Updated project metadata. SARS-CoV-2 infection has become a major public health burden and is known to affect many organs with the respiratory system being involved in a majority of cases. Here we undertook a mass spectrometry-based proteomic approach to test whether viral proteins could be detected in urine of patients with COVID-19. Urine samples from 39 patients positive for SARS-CoV-2 by RT-PCR were analyzed by mass spectrometry. We detected peptides from the nucleocapsid protein of the SARS-CoV-2 virus in 12 out of 35 urine samples. A set of five samples each from positive and negative groups were further used to study the host response. In conclusion, we demonstrated the identification of viral antigens in urine using mass spectrometry which further suggests that urine could be a potential source of infection with implications in disease transmission and also the changes in protein composition in urine may provide insights in understanding the disease pathogenesis.