Research team develops new protein mapping technique NatureComms
. The LC-MS system consists of an UltiMate 3000 gradient Micro LC system, an UltiMate 3000 Nano LC system, a WPS-3000 autosampler, and an Orbitrap Fusion Lumos Tribrid Mass Spectrometer . The peptides derived from ~2.5 µg proteins were firstly delivered onto a trapping column at a flow rate of 10 µL/min with 1% B, to selectively remove the hydrophilic and hydrophobic matrix components.
The data was collected at the positive mode using data-dependent acquisition with a 3 s cycle time. The MS1 spectra were acquired in therange of 400–1500, with a resolution of 240 K . The maximum injection time for MS1 was 50 ms, automated gain control target was 5E5. The dynamic exclusion was set to 60 s, and the mass tolerance was ±10 ppm.
Generation of protein distribution maps and further data processing using UHR-IonStar and the MAsP app Protein identification and quantification were conducted using UHR-IonStar, a unique MS1-based quantitative proteomics pipeline, which achieves accurate and robust proteomic quantification in large cohorts, including low-abundance, regulatory proteins
. UHR-IonStar measures peptide MS1 precursor ions with ultra-high-resolution , and then precisely extract UHR-MS1 signals from the typically noisy backgrounds with extremely narrow, dynamically-definedwindows without losing signal intensity.
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