFI software:
    • If you select Adobe Acrobat files to import, the password is required to import the files. Once the file is imported, you will be required to enter the password to open the report in UNIFI software.
    • If you select Microsoft Office files to import, the password is only required if you want to create report copies of the files. If you do not enter the file passwords, only one copy of each file is created, in its original format, for storage and restoration. If UNIFI software creates report copies of the files, you do not need to enter the file passwords to open the reports in UNIFI software.
  • Close files before you import them, otherwise the import process can fail.
  • If a power failure or system reboot occurs as you import files into UNIFI software, the importation can be successful, even when you do not receive a notification stating so. On the Folder Contents table toolbar, click Refresh to check if the files are present.
  • Delete unnecessary files from the Windows\Temp or %TEMP% folder before importing documents into UNIFI to avoid slowing the down process.
  • When you import UNIFI data into UNIFI software, ensure all the instrument drivers for the instruments defined in the associated method are present. Restart the UNIFI portal, if required, to update the current settings. This ensures the instrument configuration values are successfully imported.
  • When you import a Microsoft Word document into UNIFI software, it is stored in the database as a .doc and a .pdf file. If you export the .pdf file (as a .uep file) and then re-import it into UNIFI software, the file name extension for document shown in the Set name column in Explorer changes from .doc to .pdf. The change in the file name extension does not change the functionality of the captured or imported files.

Requirements:

  • Your role must include the Export/Import Data permission
  • Do not use the œfast user switchingfeature when importing documents

To import data files from other applications:

  1. On the My Work tab, in the Tasks pane, click Import Data From File System.
  2. On the Import File Data tab, select the type of data file you want to import.
  3. If you select MassLynx data, type a name and description to describe the data folders.
  4. If you select MassLynx SPL data, type a description to describe the data folders and select the check box to create a separate sample set for each SPL file you import.

Tip: UNIFI software creates sample sets with the names of the SPL files you import. If you choose not to create a separate sample set for each sample list you import, UNIFI software creates a single sample set with the name of the first SPL file in the Selected files list.

  1. Click Select Files, and then select the files you want to import while keeping these guidelines in mind:
    • To select Waters MassLynx .raw data folders, select the folders, and then click the Select .RAW Folders button.
    • To select Waters MassLynx .spl files, select the files, and then click Open.
    • To select Microsoft Office files, at the bottom of the file selection box, select the file type, and then select the files you want to import.
    • To remove selected files from the import list, right-click the files, and then click Remove Selections.
  2. In the Import Location list, select the folder into which you want to import the files, and then click Import.

Result: To verify that the files were successfully imported, on the Explorer tab, select the folder in which you imported the files. If the folder is already open, on the Folder Contents table toolbar, click Refresh to view the imported report. Because file processing times can vary, a delay can occur before you see the files in the table.

Export results for additional analysis

Export Results for Additional Analysis

Export results for additional analysis
  • My Work > double-click an analysis > Review tab> File menu > Save and mark for export
  • Alternative: My work > double-click an analysis > Acquire tab> Run Samples dialog box
You can export data to perform additional processing steps in other applications. When you mark an analysis for auto export, UNIFI software exports the analysis, as a .uep file, to a folder location specified by the export selected items automatically folder policy. This folder policy also specifies the frequency, such as every four hours, that items are exported. Typically, folder policies are configured by a system administrator.
Tip: UNIFI software exports only the analysis, which contains the analysis method and results. The sample set is not included.
Recommendation: To receive notifications of items that were exported automatically to your inbox, subscribe to the “Item exported automatically” action in the Data Management category.

 

 To export results:
Perform one of the following actions:
  • If you want to review the results before you export the analysis, on the Review tab, review the results, and then click File > Save and mark for export.
  • If you know that you want to export the analysis before you acquire data, on the Acquire tab, click Start, and then click the “Include results in automatic export” check box.
The status of an export appears in the “Auto Export Status” column in Explorer.

 

Exporting filtered results from the Review tab
You can export results from the Review tab to other file formats:
  • HUPO PSI Mass spectrometry data format (.mzml)
  • Mascot generic format (.mgf)
  • Microsoft spreadsheet (.xls)
  • Prosight PTM (.puf)
  • Waters Labelled column spectra (.lcs)
  • Waters Peak list (.pkl)
Requirement: Ensure Microsoft Excel or Microsoft Access Database Engine 2010 (32-bit) is installed on the application/database server or workstation before you export a report to a worksheet.
To export filtered results:
  1. On the Review tab, in the Analysis Center, format the Component Summary table to include the data that you want to export.
Important: If you add columns and leave them in the order in which UNIFI software places them, or if you deleted a column, the exported view matches the current view. Nevertheless, if you change the position of columns, the new order is not preserved on export until the view is saved (as part of a workflow), and the analysis is closed and then reopened.
  1. On the tool bar above the Component Summary table, click File, and then select Export filtered results.
  2. In the Export Options dialog box, select the file format, and select the path to export the data.
  3. Select these check boxes (where available for the format):
  • Overwrite existing path
  • Include header row
  • Include units row
  1. Click OK.

