MassQC Help > Metrics > Overview          
What Are All These Metrics and Why Should I Care?

Click on the Metric map below to learn more about MassQC:

Which part of LC-MS/MS the metrics monitor Peak Intensity button Dynamic Range Total Ion Current MS1 Signal to Noise MS1 Ion Injection Time Peak Width Peak Width Variability Peptides per Minute Retention spread Trigger Point Low Intensity Trigger Point Oversampling MS1 Spectrum Count MS2 Spectrum Count Peptide count Per cent semitryptic Search Score Mass Accuracy Percent Charge +1 Percent charge +3 Percent Charge +4 Spray Instability Precursor m/z Peaks per spectrum High intensity ID rate Low intensity ID rate MS2 Signal to Noise MS2 Ion Inject Time Chromatography Ion Source Peptide Identification MS1 Dynamic Sampling MS2 Chromatography Ion Source MS1 Scans Dynamic Sampling MS2 Scans Peptide Identifications

These Metrics Allow You To Answer Key Questions:
  • Are you seeing the same number of peptides for each standard run?
  • Are your current measurements up to your best practices in the past?
  • Which factors might be contributing to the variation in performance and reproducibility

Metrics in the MassQC dashboard let you monitor the performance of chromatography, ion source, MS1, dynamic sampling, MS2 and peptide identifications.

Who Established the Metrics?

NIST, National Institute of Standards and Technology, created these performance metrics for proteomics as part of a program to improve reproducibility in proteomics funded by the NCI/NIH.

This study, the "Clinical Proteomics Assessment Technologies for Cancer" (CPTAC) study also had the following institutions participating.

  • Broad Institute of MIT and Harvard
  • Memorial Sloan-Kettering Cancer Center
  • Purdue University
  • University of California, San Francisco
  • Vanderbilt University School of Medicine

NIST has spent two years refining potential MS Metrics to determine which are informative and which are not for evaluating whether a tandem mass spectrometer used for proteomics research is performing optimally.

Proteome Software has built MassQC upon the foundation that NIST provided.


If you have questions, comments and/or insights about MassQC, you can share them on the MassQC Users Forum.

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