The raw data (FASTQ files) were processed using a custom designed sequence processing tool, Altius.
All.RAW files were processed using Proteome Discoverer 2.1.0.81.
Briefly, RawMSdata files were processed using Proteome Discoverer v.1.3 (Thermo Scientific).
After Picard, BAM files were processed using the Cancer Genome Analysis tool known as "Firehose".
For data analysis all 27 raw files were processed using MaxQuant (1.3.7.4) and the implemented Andromeda search engine70.
CDF files were processed using XCMS-online (XCMS, USA).
The image files were processed using the ROVER v 2.0.51 software (ABX GmbH, Radeberg, Germany).
The raw files were processed with RMassBank [51, 52], yielding the "EA" records in MassBank.
Blot image files were processed with MultiGauge (FujiFilm Lifescience).
After video capture all files were processed with ImageJ 1.43 image viewing software.
Mass Lynx raw data files were processed with Protein Lynx Global Server 2.2 software (Waters).