Setup and Use Watson LIMS Integration

Setup and Use Watson LIMS Integration

Set up Watson LIMS
  • Administration > External Resources
For UNIFI Network configurations, you can set up Watson LIMS configuration so that users can import sample lists from LIMS into UNIFI software and export results from UNIFI software to LIMS. When you create a LIMS configuration, you select the sample keys that display to users when they select a sample list to import.
See also: UNIFI System Administrator’s Guide, Appendix B
Requirement: Your role must include the Create and modify LIMS configurations permission.
To create a new LIMS configuration:
  • Log on to UNIFI software.
  • Click Administration > LIMS configuration.
  • On the LIMS Configuration page, click Create.
  • On the General Tab of the Configuration Detail page, enter a name and description for the LIMS configuration.
Requirement: Do not select the Disable Import check box. When you want to remove the LIMS configuration, you can select this check box to prevent users from importing sample information into UNIFI software.
  • On the Custom Tab of the Configuration Detail page, enter the connection information.
Requirement: The connection information in the Custom tab must match the settings specified in the Forms Agent page of Watson LIMS Integration Manager application.
  • Type the Forms Agent Web Service URL. The FormsAgent1 Attributes dialog box in Integration Manager identifies the External Service URL.
  • In the Sample Lists IP Object Code field, type WORKLIST_TO_FORM.
  • In the Results IP Object field, type Import Object.
  • Click Test.
Result: If UNIFI can connect to LIMS, the “Connected successfully!” message appears. In the event that the connection was unsuccessful, ensure that the web service URL matches the External Service URL specified in the Forms Agent page of Watson LIMS Integration Manager application.
  • In the Sample List Keys tab of the Configuration Detail page, select the common, analytical-run assay field names. These sample list keys relate to meta data which is exported from the LIMS analytical run and are used to automatically generate UNIFI analysis name. Use the Up and Down buttons to change the order of the sample keys. (The order of selected sample keys defines the order of list and is used as a name for the new analysis.)
  • In the Result Data tab of the Configuration Detail page, select Response or both Response and Observed RT for the analysis results that will be exported to LIMS using this configuration.
Tip: UNIFI software only allows users to send Response and/or Observed RT results to LIMS.
  • Click Save.
Export sample data to Watson LIMS
You can export sample data to Watson LIMS, a laboratory-information management system that facilitates bio-analytical studies in drug development. Watson LIMS sends a sample list to UNIFI software, which runs the analysis, after which you can export the results back to Watson LIMS.
To export sample data to Watson LIMS:
  • In the Show list on the toolbar, click Folder content.
  • In the filter field below the Item Type heading, type Sample Set.
  • Right-click the analysis that you want to export, and then click Export to > LIMS.
Restriction: The Export to LIMS option is available only for analyses containing samples imported from a laboratory information management system.
  • On the Export to LIMS page, verify that the analysis details are correct, and then click Export.
Result: “Export successful” appears at the bottom of the page.
  • Open Watson LIMS.
  • Select the Run ID of the analytical run assay that matches the analysis you exported from UNIFI, and then click Import.
  • In the Instrument Parameters dialog box, from the Value column, select Watson<<Results>>.
  • From the Value column, select the analysis, and then click OK.
Tip: Match the sample list key information to the analytical run assay information.
  • To find the correct imported results in Watson LIMS, select the “Import file name” column on the “Analytical run actions” page.
Tip: NaN indicates that the value is “not a number” and that no result was found.
When you export an analysis from UNIFI software and import its results into Watson LIMS, the date and time of the export must match those of the import. You can easily identify the date an analysis was exported by creating a view for exported results in Explorer.

Import a Scientific Library

Import a Scientific Library

The scientific library is a repository of scientific information that you can use when creating or modifying analysis methods. Importing information into thelibrary from many sources saves time during method development. For example, you can import information when you want to copy a custom library from one UNIFI system to another. (In such a case, UNIFI software creates a new, custom library in the scientific library.) You can also import information from other sources, such as chemical catalogs or a third-party database of compounds.
You can import the following types of files into the scientific library.

File types for library import:

Import file type Examples Additional information on import format
UNIFI library container file A library exported from another UNIFI system, such as a .ulc file.

The following libraries are read-only, .ulc files, protected by a license:

  • Waters Pesticide Library
  • Waters Glycan GU Library
  • Waters Toxicology Library
  • Waters Traditional Medicine Library
  • Waters Natural Products Synthetic Compound Adulteration Library
 If an item tag in the .ulc file does not exist in the library, the tag is created on import.

If a library is protected by a license, the license key is included in the .ulc file. If the corresponding license is not installed in the UNIFI system, then the protected library or items cannot be imported.

