MALDI-HDMSE: A Novel ‘Data Independent’ Acquisition Method for the Enhanced Analysis of 2D-Gel Tryptic Peptide Digests

Peptide Mass Fingerprinting (PMF) is an unbiased protein identification technique that offers limited sequence information for identification purposes due to the reliance on the m/z measurement of proteolytic peptides.

An alternative technique commonly used conducts MS/MS sequencing experiments by fragmenting the tryptic peptides through sequential selection using the first analyzer of a mass spectrometer. This MS/MS approach has the following limitations:

■ Only the most intense peptides are fragmented
■ The user must choose the peptide to fragment
■ Information is limited, as peptides can be missed if the sample is depleted
■ After the sample is discarded, regaining knowledge from the sample is not feasible
■ Potentially more time consuming than PMF alone

This application note proposes a novel method of acquiring data called High Definition MSE (HDMSE). This method maintains the independent nature of PMF but extends its utility by providing molecular and MS/MS-like peptide sequence information in a simple, generic fashion.

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