LC-MS has been used for comprehensive identification of proteins in tissues or biofluids by LC separation of peptides for a long gradient time (~2 hours). On the other hand, recent development of LC and MS may propose an application of LC-MS for measurement of biomarkers in clinical samples at clinical laboratories in hospitals. For the clinical application high-throughput LC-MS measurement should be required.
To make it possible, we analyzed proteomes of 30 urine samples in 24 hours by using a new high-throughput LC (Evosep One) and a new efficient MS (Bruker tims TOF pro) with a 48 min measurement method. Our standard measurement LC-MS (nanoElute-timsTOFpro, Bruker) system was also used in a short gradient time method such as 30 min, 68 min, or 120 min.
~ 2,000 proteins were identified by our standard measurement using the nanoElute-timsTOFpro with 120 min gradient time for a 200 ng protein urine sample measurement. With shortening the gradient time to 68 min or 30 min, ~1,100 or ~900 proteins were identified by using a nanoElute LC system. With a new LC, Evosep One, ~1,000 urine proteins were identified with the 48 min measurement time for consecutive three days. These LC-MS measurements may propose an comprehensive analysis of clinical samples for understanding patients or diseases.