UNIFI 1.8 libraries cannot include acquired data. If you import a licensed library from UNIFI version 1.6 or 1.7 that includes acquired data, then the data are saved in a separate, custom library as they are imported. The custom library contains only library item names and acquired data.
UNIFI 1.0 or 1.5 library file Library items exported from UNIFI 1.0 or 1.5 as a .zip file. The .zip file is converted to a .ulc file on import.

Human Metabolome database file

 Files downloaded from the The Human Metabolome Database (HMDB), a freely available, electronic database containing detailed information about small-molecule metabolites found in the human body. See the Human Metabalome Project for more information (www.hmdb.ca). Files in .sdf format provide structure, name, and mass.

To associate metadata with structures, include a metabocard.txt file in the same folder as the .sdf file. The following tags are imported from the metabocard file:

  • Compound ID (added to library item identifiers)
  • Taxonomy (added to library item tags)
  • References (added to library item references)
  • IUPAC name (added to library item IUPAC name)
  • Synonyms (added to library item synonyms)
  • Secondary ID (added to library item synonyms)

LipidMAPS database file

 Files downloaded from the LIPID MAPS (Lipid Metabolites and Pathways Strategy) consortium library of lipids. See the LIPID MAPS Lipidomics Gateway, for more information (www.lipidmaps.org). Files in .sdf format provide structure, name, and mass. The following tags are also imported from the .sdf file:

  • Systematic name (added to library item IUPAC name)
  • Compound ID (added to library item identifiers)
  • Lipid maps classification (added to library item tags)
  • Synonyms (added to library item synonyms)
SDF file Any SDF file that contains a sequence of chemical structures in MOL file format with a list of text properties for each chemical structure. Files in .sdf format must use the same field definitions as HMDB files or LipidMAPS files.
Spreadsheet file Spreadsheet files created manually in programs such as Microsoft Excel or created for exchanging information with other scientific applications, for example, chemical databases, MassLynx software and MacCoss Lab Skyline.

Two spreadsheet formats for .xls or .xlsx files are valid:

  • Tof Screening, used for creating Tof Screening and 2D Quantify Tof methods. It includes detection results containing formulas, masses, adducts, and fragments.
  • Quandrupole MRM, used for creating Small Molecule and Peptide Quantify MRM methods. It includes optimization results containing masses, cone voltage, collision energy, and labels.
 Requirement: Files must be in the correct format. See “Format a spreadsheet file for library import”.

 

Requirements:

  • To import a library, your role must include the Create Scientific Library permission.
  • To import a third party library, such as the Waters Pesticide Library, Waters Toxicology Library, Waters Traditional Medicine Library, or Waters Glycan GU Library, you must have a license for the library on the target UNIFI system.
  • To import a library that includes new tags or synonyms that will be created in the scientific library, your role must include the Configure Scientific Library permission.
  • To import an Excel file, if Excel is not installed on the target system, the Microsoft Access Database Engine 2010 Redistributable (32-bit version) must be installed on the UNIFI server.

To import a library:

  1. From the Scientific Library home page, click Import library items.
  2. In the Import Files pane, from the Type of import list, select the type of file that you want to import.
  3. From the “File to import” box, browse to the file that you want to import.
  4. In the “Library to create” box, enter a name for the imported library.Tip: If the library name that you enter already exists, the Import function creates a new library with a number appended to the library name.
  5. For spreadsheet files,
    • From the “Detection results” list, select the ionization mode for the data.
    • Click Verify.

    Result: A report opens, listing any format issues that you should resolve before you import the file.

  6. Click Import.

Format a Spreadsheet for Scientific Library Import

Format a Spreadsheet for Scientific Library Import

You can import spreadsheet files created manually in programs such as Microsoft Excel or files created for exchanging information with other scientific applications, for example, chemical databases, MRM transition lists exported from MassLynx software or MacCoss Lab Skyline software. Importing information from these sources into the scientific library can save time when you develop methods.

Before you import content from a spreadsheet file to a library, the headers must be in the correct format, to ensure that the information maps correctly. The correct format ensures that the spreadsheet files transfer to UNIFI software. Two spreadsheet file formats are valid:
  • Tof screening, for mass-fragment data, in the form of detection results.
  • Quadrupole MRM, for MRM data, in the form of optimization results.
You can use the Verify function to confirm that the spreadsheet file is in the correct format before you import it. The function produces a report that includes the following information:
  • Details of items that are valid for import.
  • Any item tags or synonym types created during import.
  • Details of any items or columns not in the correct format.
Rules:
  • The first row of the worksheet is a header row and is not imported.
  • Header-row column names are not case sensitive and spaces are ignored.
  • If a column name is empty or preceded by $$, the column is ignored.
  • Each row subsequent to the header row corresponds to a library item.
  • If the item name and isotope are not specified for a row, the row is ignored.
  • If a particular item name is identical for contiguous rows, the rows are imported as one library item. All the item’s details are adopted from the first contiguous row labeled with that item’s name.
  • If the item name and isotope are identical for contiguous rows, the rows are imported as one detection result in the library item.
  • Noncontiguous rows labeled with the same item name are imported as separate library items.
  • You can import an unlimited number of rows.
  • Each row of the worksheet can include the name of a MOL file, which contains the chemical structure. The structure file must be in the same directory as the spreadsheet file. When you import the spreadsheet file, all MOL files in the directory are also transferred to the server.
Important: To import spreadsheet files that are in the correct format for UNIFI version 1.6 or 1.7, you must rename the columns referring to the tables below.
The following table lists headers and descriptions of the information that you can enter into a spreadsheet before you import it.

