Boxcar? Carmax?? BoxCarmax!

The Liu Lab recently published a new DIA method named BoxCarmax, which is a high-selectivity data-independent acquisition mass spectrometry method for the analysis of protein turnover and complex samples!

The method is highly multiplexing at both MS1 and MS2 levels. BoxCarmax incorporates the sensitivity improvement of BoxCar MS1 acquisition (Initially developed by Mann group) through four sample injections and the selectivity improvement of MS2 through non-consecutive acquisition small DIA windows (MSX, initially developed by MacCoss group). BoxCarmax reaches the sensitivity of nominal isolation width of 2-2.5 m/z, but with a measurement of only four hours per sample due to its multiplexity capacity.

Compared to the high-performance classic DIA method (4hr-DIA in this report as an example), BoxCarmax modestly increased the identification rate for label-free and labeled samples but significantly reduced the interference and improved the quantitative accuracy in SILAC and pSILAC samples. Combing with pSILAC, BoxCarmax data deciphered how cells maintain the critical balance between protein synthesis and degradation, to meet the serum depletion stress during tissue culture.

We expect potential applications of BoxCarmax in analyzing small protein PTMs such as oxidation and methylation, as well as samples of high-dynamic range (e.g., plasma proteomics), high complexity (e.g., metaproteomics), and samples containing lots of peptide isomers (e.g., histone modification analysis).