Journal Highlight: Applying multiple proteases to direct digestion of hundred-scale cell samples for proteome analysis

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  • Published: Sep 21, 2015
  • Author: spectroscopyNOW
  • Channels: Proteomics
thumbnail image: Journal Highlight: Applying multiple proteases to direct digestion of hundred-scale cell samples for proteome analysis
Multiple proteases were applied to the direct digestion of a few hundred cells and the identified proteins were compared both qualitatively and quantitatively to find the best combination.

Applying multiple proteases to direct digestion of hundred-scale cell samples for proteome analysis

Rapid Communications in Mass Spectrometry, 2015, 29, 1389-1394
Qi Chen, Guoquan Yan and Xiangmin Zhang

Abstract: Analyzing the proteome on the scale of only several hundred cells with mass spectrometry has great significance for applications with limited sample amounts. We applied multiple proteases to the direct digestion of cells and compared the identified proteins both qualitatively and quantitatively. Three hundred cells were directly digested by trypsin, chymotrypsin, or the combination of trypsin and chymotrypsin. The peptides were identified using a LTQ-Orbitrap XL, and data were analyzed using MaxQuant software. Different proteases produced different identified protein numbers. Trypsin proved to be the best choice for generating the largest protein number, while other proteases complemented the identification results of trypsin by increasing protein sequence coverage. Concerning the quantitative perspective, using trypsin would produce the biggest number of proteins quantifiable by intensity-based absolute quantification (iBAQ). When hundred-scale cell samples are analyzed, an optimum choice of proteases should be made to realize different analytical objectives.

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