Stable Isotope-Labeled ApoA-1 as a Global Standard for Quantitative Proteomics Studies (Application Note 46)

  • Stable Isotope-Labeled ApoA-1 as a Global Standard for Quantitative Proteomics Studies (Application Note 46)
The majority of research within the field of MS-based proteomics has focused on the relative quantitation of candidate protein biomarkers using bottom-up LC-MS methodologies in conjunction with stable isotope-labeled standards (SIS). Though significant progress has been made in the field of quantitative proteomics, bottlenecks, such as assessing variability associated with proteolytic digestion and employing adequate quality control checks, often slow the process. In an effort to overcome these issues, Cambridge Isotope Laboratories, Inc. (CIL) is pleased to offer ProteusQC™, a kit designed to improve data quality and analytical reproducibility in quantitative proteomics.


This kit can:

  1. Enable retention time calibration
  2. Assess system suitability
  3. QC the digestion process
  4. Provide a global normalization standard of a user’s peptides /proteins of interest without the need for individual SIS peptides or proteins for each given target.
Kit Features and Benefits:
  • Precise retention and indexing
  • Digestion efficiencey check of ApoA-I
  • LC-MS system suitability 
  • Absolute/relative protein quantification
  • Reduced experimental cost 
  • Improved overall data quality


Given the importance of QC in LC-MS/MS-based proteomics experiments (from basic R&D to clinical applications), MacCoss and colleagues developed an external Skyline tool for evaluating and tracking platform performance in a systematic and longitudinal fashion.  Their newly launched pipeline, termed Panorama AutoQC (PMID: 27700092), builds on earlier work in Statistical Process Control in Proteomics (SProCoP; PMID: 24496601), enabling automated system/assay assessment in real time.  The pipeline is vendor and instrument independent, and supports an array of acquisition techniques (e.g., MRM, PRM).  Described in the Panorama AutoQC article is the QC workflow and its utility in system suitability, new technology evaluation, and long-term instrument performance with peptide mass spectral data.



Percy, A.J. et al. 2016. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential. Expert Rev Proteomics, 13(7):673-84. PMID 27341553

Bereman, M.S. et al. 2016. An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments. J Proteome Res., Oct 4. [Epub ahead of print]. PMID: 27700092

Wang, X. et al. 2014. QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics. Anal Chem, 4, 86(5): 2497-509. PMID: 24494671

Bereman, MS. et al. 2014. Implementation of statistical process control for proteomic experiments via LC MS/MS. J Am Soc Mass Spectrom, (4):581-7. PMID: 24496601 

Abbatiello, S.E. et al. 2013. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics, 12(9): 2623-39. PMID: 23689285

Escher, C. et al. 2012. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics, 12(8),1111-1121. PMID: 22577012

Hoofnagle, A.N. et al. 2012. Multiple-Reaction Monitoring–Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures. Clin Chem, 58(4), 777-781. PMID: 22307200

Kevin Millis, PhD

Kevin Millis, PhD

Senior Scientist, Application Development Manager

Kevin Millis, PhD, is the Senior Scientist and Market Development Manager for all NMR and Mass Spectrometry product lines. Kevin is responsible for Technical Services both internally and externally for all CIL customers as well as being responsible for the application and market development for the CIL products.

Andrew Percy, PhD

Andrew Percy, PhD

Senior Applications Chemist - Mass Spectrometry

Dr. Andrew Percy is the Senior Applications Chemist for Mass Spectrometry. His responsibilities minimally involve overseeing product development, identifying new product market opportunities, assisting in the analysis of products for MS ‘omics applications, and providing technical support to customers.

Tasha Agreste

Tasha Agreste

Proteomics Product Manager, Deuterated Reagents & Intermediates Product Manager, China Sales - Research Products

Tasha Agreste, Product Manager for the Proteomics product line, has been with CIL since 1989. During her tenure at CIL, Tasha has held various positions including customer service, sales and marketing, where she has proven to be instrumental in enhancing CIL’s customer relationships.