Q2C

We present Q2C, an open-source software designed to streamline mass spectrometer queue management and assess performance based on quality control metrics.
Q2C provides a fast and user-friendly interface to visualize projects queues, manage analysis schedules and keep track of samples that were already processed. Our software includes analytical tools to ensure equipment calibration and provides comprehensive log documentation for machine maintenance, enhancing operational efficien-cy and reliability.
Additionally, Q2C integrates with Google® Cloud, allowing users to access and manage the software from different locations while keeping all data synchronized and seamlessly integrated across the system.

Data are available from the ProteomeXchange consortium (identifier PXD055186).

Please cite our paper:
Lima, DB, et al., “Q2C: A software for managing mass spectrometry facilities”, Journal of Proteomics, 2025.

Equipment

Hardware

• A computer with a minimum of 16 GB RAM and 4 computing cores is recommended. However, the software can take advantage of superior configurations.

Software

• Windows 10 (64 bits) or later.
• The .NET Core 9 or later.
• For reading Thermo® RAW files, the MSFileReader must be installed. To do so, create an account on Thermo®, register, choose Other Releases → MSFileReader 3.1 SP4 and download MSFileReader_x64.exe.
• The Q2C software, available for download at https://github.com/diogobor/Q2C/releases
• A Google® account (for online mode)

Data files

• Q2C is compatible with data files in the formats mzML (proposed by HUPO Proteomics Standard Initiative) and Thermo® RAW files.

Procedures

1. Software installation:

There are two modes to run Q2C: online and offline. To setup the first one, start from 1.1, otherwise, go to 1.2.

1.1 Set up a Google cloud project:
 Note: If the Google cloud project has already been established, proceed to step 1.2.

 1.1.1 Go to Google account and sign up or log in.

 1.1.2 Go to Google cloud platform and create a new project.
  1.1.2.1 To do so, go to Select a project. (Figure 1)

Figure 1: Access Google cloud platform.

  1.1.2.2 Click on 'New Project'. (Figure 2)

Figure 2: Create a new project.

  1.1.2.3 Set a project name (q2c-software) and click on 'Create' button. (Figure 3)

Figure 3: Set a project name.

 1.1.3 Go back to Applications (Figure 1) and click on q2c-software to set it up. (Figure 4)

Figure 4: Set a project up.

 1.1.4 On the left side of the Google Cloud icon, click on the menu to display the options. Then, go to APIs and services → OAuth consent screen (Figure 5) and go to Create an External User Type. (Figure 6)

Figure 5: Go to APIs and services → OAuth consent screen.

Figure 6: Create an external user type.

  1.1.4.1 Set up an app name (q2c-software) and select a valid Gmail. (Figure 7)

Figure 7: Start to set up an external user type by giving an app name and selecting a valid Gmail.

  1.1.4.2 Set an email for the developer contact information (set the same used in the previous setp) and click on the 'Save and Continue' button. (Figure 8)

Figure 8: Save the external user type.

  1.1.4.3 Click on 'Save and Continue' button in Scopes and Test users steps. Finally, in 'Summary' step, go to the bottom and click on the 'Back to dashboard' button.

  1.1.4.4 On the dashboard, click on the 'Publish App' button (Figure 9a) and confirm the publication. (Figure 9b)

 
Figure 9: Publish q2c-software app.

 1.1.5 Go to Credentials, click on Create Credentials, then on OAuth client ID. (Figure 10)

Figure 10: Create credentials.

  1.1.5.1 In Application type, select Desktop app (Figure 11a), then type a name (q2c-software) and click on Create button. (Figure 11b)

 
Figure 11: Create OAuth client ID.

  1.1.5.2 Once the OAuth client ID is created, a new window is displayed with the Google Client ID and Google Secret ID. (Figure 12) Both IDs will be used to set up the database on Q2C.

Figure 12: Client and Secret IDs. Both of them are used to set up the database on Q2C.

 1.1.6 Go to Enabled APIs and services and click on Enable APIs and Services. (Figure 13)

Figure 13: Enable APIs and Services.

  1.1.6.1 In the API Library, search for google drive api (Figure 14a) and enable it. (Figure 14b)

 
Figure 14: Enable Google Drive API.

  1.1.6.2 In the API Library, search for gmail api (Figure 15a) and enable it. (Figure 15b)

  
Figure 15: Enable Gmail API.

