Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting

Microflow liquid chromatography tandem mass spectrometry (mu LC-MS/MS) is becoming a viable alternative to nanoflow LC-MS/MS for the analysis of proteomes. We have recently demonstrated the potential of such a system operating with a 1 mm i.d. X 150 mm column and at a flow rate of 50 mu L/ min for high-throughput applications. On the basis of the analysis of similar to 38 000 samples measured on two instruments over the past two years, we now show that the approach is extremely robust. Up to 1500 analyses were performed within one month, and >14 000 samples could be analyzed on a single column without loss of chromatographic performance. Samples included proteomes of cell lines, tissues, and human body fluids, which were analyzed with or without prior peptide fractionation or stable isotope labeling. We show that the mu LC-MS/MS system is capable of measuring 2600 proteins from undepleted human plasma and similar to 5000 proteins from crude human urine in 1 day, demonstrating its potential for in-depth as well as high-throughput clinical application.

Automated summary

Microflow liquid chromatography tandem mass spectrometry (mu LC-MS/MS) has been shown to be a robust and high-throughput method for analyzing proteomes, capable of measuring thousands of proteins from various samples. The system demonstrated the potential for in-depth and high-throughput clinical applications through analyzing a large number of samples over a period of two years.