List of differentially-expressed proteins in rat brain sections observed on MALDI-TOF/TOF and identified by mass matching.

• The italicized protein sequences have been verified by top-down tandem mass spectrometry. The rest of the identity assignments are solely based on mass matching. The proteins that can be identified by neither approach were shown as unknown.
• The bolded sequences represent the proteins that were reported from rat brain in a MALDI-MS-based platform for the first time.
The proteins that were further identified by top-down MS/MS were highlighted in italics and annotated with UniProt entry, accession number, calculated mass based on the m/z observed on Orbitrap Elite, expected mass based on the matched protein sequence and the mass difference between the calculated mass and expected mass. All MALDI-MS profiling spectra have been processed by ClinProTools and summarized here by “peak statistic” function. PTTA represents p-value of t-test (2 classes); Ratio represents the relative abundance changes of these proteins in the brain sections of rats treated with MK801 and vehicle, calculated based on the average intensity of the ion observed in the MK801-treated class over the vehicle-treated class.