Column headers valid for all spreadsheet import files:
First row header item Description
Item Name Name of library item (required). Synonyms can be defined in this column by enclosing them in curly brackets. Alternatively, add synonyms in the Synonym column.
Item type Item type determines the properties available in the library. If the item type is empty for a row, the default item type “Compound” is specified.
Formula Chemical formula, from which molar mass and monoisotopic mass are calculated.
Peptide Peptide sequence, from which molar mass and monoisotopic mass are calculated. If used, the item type is specified as “Peptide Sequence”.
Structure Name of chemical-structure file, in MOL file format. If the structure file exists, then the formula is calculated from the structure file, and the sum formula specified in the Formula column is ignored.
IUPAC Name IUPAC synonym for the library item.
Description Description of the library item.
Retention Time If used, must be a number greater than 0. Retention time is added to the detection results for the library item.

Alternative column headings “Observed RT” or “RT” are also valid.
Instrument model Instrument model is added to the details of the detection result for the library item.
Instrument Serial No Instrument serial number is added to the details of the detection result for the library item.
Comment Comments are added to the details of the detection result for the library item.
Adduct If the column is included, any adducts that you specify must be defined in the UNIFI software’s list of adducts. The polarity you select for the ionization mode determines the default adduct, +H or -H. If you do not specify an adduct, the default adduct is used in the detection result for the library item.
Observed CCS If used, must be a number greater than 0. Collision cross-section is added to the detection results for the library item.

Alternative column headings “CCS” or Cross collision section” are valid.
Charge Charge state for the detection result.

Alternative column heading “Charge state” is also valid.
Synonym Synonyms which are not specified as a special type. For additional synonyms, each column must have a different header beginning with “Synonym”, for example, Synonym 1, Synonym 2, Synonym abc, Synonym common.
Synonym “identifier name” Identifiers for the library item. The identifier name must appear within quotation marks in the column header. For example, Synonym “ChemSpider”, Synonym “LipidMAPS”.
Synonym “synonym type” Synonyms with an assigned type are verified against the synonym type. The synonym type must appear within quotation marks in the column header. For example, Synonym “German name”.

If the synonym type does not exist in the scientific library, it is created when you import the spreadsheet file.
Item tag “Tag path” Item tags identify library items by use or class. You can specify the tag as a sub-tag of another item tag by separating the tags by means of a forward slash. For example, Pesticide/herbicide/amide herbicide/chloroacetanilide herbicide.

For additional tags, each column must have a different header beginning with “Item tag”, for example, Item tag 1, Item tag 2, Item tag abc.

You can optionally include the hierarchy for the tag in the column header. The hierarchy must appear within quotation marks, with the tags separated by a forward slash. For example, Item tag “Pesticide/Insecticide”. If an entry in the column also includes a tag hierarchy, then the two paths are combined.

If the item tag does not exist in the scientific library, if the tag is defined as a sub-tag of an existing item tag, then the new sub-tag is created when you import the spreadsheet file.
Isotope Precursor value for a detection result. If used, the precursor value is not calculated using the monoisotopic molar mass of library item, adduct and charge.

Tof screening format

When you import spreadsheet files in Tof screening format, detection results are created for the imported library items.
Column headers valid for spreadsheet (Tof screening format) import files only:
First row header item Description
Cone voltage low Low cone voltage, for fragmentation experiments.

Alternative column heading “CV low” is valid.
Cone voltage high High cone voltage, for fragmentation experiments.

Alternative column heading “CV high” is valid.
Collision voltage low Low collision voltage, for fragmentation experiments.

Alternative column heading “CE low” is valid.
Collision voltage high High collision voltage, for fragmentation experiments.

Alternative column heading “CE high” is valid.
Observed RCCS Relative collision cross-section, for ion mobility experiments.
Observed drift Drift time, for ion mobility experiments.
Fragmentation type Specify one of these following fragmentation types:

  • Unknown
  • CV – Cone voltage, applies energy in the instrument source to fragment ions.
  • CID – Collision induced dissociation, applies energy stepwise in the collision cell to fragment ions.
  • ETD – Electron transfer dissociation, ions fragment through a chemical process.
  • SID – Surface induced dissociation, applies energy in the collision cell to accelerate ions into a surface and cause fragmention.
  • Trap – For dual collision cell systems, CID in the first collision cell.
  • Transfer – For dual collision cell systems, CID in the second collision cell.
  • TAP – Time aligned parallel fragmentation, for dual collision cell systems, CID in both collision cells.
  • None – Not a fragmentation experiment.

