AI Article Synopsis
- An integrated platform was developed that combines machinery and software to analyze large datasets from nanoflow LC-MS for studying protein expression.
- Unlabeled proteins were fully digested and separated using low-speed HPLC, with mass spectra collected every second and visually represented in a two-dimensional format.
- The platform demonstrated high comprehensiveness, reproducibility, and accurate quantification, making it suitable for diverse experimental and translational proteomics applications.
Article Abstract
We developed an integrated platform consisting of machinery and software modules that can apply vast amounts of data generated by nanoflow LC-MS to differential protein expression analyses. Unlabeled protein samples were completely digested with modified trypsin and separated by low speed (200 nl/min) one-dimensional HPLC. Mass spectra were obtained every 1 s by using the survey mode of a hybrid Q-TOF mass spectrometer and displayed in a two-dimensional plane with m/z values along the x axis, and retention time was displayed along the y axis. The time jitter of nano-LC was adjusted using newly developed software based on a dynamic programming algorithm. The comprehensiveness (60,000-160,000 peaks above the predetermined threshold detectable in 60-microg cell protein samples), reproducibility (average coefficient of variance of 0.35-0.39 and correlation coefficient of over 0.92 between duplicates), and accurate quantification with a wide dynamic range (over 10(3)) of our platform warrant its application to various types of experimental and translational proteomics.
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| http://dx.doi.org/10.1074/mcp.T500039-MCP200 | DOI Listing |
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