Data-dependent acquisition (DDA) is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, it presents major drawbacks in terms of detectable dynamic range. Recently, we demonstrated the superior performance of a data-independent acquisition (DIA) method that we termed precursor acquisition independent from ion count (PAcIFIC), which showed increased protein identification as well as extended detectable dynamic range over DDA methods. In this chapter, we discuss recent improvements to PAcIFIC that make it faster, more accurate, and quantitative. Currently, the time needed to perform a PAcIFIC experiment can be reduced to less than two days using an ion trap with an overall tandem mass spectral acquisition rate of 0.2 seconds or less.
|Title of host publication||Proteomic and Metabolomic Approaches to Biomarker Discovery|
|Number of pages||12|
|State||Published - Jun 2013|
- Data-independent acquisition (DIA)
- Dynamic range
- Precursor acquisition independent from ion count (PAcIFIC)