  1.1.6.3 In the API Library, search for google sheets api (Figure 16a) and enable it. (Figure 16b)

  
Figure 16: Enable Google Sheets API.

 1.2 Download Q2C by clicking on Q2C_setup_64bit.msi in the latest release.

 1.3 Install it by double-clicking the previous downloaded file.

2. Workflow:

 2.1 Set up Q2C:
  2.1.1 As mentioned in Software installation section, Q2C can be run either online or offline. To setup the offline mode, on the Database settings screen, check Offline Mode option.

   2.1.1.1 Click on the 'Confirm' button (Figure 17a), and click on 'Yes' to accept the modified entries. (Figure 17b)

   2.1.1.2 Go to 2.1.3.

 
Figure 17: Set up the database.

  2.1.2 On the other hand, the online mode requires Google Client ID and Google Client Secret according to the IDs obtained in 1.1.5.2 section.
   2.1.2.1 If you are not the administrator, uncheck the Create spreadsheet option, and set the Spreadsheet ID obtained when the administrator set up the Q2C for the first time.
   2.1.2.2 Click on the 'Confirm' button. Similar to 2.1.1.1.
   2.1.2.3 Q2C will be redirected to Google login page. Type the created email in 1.1.1 section, click on the 'Next' button and enter the password. (Figure 18)
PS1: Make sure the message 'Sign in to continue to q2c-software' is displayed.
PS2: You have 90 seconds to complete this step.

Figure 18: Enter the credentials.

   2.1.2.4 Give Google permission to access the app by clicking on 'Advanced' link (Figure 19a). Then, click on the 'Go to q2c-software (unsafe)' link. (Figure 19b)

 
Figure 19: Give Google permission to access Q2C.

   2.1.2.5 On the next page, 'q2c-software wants access to your Google Account', check the 'Select all' option, then click on the 'Continue' button. (Figure 20)

Figure 20: Select all option to give Google permission.

   2.1.2.6 Once the permission is done, the next page will display the following message 'Received verification code. You may now close this window'. Go back to Q2C. (Figure 21)

Figure 21: Google permission is complete.

  2.1.3 Q2C will display a new window to add new users. Click on 'Add User' button. (Figure 22)

Figure 22: List of registered users.

   2.1.3.1 To add a new user, enter a username (must be the same as the Windows® username.), a valid email and set a category. Then, click on 'Confirm' button. Q2C will be restarted. (PS: the first registered user is configured as Administrator.) (Figure 23)

Figure 23: Add new user.

    2.1.3.1.1 There are 8 different types of category:
     2.1.3.1.1.1 User: the basic category. Only allows the user to view the project queue (section 2.2).
     2.1.3.1.1.2 User Sample: Allows the user to add/edit/remove projects to the queue (section 2.2).
     2.1.3.1.1.3 Super User Sample: Allows the user to add/edit/remove projects to the queue. In addition, it also allows the user to view the runs (section 4).
     2.1.3.1.1.4 Super User Machine: Allows the user to add/edit/remove runs (section 2.3).
     2.1.3.1.1.5 Super User Sample & Machine: Allows the user to add/edit/remove projects and runs (sections 2.2 & 2.3).
     2.1.3.1.1.6 Master User Sample: Allows the user to add/edit/remove projects and put them in the machine queue (sections 2.2).
     2.1.3.1.1.7 Master User Sample & Machine: Allows the user to add/edit/remove projects and runs and put projects in the machine queue (sections 2.2 & 2.3).
     2.1.3.1.1.8 Administrator: Allows the user to add/edit/remove databases, users and machines. In addition to having all the Master User Samples & Machine functions (sections 2.2 & 2.3).

  2.1.4 Q2C will display a new window to add new machines. Click on 'Add Machine' button. (Figure 24)

Figure 24: List of registered machines.

   2.1.4.1 To add a new machine, enter a name, set the frequency of the mass calibration time (default is 2 weeks), set the frequency of the full calibration time (default is 1 month), set the interval time (in minutes) for each project (default is 20), and check the options that satisfy the machine: Evaluation, FAIMS, OT (high resolution) & IT (low resolution). Then, click on 'Confirm' button. Q2C will be restarted. (Figure 25)

Figure 25: Add new machine.

 2.2 Projects:  

The main Q2C interface shows all registered projects. (Figure 26)

Figure 26: Graphical User Interface of Q2C’s main window.

