Application Note

Identify Over 40% More Proteins With The Zeno MS/MS

Source: SCIEX

By Alexandra Antonoplis, Bradley Schneider, and Christie Hunter, SCIEX

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Proteomics samples are some of the most complex samples encountered by the mass spectrometry community. The ability to collect high quality MS/MS at very high acquisition rates is key to achieving high numbers of peptide and protein identifications.

Sensitivity (particularly, MS/MS sensitivity) is a key performance specification for proteomics experiments. High sensitivity MS/MS leads to the broad and deep coverage for protein identification (ID).

The data acquisition strategy is another key factor that can influence proteomics experiments. One of the main acquisition workflows for discovery proteomics is data dependent acquisition (DDA), also known as information dependent acquisition (IDA). During data acquisition, the highest-ranking ions that pass certain criteria in each cycle are sent for MS/MS analysis. With many factors to consider, an important consideration is how to specify the selection criteria in order to maximize the number of unique, high confidence peptide and protein IDs.

In the current study, the sensitivity gains using the Zeno trap technology were evaluated for the impact on protein ID results. Additionally, Zeno IDA acquisition parameters were optimized for 4 different microflow gradient lengths using a design of experiments (DOE) approach.

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