If the column is not included, or the cell is empty, the default-value CID is used for the detection results.
Fragment This column and additional columns contain the high energy m/z values for detection results. Each column must have a different header beginning with “Fragment”, for example, Fragment 1, Fragment 2, Fragment 3, Fragment abc, Fragment XYZ.

Alternative column headings F1, F2, F3, F4, F5, Frag1, Frag2, Frag3, Frag4 and Frag5 are also valid.

Tips:

  • You can add a comment to this column by enclosing it in curly brackets. Alternatively add a comment using the Fragment Comment column.
  • To use m/z values from a MassLynx screening .xls file, you must account for the mass of an electron. For example, in positive ion mode, subtract 0.0005 Da from a MassLynx mass; in negative ion mode, add 0.0005 Da to a MassLynx mass.
  • For contiguous rows with identical item names, fragments are added to separate detection results.
  • Fragments in the same row are added as peaks in a single detection result.
  • If no formula is specified for the row, no precursor is added to the detection result.
  • If no formula or peptide sequence is specified for the row, no mass values except fragment-expected ones are added to the detection result.
Fragment formula This column, and additional columns, contain the sum formula for high-energy fragments. For example, FragmentFormula 1, FragmentFormula 2, FragmentFormula 3, and so on. Mass values are calculated from each chemical formula and added to the detection results.
Ion ratio This column, and additional columns, contain the ratio of fragment ion intensity to precursor ion intensity for high-energy fragments. For example, Ion ratio F1, Ion ratio F2, or Ion ratio Frag1, Ion ratio Frag2, and so on. The ion ratio value must be greater than 0. The ion ratio is added to the corresponding fragment in the detection results.
Ion ratio tolerance This column, and additional columns, contain the percentage of the expected ion ratio within which the observed ion ratio must occur for a fragment to be identified. For example, Ion ratio tolerance F1, Ion ratio tolerance F2, or Ion ratio tolerance Frag1, Ion ratio tolerance Frag2, and so on. The ion ratio tolerance is added to the corresponding ion ratio in the detection results.
Fragment comment Add a comment about a fragment. Use this column as an alternative to using curly brackets to add a comment within a fragment column.

When a spreadsheet row includes multiple fragment columns, you can add a comment for each fragment.

Examples:

  • To add a comment to the column Fragment 1, use the column heading Fragment Comment 1.
  • To add a comment to the column Fragment abc, use the column heading Fragment Comment abc.
  • To add a comment to the column F1, use the column heading Fragment Comment F1.
  • To add a comment to the column Frag1, use the column heading Fragment Comment Frag1.
Peptide fragment This column, and additional columns, contain the peptide sequence for a fragment.

When a spreadsheet row includes multiple fragment columns, you can add a peptide sequence for each fragment.

Examples:

  • To add a peptide sequence to the column Fragment 1, use the column heading Peptide Fragment 1.
  • To add a peptide sequence to the column Fragment abc, use the column heading Peptide Fragment abc.
  • To add a peptide sequence to the column F1, use the column heading Peptide Fragment F1.

 

 

 

 

 

 

 

 

 

 

Example of Tof screening format spreadsheet file for import:
example-of-tof-screening-format-spreadsheet-file
Library item created from Tof screening format .xls import:
 example-of-tof-screening-format-xls-import

Quadrupole MRM format

When you import spreadsheet files in Quadrupole MRM format, optimization results are created for the imported library items.

Column headers valid for spreadsheet (Quadrupole MRM format) import files only:

First row header item Description
Cone voltage Cone voltage for the MRM transition (required).

Alternative column heading “CV” is valid.
Precursor Mass (m/z) of the precursor ion (required).
Precursor label Peak description for the precursor ion.
Collision Collision energy for the MRM transition (required).

Alternative column heading “Collision energy” is valid.
Product Mass (m/z) of the product ion (required).
Product label Peak description for the product ion.
MRM comment Adds a comment to the MRM transition in the detection results.
Priority When you import library items to a Quantify Assay analysis method, if the ion mode you select has more than one MRM transition, the priority determines the order of the transitions that are imported. When you specify a priority of 1 the transition is the highest priority and is imported as the first transition.

If used, you must specify an integer value.

Alternative column heading “prio” is valid.

Spreadsheet formats for importing Skyline .csv files

Skyline software is a third-party tool that provides the ability to manage and predict peptide MRM transitions. You can use it as a source of peptide information to create 2D QuanTof and 2D Quan MRM analysis methods that support the quantification of peptides.

You can use Skyline software to export MRM transition lists as .csv files from several LC/MS data systems, including MassLynx software. You can open the .csv file in Microsoft Excel, and then save it as an .xls or .xlsx file for import into the scientific library. You can convert the file to either of the valid spreadsheet file formats (Tof or Quadrupole MRM) by using the appropriate column headers.