  2.2.1 To add a new project and put it in the general queue, click 'Add Project' and a new pop-up window will open. (Figure 27)

Figure 27: Add a new project.

   2.2.1.1 Project name: Specify a name for the project.
   2.2.1.2 Amount of MS time (hours): The total time for this project will be displayed here according to the number of samples and the selected method.
   2.2.1.3 Number of Samples: Specify the number of samples.
   2.2.1.4 Method: Select a pre-defined method.

    2.2.1.4.1 A new method can be defined. To do so, click '+'. A new pop-up window will open. (Figure 28)

Figure 28: Define a new method or edit an existing one.

     2.2.1.4.1.1 To add a new method, press CTRL + I, set the parameters and click on 'Confirm'.
     2.2.1.4.1.2 To modify a pre-defined method, select the desired one, change the parameters and click on 'Confirm'.
     2.2.1.4.1.3 To delete a method, press DEL. A pop-up message will appear to confirm the deletion; click on 'Yes'.
     2.2.1.4.1.4 Parameters:
      2.2.1.4.1.4.1 Quantification:Select a pre-defined quantification or select 'Customize' to create a new one. If the method does not refer to a quantification, select 'None'.
      2.2.1.4.1.4.2 Purpose / Modification: Select a purpose of the new modification.
      2.2.1.4.1.4.3 Comment: Type a comment for the new method (optional).
      2.2.1.4.1.4.4 Gradient length (min): Set a gradient legth (in minutes) for the method. This value will be used for computing the 'Amount of MS time'.
      2.2.1.4.1.4.5 To confirm a new method, click 'Confirm'.
      2.2.1.4.1.4.6 Export: Choose this option to save the current methods to a file.
      2.2.1.4.1.4.7 Load: Select this option to import methods from a file. (Default settings can be imported from q2c_initital_methods.json)

   2.2.1.5 Machine: Select one or more machines that will acquire the data. If FAIMS will be used for acquiring the data, select 'Yes' for the respective machine(s).
   2.2.1.6 Status: Select the status for the project. New project will have 'Wait for acquisition' as status.
   2.2.1.7 Comments: Type an optional comment for the new project.
   2.2.1.8 Receive notification(s) by e-mail: Check this option if you want to receive by e-mail when the project changes its status.
   ⇒ Click on 'Confirm' to add the new project.

  2.2.2 To queue a project to a specific machine, right-click* on a project and click 'Add to machine queue'. (Figure 29a)
   2.2.2.1 If more the one machine has been set up for the project, a new window will open. At that moment, select which machine will acquire the data. (Figure 29b)
  * This option is only available for 'Master User Sample', 'Master User Sample & Machine' and 'Administrator'.
  ⇒ Once the project is queued, its color changes to blue.

 
Figure 29: Put a project to a machine queue.

  2.2.3 To remove a project, select it and press Delete.
  2.2.4 Statistical analysis → Queue: To check the machines' usability over a specific period, go to 'Statistical analysis → Queue' (or press SHIFT + Q)*.
   2.2.4.1 Set a specific period or a month or a year and click 'Confirm'. Your can check the plots per period or per user. (Figure 30)
  * This option is only available for 'Super User Machine', 'Super User Sample & Machine', 'Master User Sample & Machine' and 'Administrator'.

Figure 30: Statistic analysis → Machines' Queue.

 2.3 Machine:  

In this module, you can check the mass spectrometers' queue as well as assess the machines' efficiency by running quality control samples.

  2.3.1 Machines' queue:
  Each mass spectrometer has its own queue. When a project is added, it appears in this tab. (Figure 31)

Figure 31: Machines' Queue.

  When all samples for a specific project have been acquired, the responsible for the samples must delete the project from the machine's queue.
  To do so, click on the project and press delete. A message will appear asking if the samples have been measured.
  If so, click 'Yes' and the samples will be removed from the queue, with the status changed to 'Measured' (the project color will be changed to grey).
  If not, click 'No'; the samples will be removed from the queue and the status will return to 'Wait for acquisition'.

  2.3.2 Machines' Evaluation:

Figure 32: Machines' Evaluation

  2.3.3 Machines' Log:

Figure 33: Machines' Log

 2.4 Reset settings:  

Q2C allows to reset methods and fasta settings. To do so, go to Help → About → Reset Settings. The software will restart to complete the process.

Watch this tutorial video, which explains how Q2C works.

Tutorial_Video.mp4