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Bottom-up proteomics using mass spectrometry faces significant challenges due to dynamic range limitations, where high-abundance peptides can saturate ion capacity and suppress detection of low-abundance species. This issue is particularly pronounced in trapping instruments like Orbitraps, where ions accumulate for extended periods before analysis.

To overcome these dynamic range limitations and improve both peptide identification and quantification in proteomics workflows, the Searle lab introduced Multiple Accumulation Precursor Mass Spectrometry (MAP-MS), which multiplexes precursor ions into multiple m/z range packets during the long transient recording times of Orbitrap instruments. The experiments were performed using an Exploris 480 with an EASY-nLC 1200 and Aurora Ultimate XT 25×75 C18 UHPLC column.

This was primarily a methodological development study with quantitative validation. The MAP-MS approach demonstrated significant improvements in both protein detection and quantitative precision. In data-dependent acquisition (DDA) mode, MAP-MS increased protein identifications by 9% while reducing the quantitative coefficient of variation (CV) by more than 50% compared to standard DDA method. For data-independent acquisition (DIA), MAP-MS achieved a 4% increase in total protein identifications relative to a standard DIA analysis (using 3×10⁶ MS1 AGC targets), while maintaining equivalent precursor integration accuracy to DDA measurements.

MAP-MS effectively utilises previously wasted instrument time by accumulating ions from different mass ranges in parallel, producing precursor spectra with enhanced dynamic range without additional measurement cost. This approach represents a significant advancement for proteomics applications requiring high sensitivity, particularly in complex biological samples with wide dynamic ranges such as plasma, metaproteomics, and single-cell proteomics studies.

Publication
bioRxiv

Authors

Teeradon Phlairaharn, Ariana E. Shannon, Xinlei Zeng, Dong-Jiunn Jeffery Truong, Erwin M. Schoof, Zilu Ye, & Brian C. Searle;

Title

Improving proteomic dynamic range with Multiple Accumulation Precursor Mass Spectrometry (MAP-MS)