QCAL—a Novel Standard for Assessing Instrument Conditions for Proteome Analysis

• Published in: Journal of the American Society for Mass Spectrometry Vol. 19; no. 9; pp. 1275 - 1280
• Main Authors: Eyers, Claire E., Simpson, Deborah M., Wong, Stephen C.C., Beynon, Robert J., Gaskell, Simon J.
• Format: Journal Article
• Language: English
• Published: New York Elsevier Inc 01.09.2008; Springer-Verlag; Elsevier Science; Springer Nature B.V
• Subjects: Amino Acid Sequence; Analytical Chemistry; Analytical, structural and metabolic biochemistry; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bioinformatics; Biological and medical sciences; Biotechnology; Chemistry; Chemistry and Materials Science; Chromatography, High Pressure Liquid; E coli; Escherichia coli - metabolism; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Mass spectrometry; Molecular Sequence Data; Nanotechnology; Organic Chemistry; Peptides; Peptides - analysis; Proteins; Proteomics; Proteomics - methods; Proteomics - standards; Reagents; Reference Standards; Short Communication; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods; Spectroscopy, Fourier Transform Infrared - methods; Standardization; Tryptic Peptide; Instrument Resolution; Artificial Protein; Peptide; Homoarginine; Tandem mass spectrometry; Fourier transformation; Peptides; Coupled method; HPLC chromatography; Proteome; Matrix assisted laser desorption ionization; Ion cyclotron resonance spectrometry; Electrospray; Optimization; Protein; Operating conditions; Reversed phase chromatography; Analysis method; Synthetic product; Peptide fragment; Time of flight method; Polypeptide; Proteomics; Mass spectrometry
• ISSN: 1044-0305; 1879-1123
• DOI: 10.1016/j.jasms.2008.05.019

If proteome datasets are to be collated, shared, and merged for higher level proteome analyses, there is a need for generally accepted strategies and reagents for optimization and standardization of instrument performance. At present, there is no single protein or peptide standard set that is capable of assessing instrument performance for peptide separation and analysis in this manner. To create such a standard, we have used the recently described QconCAT methodology to generate an artificial protein, QCAL. This protein, a concatenation of tryptic peptides that is expressed in E. coli, provides a stoichiometrically controlled mixture of peptides that are amenable to analysis by all commonly used instrumentation platforms for proteomics. QCAL1 is described as a novel tool for the assessment and optimization of instruments used in proteome analyses, providing a platform for standardization.