Application of the half decimal place rule to increase the peptide identification rate

Abstract

Rationale: Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the digits after the decimal point to the full molecular mass and results in a relatively small permitted mass window for most peptides. Methods: First, the HDPR mass filter was calculated for the human and other proteomes. Subsequently, the HDPR was applied to three technical replicates of an in-solution tryptic digest of HeLa cells which were analysed by liquid chromatography/mass spectrometry (LC/MS) using a quadrupole-orbitrap mass spectrometer (Q Exactive). In addition, the same sample was analysed three times with a fixed exclusion list. The exclusion list was based on only choosing doubly charged ions for fragmentation. Results: The peptide spectrum match (PSM) rate increased by 2–4% applying HDPR filters from 0.1–0.25 Da and 75–150 ppm, respectively. Excluding all MS2 events by applying an HDPR filter of doubly charged ions, we were able to improve PSMs by 0.9% and the PSM rate by 2.5%. Conclusions: An algorithm to filter precursors based on the HDPR was established to improve the targeting of the acquisition of MS2 spectra in data-dependent acquisition (DDA) experiments. According to our data, a total gain of PSMs of 1–5% might be achievable if the HPDR filter would already be applied during MS data acquisition. Copyright © 2016 John Wiley & Sons, Ltd. The final version of this research has been published in Rapid Communications in Mass Spectrometry. © 2016 Wiley