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 nf-SearchEngine executes the MSFragger search engine for peptide identification (https://github.com/CNIC-Proteomics/nf-SearchEngine). The available sample files are as follows: heteroplasmic_heart.zip: Heart tissues. Input files for nf-SearchEngine, derived from the study by Bagwan N, Bonzon-Kulichenko E, Calvo E, et al. (*), including Thermo raw files in mzML format and other data. heteroplasmic_liver.zip: Livertissues. Input files for nf-SearchEngine, derived from the same study (*), including Thermo raw files in mzML format and other data. heteroplasmic_muscle.zip: Muscle tissues. Input files for nf-SearchEngine, derived from the same study (*), including Thermo raw files in mzML formatand 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