DIA is the most widely used acquisition strategy to resolve the missing value problem. However, using it requires the construction of spectral libraries – which can be timely and difficult when it concerns an uncommon organism – and traditional DIA methods are too slow to be compatible with short gradient analysis. In such cases, the PASEF-LFQ delivers speed, flexibility and reliability. Nonetheless, even with > 100Hz MS/MS, some peptides might not be selected for fragmentation in every analysis, especially while using short gradients.
The Match Between Runs (MBR) approach has been developed to resolve this missing value issue. MBR extracts intensity information for all peptides to be quantified using narrow m/z and retention time windows. This combination of filters, previously suggested as not being specific enough, is resulting in inaccurate ratio measurements. 4D-MBR adds an extra CCS filter to the first m/z and retention time ones, allowing for much greater specificity as illustrated in our application note LC-MS 151.
4D-MBR applied on high-throughtput plasma proteomics
Outcome for the quantitation of 192 patient and 20 QC plasma samples digests, separated with an 11.5 min gradient using an Evosep One LC system. (click to enlarge)