MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments
Authors: Eralp Dogu, Sara Mohammad-Taheri, Susan E. Abbatiello, Michael S. Bereman, Brendan MacLean, Birgit Schilling*, Olga Vitek*
Acquisition of System Suitability Samples (SSS) over course of 1 week on Triple Quadrupole Instruments.
SSS were interspersed into biomarker plasma assessment study samples throughout the week (Abbatiello et al., MCP 2015), study total runs ~ 300 acquistions
6 sites selected to show SSS performance (QC), monitoring digested 6 protein mix (15 peptides) as part of the larger study:
Comments and notes about uploaded files (also see slides attached):
86: Site86_Study9.1_SSS_QCED, quite nice and robust SSS performance throughout the study, basically for all monitored peptides
54: Site54_Study9-1_SSS_111611_QCED, quite nice SSS, very nice and robust for majority of peptides, One ‘empty’ run called SSS_run_109, also Slight ‘random’ problems with 2 hydrophobic, late eluting peptides VGP and also FFV (note a 3 letter code is used for any of the 15 monitored peptides, first 3 amino acids)
65: Study9.1 Site65 SSS runs_QCED, quite nice SSS, some slight variation that for the study heavy peptide spikes could account for.
56C: Study9_1_Site56C_SSS_Final_101711_QCED, quite nice SSS, Some of the SSS runs in the beginning have signal loss on some late eluting peptides (VGP, FFV), Most other peptides are fine, even for problem peptides things stabilized after several runs in the beginning, and the study could be performed fine.
56A: Study9p1_site_56A_5500_SSS_runs_final_QCED, overall ok. some sensitivity loss observed over the study, notes from operator :
- Changed the chip in pos 1 before the run # 155
- Cleaned the Mass Spec before the run # 255.; sensitivity jumped up nicely after cleaning to anticipated performance.
90: Study9S_Site90_SSS_QCED, SSS is borderline as signal goes up and down .... heavy peptides in study can account for a lot, but LOD/LOQ suffered a little bit