Details of the ProFI Yeast-UPS1 spiked-in experiment...

Samples (2 μg of yeast cell lysate + different spiked levels of UPS1) were analyzed in triplicate by nanoLC–MS/MS on an LTQ-Orbitrap Velos mass spectrometer. For more information on samples preparation and LC-MS/MS analyses, please refer to Ramus et al., J Proteomics. 2016 Jan 30;132:51-62. doi: 10.1016/j.jprot.2015.11.011.

SAMPLERAW FileMascot dat FilemzDB File
2µg levure UPS1 100fmol- Replicat 1OEMMA121101_61b.rawF083068.datOEMMA121101_61b.mzdb
2µg levure UPS1 100fmol- Replicat 2OEMMA121101_63b.rawF083069.datOEMMA121101_63b.mzdb
2µg levure UPS1 100fmol- Replicat 3OEMMA121101_65b.rawF083070.datOEMMA121101_65b.mzdb
2µg levure UPS1 10fmol – Replicat 1OEMMA121101_36b.rawF083064.datOEMMA121101_36b.mzdb
2µg levure UPS1 10fmol – Replicat 2OEMMA121101_38b.rawF083066.datOEMMA121101_38b.mzdb
2µg levure UPS1 10fmol – Replicat 3OEMMA121101_40b.rawF083067.datOEMMA121101_40b.mzdb

Short protocol description: Peaklist were generated using the Extract_msn.exe macro provided with Xcalibur. Peaklists were submitted to Mascot database searches (version 2.5.1). ESI-TRAP was chosen as the instrument, trypsin/P as the enzyme and 2 missed cleavages were allowed. Precursor and fragment mass error tolerances were set at 5 ppm and 0.8 Da, respectively. Peptide variable modifications allowed during the search were: acetyl (Protein N-ter), oxidation (M), whereas carbamidomethyl (C) was set as fixed modification. Databases used were yeast database from UniprotKB (S_cerevisiae_ 20121108.fasta, 7798 sequences), a compiled database containing the UPS1 human sequences (48 sequences) and the corresponding reversed databases in order to calculate FDR.