The following example shows a .csv file exported from Skyline software, the recommended changes to the column headers required for import as a Quadrupole MRM spreadsheet file, and a library item resulting from the import.

Tips:

  • In the example, the columns Itemtag “Protein” (used to record the name of the protein), RT, and precursor label charge are optional changes to the spreadsheet file.
  • Use $$ change a column to a comment, which is not imported to the scientific library.
  • For large numbers of file conversions, use an Excel macro to change the column headers.
Example of a .csv file exported from Skyline software:

excel_import_csv

Recommended column header changes for import as a Quadrupole MRM spreadsheet file:

excel_import_csv_reformatted

Library item created from .xls import:

excel_import_library_item_skyline

LIMS Configuration

LIMS Configuration

Before you begin

You can process and report UNIFI® analysis results using Watson LIMSTM. You can import a Watson LIMS-generated analytical run into UNIFI software and use it as a sample list for an analysis. You can export the analysis results back into the analytical run, to enable processing and reporting of those results in Watson LIMS. Before you can perform these actions, you must configure UNIFI software to recognize Watson LIMS.

Prerequisites:

  • Thermo Fisher personnel installed Watson LIMS on a computer other than the UNIFI server.
  • If the application/database server is in a different domain than that of the LIMS server, ensure that the date and time-stamps are synchronized to a time server. In a Windows® Server 2012 R2-based domain, the domain controllers are automatically configured as time servers for the domain.
  • You or a Waters Service Engineer can access the Watson LIMS Integration ManagerTM Admin Client and Watson LIMS Integration Manager Service Manager applications.See also: These Thermo Scientific guides and their associated release notes:
  • Integration Manager 3.0 Administration Guide, Revision A
  • Integration Manager 3.0 Watson Agent Configuration Guide, Revision A
  • Integration Manager 3.0 Forms Agent Configuration Guide, Revision A
  • Integration Manager 3.0 Installation and Configuration Guide, Revision A
  • Integration Manager 3.0 Web Service Agent Configuration Guide, Revision A

Configure Watson LIMS to work with UNIFI software as follows:

  • Configure a Watson agent as instructed in the Integration Manager 3.0 Watson Agent Configuration Guide, Revision A.
  • Configure a Forms Agent as instructed in the Integration Manager 3.0 Forms Agent Configuration Guide, Revision A.
  • Connect the import IPO from the Watson agent to an export IPO on the forms agent by means of an interface and interface map.
  • Record the external interface URL for the Forms Agent.

Result: UNIFI interface software reads the LIML sent by Watson from the URL and IPO specified in the Forms Agent.

  • Using the Forms and Watson agents previously created, create an interface and interface map from an IMPORT IPO on the forms agent to an Export IPO on the Watson agent. These interface maps transfer data pushed into the forms agent URL (to the Unique Import IPO) to the Watson agent where it is queued for import.
  • Add instrument interface to Watson LIMS.
  • Update instrument parameter file.

Configuring Watson agent

Watson agents connect the Integration Manager and the Watson LIMS via the Watson IM Gateway.

You must perform these tasks to create and configure a Watson agent:

  • Create a new Watson agent, using the IM Service Manager as specified in the Watson Agent Configuration Guide, Revision A.
  • Configure the Watson agent, using the IM Administration as specified in the Watson Agent Configuration Guide, Revision A.

Configuring Forms agent

You must configure the Forms agent, as specified in the Integration Manager 3.0 Forms Agent Configuration Guide, Revision A.

The Forms agent contains the external service URL.

Requirement: Record the external service URL. You must specify this value when you configure LIMS in UNIFI software.

You must add a new integration point to export analytical assays into UNIFI software.

To configure Forms agent to work with UNIFI software:

  1. Open Integration Manager and then click System Configuration > Configure Agents.
  2. On the Integration Manager Form Agents tab, select FormsAgent1, and then click Attributes.Result: The FormsAgent1 Attributes dialog box lists the External Service URL value.

    forms-agent-attributes

  1. Add a new Integration Point Object by performing these steps:
  • Right-click Forms Agent 1 > New Integration Point.
  • In the New dialog box, enter “Export to UNIFI” for the name, an optional description, and then click OK.
  1. For these items, keep the default values as specified in the Forms Agent Configuration Guide, Revision A.
  • Forms Interaction Worklist Object and its attributes.Tip: When you configure LIMS in UNIFI software, you must enter the Integration Point Object Code (WORKLIST_TO_FORM) in the Sample Lists IP Object Code field of the Custom Tab in the Configuration Detail page.
  • Import Object and its attributes.Tip: When you configure LIMS in UNIFI software, you must enter the Import Object name (Import Object) in the Results Object field of the Custom Tab in the Configuration Detail page.

