Exact p‐value calculation for XCorr scoring of high‐resolution MS/MS data

• Published in: Proteomics (Weinheim) 2024-03, Vol.24 (5), p.e2300145-n/a
• Main Authors: Bhimani, Kishankumar, Peresadina, Arina, Vozniuk, Dmitrii, Kertész‐Farkas, Attila
• Format: Article
• Language: English
• Subjects: Annotations; Bins; Calibration; Database searching; exact p‐value; Fragmentation; high resolution; Mass spectrometry; Mass spectroscopy; PSM scoring; score calibration; Spectrometers; tandem mass spectrometry
• ISSN: 1615-9853; 1615-9861
• DOI: 10.1002/pmic.202300145

Exact p‐value (XPV)‐based methods for dot product‐like score functions—such as the XCorr score implemented in Tide, SEQUEST, Comet or shared peak count‐based scoring in MSGF+ and ASPV—provide a fairly good calibration for peptide‐spectrum‐match (PSM) scoring in database searching‐based MS/MS spectrum data identification. Unfortunately, standard XPV methods, in practice, cannot handle high‐resolution fragmentation data produced by state‐of‐the‐art mass spectrometers because having smaller bins increases the number of fragment matches that are assigned to incorrect bins and scored improperly. In this article, we present an extension of the XPV method, called the high‐resolution exact p‐value (HR‐XPV) method, which can be used to calibrate PSM scores of high‐resolution MS/MS spectra obtained with dot product‐like scoring such as the XCorr. The HR‐XPV carries remainder masses throughout the fragmentation, allowing them to greatly increase the number of fragments that are properly assigned to the correct bin and, thus, taking advantage of high‐resolution data. Using four mass spectrometry data sets, our experimental results demonstrate that HR‐XPV produces well‐calibrated scores, which in turn results in more trusted spectrum annotations at any false discovery rate level.