How to setup mixed authentication for Web API application (.net framework 4.7)?

I need to add additional authentication method to the existing Web API application that already has the Windows authentication. I have added a Startup file with the code:

using System.Configuration;
using Microsoft.IdentityModel.Tokens;
using Microsoft.Owin;
using Microsoft.Owin.Security.ActiveDirectory;
using Owin;

[assembly: OwinStartup(typeof(TodoList_Web.Startup))]
namespace TodoList_Web
{
    public class Startup
    {
        public void Configuration(IAppBuilder app)
        {
            app.UseWindowsAzureActiveDirectoryBearerAuthentication(
                new WindowsAzureActiveDirectoryBearerAuthenticationOptions
                {
                    Tenant = ConfigurationManager.AppSettings["ida:Tenant"],
                    TokenValidationParameters = new TokenValidationParameters
                    {
                        ValidAudience = ConfigurationManager.AppSettings["ida:Audience"]
                    },
                });
        }
    }
}

Windows authentication is turned on IIS level and it seems that I should turn of it in IIS and add on the application level - add the configuration to the web.config file:

<system.webServer>
  <security>
    <authentication>     
       <windowsAuthentication enabled="true" />
    </authentication>
  </security>

Will it work at all? Can I somehow use an Authorize attribute to specify what authentication should be applied to particular method/controller? Something like this:

[Authorize(AuthenticationType=Windows)] 
or 
[Authorize(AuthenticationType=WindowsAzureActiveDirectoryBearer)]