identifying short open reading frames: a high/low pH reversed phase LC-MS bottom-up approach and a semi-top-down strategy involving separation of proteins in a GelFree system followed by digestion and LC-MS analysis . The experiments were carried out using the methane producing archaeon Methanosarcina mazei. All nine studies were performed using a Thermo Scientific Q Exactive mass spectrometer. We downloaded the RAW files from the corresponding PRIDE projects (Table ) and converted them to MGF format using the ThermoRawFileParser v1.3.4. We downloaded the corresponding nine UniProt reference proteomes and constructed a Tide index for each one, using Crux version 4.2. Note that, for one species (Vigna mungo) no reference proteome is available, so we used the proteome of the closely related species Vigna radiata.