Important considerations for each stage of quantitative proteomics

Important considerations for each stage of quantitative proteomics

Sample Preparation. To maximize quality protein identifications and reproducibility, MSF clients should ensure:

  • Careful handling and storage of samples to ensure equal treatment between all replicates and sample groups
  • Protease inhibitors should be used early in sample preparation to reduce non-specific protein degradation prior to targeted digestion
  • Accurate quantitation of starting material (protein) and/or injection material (peptides). Recommend BCA assay.
  • Avoidance or removal of non-peptide substances such as detergents and salts that can interfere with chromatographic separation, ionization efficiency, and detection, resulting in reduced instrument sensitivity
  • Please note: MSF can provide optimized sample preparation protocols for users, full-service sample preparation, and/or advice on efficient extraction, digestion, and cleaning of sample for quantitative LC-MS. Please reach out with any questions or concerns before designing your quantitative proteomics experiments


Instrument maintenance, calibration, and quality control (QC) standards. Clients that submit samples to MSF can be confident that:

  • Instruments used for quantitative proteomics receive scheduled preventative maintenance and cleaning, mass calibration (weekly minimum) and monthly system calibration
  • Protein identification statistics from a standard QC sample (complex human proteome) are reviewed by MSF staff weekly (minimum) for overall system performance based on pre-defined criteria
  • MSF staff monitors chromatographic standards and instrument status daily for optimal functioning of all components in real-time


Data processing. LC-MS/MS of complex proteomes generates complex data sets. Assessment and analysis by MSF staff ensure high quality data from start to finish:

  • Initial quality control steps include a manual confirmation of effective sample separation based on total ion chromatogram features
  • Full analysis using PEAKS Q software with assessment of QC statistics, selection of appropriate data filters, and review of output data
  • Assistance with Minimum Information about a Proteomics Experiment (MIAPE) reporting guidelines when required