Program

Oral Sessions

Day 1, May 15（Tue.）　15:45-16:05　Room A (OrBit Hall)

1A-O1-M-1545　　PDF

Validation of the label-free quantification (LFQ) with data-dependent acquisition (DDA)

(RIKEN CSRS)
^oNaoshi Dohmae, Takehiro Suzuki

Combination with the other omics, large scale proteome research has lead a great progress in life science. In order to conduct comprehensive proteome research even in a small laboratory, we examined proteome analysis in a small scale (one mass spectrometer) using the label-free quantification (LFQ) method. The digests were applied to data dependent analysis with ordinary shotgun system that were repeated 3 times for each analysis of 3-4 conditions. The MS/MS data was identified with MASCOT (Matrix Science). The identified peptide amount was quantified by area of the peptide ion mass chromatogram and the protein amount was determined by a median of peptide amount using Proteome Discoverer 2.2 (Thermo Scientific).
Approximately 6600 proteins were identified (p-value = <0.01) using the Q–Exactive HFX hybrid mass spectrometer (Thermo Scientific), and quantitative values were attached to about 6000 proteins. In the CV value, nearly 50% of the 3 times repetition data was 10% or less.
The Many methods have been adopted for the quantitative proteome, but LFQ by DDA is the simplest, it is possible to clear the state of cells and it is expected to be applied to drug discovery research and the like.