Samples for CNIC-Proteomics Nextflow pipelines

We present several input sample files for the execution of various Nextflow pipelines developed by the Cardiovascular Proteomics Lab/Proteomics Unit at the National Centre for Cardiovascular Research (CNIC, https://www.cnic.es). The list of developed Nextflow pipelines includes: nf-PTM-compass: Enhances the identification and quantification of Post-Translational Modifications (PTMs) (https://github.com/CNIC-Proteomics/nf-PTM-compass). nf-SearchEngine: Executes the MSFragger search engine for peptide identification (https://github.com/CNIC-Proteomics/nf-SearchEngine). The available sample files are as follows: nf-PTM-compass_Heteroplasmic_Muscle.zip: Input files for nf-PTM-compass, derived from the study by Bagwan N, Bonzon-Kulichenko E, Calvo E, et al. (*), with results from an open search conducted using MSFragger. nf-SearchEngine_Heteroplasmic_Muscle.zip: Input files for nf-SearchEngine, derived from the same study, including Thermo raw files and other data. (*) Bagwan N, Bonzon-Kulichenko E, Calvo E, et al. Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy. Cell Reports. 2018;23(12):3685-3697.e4. doi:10.1016/j.celrep.2018.05.080