Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

Abstract

Data independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.

Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020

“…Various schemes of DIA strategies have been implemented since the beginning of this century, including but not limited to Shotgun CID, [9] DIA, [5] MS E , [10] PAcIFIC, [11] AIF, [12] SWATH-MS, [6] MSX, [13] SONAR, [14] WiSIM, [15] BoxCar DIA, [16] Scanning SWATH, [17] diaPASEF, [18] and PulseDIA [19] (Figure 1, Table 1), but not all schemes have been widely revisited. In Shotgun collision-induced dissociation (Shotgun CID) [9] induces in-source fragmentations where all ions co-eluting from chromatographic separation into the mass spectrometer are fragmented in parallel.…”

Metaproteomics insights into traditional fermented foods and beverages

“…After the introduction of ion mobility separation, proteomics entered the 4D era. The performance of 4D proteomics has been extensively improved in terms of identification depth, quantitative accuracy, and other aspects (Meier et al., 2019). The fermentation environment has a great influence on the posttranslational modification of proteins, which is closely related to time and space.…”

Microdissection—An Essential Prerequisite for Spatial Cancer Omics

“…[ 78 ] The identification is usually done on quadrupole Orbitrap mass spectrometer. The new parallel accumulation‐serial fragmentation (PASEF) combined with the trapped ion mobility spectrometry (TIMS) technology has also the potential to identify masses from a few cells [ 79 ] due to its high sensitivity. The results from MALDI MSI can be directly projected on the corresponding H&E stained section.…”