Open AccessDeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results
Author(s) -
Dmitry M. Avtonomov,
Andy T. Kong,
Alexey I. Nesvizhskii
Publication year - 2018
Publication title -
journal of proteome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.644
H-Index - 161
eISSN - 1535-3907
pISSN - 1535-3893
DOI - 10.1021/acs.jproteome.8b00728
Subject(s) - computer science , software , data mining , identification (biology) , graphical user interface , visualization , interface (matter) , mass spectrometry , kernel density estimation , chemistry , chromatography , operating system , statistics , mathematics , botany , bubble , maximum bubble pressure method , estimator , biology
Routine identification of thousands of proteins in a single LC-MS experiment has long become the norm. With these vast amounts of data, more rigorous treatment of modified forms of peptides becomes possible. "Open search", a protein database search with a large precursor ion mass tolerance window, is becoming a popular method to evaluate possible sets of post-translational and chemical modifications in samples. The extraction of statistical information about the modification from peptide search results requires additional effort and data processing, such as recalibration of masses and accurate detection of precursors in MS1 signals. Here we present a software tool, DeltaMass, which performs kernel-density-based estimation of observed mass shifts and allows for the detection of poorly resolved mass deltas. The software also maps observed mass shifts to known modifications from public databases such as UniMod and augments them with additionally generated possible chemical changes to the molecule. Its interactive graphical interface provides an effective option for the visual interrogation of the data and the identification of potentially interesting mass shifts or unusual artifacts for subsequent analysis. However, the program can also be used in fully automated command-line mode to generate mass-shift peak lists as well.