Creating an interface for the Integration Manager

After the Watson agent and Forms agent are configured correctly, you must connect the import IPO from the Watson Agent to an export IPO on the Forms agent by means of an interface and interface map. You must create and map an Integration Manager interface between Watson LIMS and UNIFI software and UNIFI software and Watson LIMS.

See also: Thermo Scientific Integration Manager 3.0 Administration Guide, Revision A

To create and map an IM interface between Watson LIMS to UNIFI software:

  1. Open Integration Manager, and then click System Configuration > Manage Interfaces.
  2. From the Interfaces page, right-click an empty area of the tree view pane, and then select Add New Interface.
  3. In the New Interface wizard page, enter “Watson to UNIFI” for the name, leave the description blank, and then click Next.
  4. Select Integration Points, and then click Next:
  • For Integration point 1 select “Watson” on agent WatsonAgent1
  • For Integration point 2, select “Export to UNIFI” on agent FormsAgent1
  1. Specify “30 seconds” as the Polling Interval and Unit and then click Next.
  2. Enter the following values, click Add Map, and then click Finish.

Interface map values:

Name Properties
Name Watson to UNIFI_Map1
Description Leave blank
Interface map code Leave blank
IP 1 Object Sequence
IP 2 Object Form Interaction Worklist Object

To create and map an IM interface between UNIFI software and Watson LIMS:

  1. Open Integration Manager, and then click System Configuration > Manage Interfaces.
  2. From the Interfaces page, right-click an empty area of the tree view pane, and then select Add New Interface.
  3. In the New Interface wizard page, enter “UNIFI to Watson” for the name, leave the description blank, and then click Next.
  4. Select Integration Points and then click Next:
  • For Integration point 1 select “Export to UNIFI” on agent FormsAgent1.
  • For Integration point 2, select “Watson” on agent WatsonAgent1.
  1. Specify “30 seconds” as the Polling Interval and Unit, and then click Next.
  2. Enter the following values, click Add Map, and then click Finish.

Interface map values:

Name Properties
Name UNIFI to Watson_Map
Description Leave blank
Interface map code Leave blank
IP 1 Object Form Interaction Worklist Object
IP 2 Object Sequence

Adding instrument interface to Watson LIMS

You must create an instrument interface to export your analytical run assays to use in software. You can make the sample tray of the instrument interface specific to your instrument system. You can create multiple instrument interfaces for other sample trays and titer plates.

To add a new instrument interface:

  1. Log on to Watson LIMS.
  2. Click Options > Instrument Interface.
  3. In the Add Instrument Interface dialog box, enter the following values, and then click Save.

    Instrument interface values:

    Name Properties
    Instrument Name Enter a name that describes your instrument configuration and include the word “UNIFI” in the name.

    Example: UNIFI Interface 48 Position Plate.
    Assay Type LC/MS
    Data Import Type Raw and Concentration
    Number of Rows Enter the number of rows in a sample tray or titer plate.

    Example: Enter 6 for a 48-position vial tray.
    Number of Columns Enter the number of columns in a sample tray or titer plate.

    Example: Enter 8 for a 48-position vial tray.
    Sequence File Yes
    Interface type Gateway
    Gateway Executable IM Gateway

    Add instrument interface dialog box:

    add-instrument-ui

Updating the instrument parameter file

When you create a new instrument interface, you must update the IM Instrument Parameters file to include the name of the newly created instrument interface (UNIFI Interface 48 Position Plate in the previous example) and the corresponding WatsonAgentURL (Integration Manager connection). If you do not update this file, an error message informs you that the new instrument interface is missing and that the Watson agent cannot read the Watson Agent URL.

To update the IM Instrument Parameters File:

  1. Browse to Program Files\Thermo\Watson directory, and open the IMInstrumentParameters.XML file in Notepad.
  2. Add these lines to this file:<Instrument InstrumentName=”UNIFI Interface 48 Position Plate”><!–where “UNIFI Interface 48 Position Plate” equals the name of the newly created instrument interface–><Parameter ParameterName=”WatsonAgentURL” ParameterRequired=”Y”>

    <Value ParameterValue=”soap.tcp://10-162-35-25.:50006/WatsonAgent1″/>

    </Parameter>

    </Instrument>

 

Creating new LIMS configuration in UNIFI software

Requirement: Your role must include the Create and modify LIMS configuration permission.

