As mentioned previously, application letters and cover letters are not the same. A cover letter identifies an item being sent, the person to whom it is being sent, and the reason for its being sent. A cover letter provides a permanent record of the transmittal for both the writer and the reader.
Quick Tip: Don't use your work email address for job searching. Use your personal email account, or set up a unique account to use just for your job hunt. Many free online email services exist, like Gmail and Yahoo mail, that you can use to set up a new email account exclusively for your job search.