To create a new LIMS configuration:

  1. Log on to software.
  2. Click Administration > LIMS configuration.
  3. On the LIMS Configuration page, click Create.
  4. On the General Tab of the Configuration Detail page, enter a name and description for the LIMS configuration.Restriction: Do not select the Disable Import check box. When you want to remove the LIMS configuration, you can select this check box to prevent users from importing sample information into UNIFI software.
  1. On the Custom Tab of the Configuration Detail page, enter the connection information.Requirement: The connection information in the Custom tab must match the settings specified in the Forms Agent page of Watson LIMS Integration Manager application.
  • Type the Forms Agent Web Service URL. The FormsAgent1 Attributes dialog box in Integration Manager identifies the External Service URL.
  • In the Sample Lists IP Object Code field, type WORKLIST_TO_FORM.
  • In the Results IP Object field, type Import Object.custom-tab
  1. Click Test.Result: If UNIFI software can connect to LIMS, the “Connected successfully!” message appears. If the connection is unsuccessful, ensure that the Web service URL matches the External Service URL specified in the Forms Agent page of Watson LIMS Integration Manager application.
  1. In the Sample List Keys tab of the Configuration Detail page, select the common, analytical-run assay field names. These sample list keys relate to metadata exported from the LIMS analytical run, which are used to automatically generate UNIFI analysis name. Use the Up and Down buttons to change the order of the sample keys. (The order of selected sample keys defines the order of list and is used as a name for the new analysis.)

    sample-list-keys

  1. On the Result Data tab of the Configuration Detail page, select Response, or both Response and Observed RT, specifying analysis results for export to LIMS using this configuration.

    result-data

  1. Click Save.

Creating an analysis for LIMS

After you configure the LIMS interface, you can create an analysis to be used by LIMS.

To create an analysis for LIMS:

  1. From Watson LIMS, click File > Select Project.
  2. Click Analytical > Analytical Run Actions.
  3. Select a Run ID, and then click the Sequence File button.create-an-for-lims-step-3Result: This message appears: “Preparing to create MassLynx DataBridge Sequence Data”.Tip: “MassLnyx Databridge Sequence” is a configurable name that is specified on the Import IPO page in the Watson Agent.
  1. In the Value column of the instrument Parameters dialog box, select Watson <<Sequence>>, and then click OK.
  1. When the “Sequence data submitted to Masslynx DataBridge” message appears in the Watson Message dialog box, click OK.

Result: A UNIFI-compatible sample list is available to pick from the “Use sample list from LIMS” section of the Create Analysis wizard in UNIFI software.

Creating an analysis in UNIFI

You can now create an analysis in UNIFI software to use with LIMS.

To create an analysis to use with LIMS:

  1. Log on to UNIFI software.
  2. On the My Work tab, click Create > Analysis.
  3. On the Create Analysis wizard page, click “Create analysis by acquiring new data”, and then click Next.
  4. In the Create Analysis wizard on the page “What sample list and analysis method do you want to use?”, click “Use sample list from LIMS”, and then select the LIMS configuration you created previously created.

    use-sample-list-from-lims

  1. In the LIMS Sample Lists dialog box, select the sample list that you created in LIMS, and then click OK.

    lims-sample-lists

Result: Doing so ensures the LIMS-created sample list is used as the sample list for the current analysis.

Exporting analysis to LIMS

When a LIMS-generated analysis is completed, you can export it back into the original LIMS Analytical Run Assay for processing.

To export the LIMS analysis into Watson LIMS:

  1. Log on to UNIFI software.
  2. Open Explorer, select the analysis, and then right-click Export to > LIMS.
  3. In the Export to LIMS page, click Export.Result: The “Export successful” message appears at the bottom of the page.export-successful
  1. Open Watson LIMS.
  2. Select the Run ID of the analytical run assay that matches the analysis results being exported, and then click the Import button.
  3. In the Instrument Parameters dialog box, click Watson <<Results>> in the Value column.analysis-result
  1. In the second Instrument Parameters dialog box, select the analysis result in the Value column.analysis-result-in-limsRequirement: You can import the UNIFI analysis only to the matching Analytical Run Assay. The date and time that the analysis was exported from UNIFI software must match that the date and time the result was imported into Watson LIMS.Tip: Match the sample list key information to the analytical run assay information.
  1. Click OK.
  2. To find the correct imported results in Watson LIMS, search the Import File Name column in the Analytical Run Actions page.Results: The imported data appear in LIMS.Tip: NaN indicates that the value is not a number and that, consequently, no result was found.imported-data-inlims

Viewing exported results

When you export an analysis from UNIFI software and import it into Watson LIMS, you must match the UNIFI analysis to the analytical run assay in LIMS. You do so by comparing the date and time stamps that report when the analysis was exported from UNIFI and the result imported into LIMS. To easily identify the date the analysis was exported, create a specialized view in UNIFI’s Explorer window.

To create a specialized view in Explorer:

  1. Log on to UNIFI software.
  2. Open Explorer, click the View list on the toolbar, and then click Select View > Analyses and Reports.
  3. Right-click any column heading in the table, and then click Add Column.
  4. In the Add Columns dialog box, perform the following tasks, and then click OK:
  • Expand Common Fields
  • Click Last result export
  • Click Add
  1. From the View list on the toolbar, click Current View > Save As.
  2. In the Save View dialog box, enter a description for the view, make it public or private, and then click OK.

folder-contents

Tip: You can move the “Last result export” column by dragging and dropping it to the desired location in the Folders Contents table. By default, the column is positioned as the last right-hand column.

Result: The “Last result export” column displays the date and time that the analysis was exported from UNIFI software into LIMS.