Developing a peptide concatemer (PepCon) as a process control for LC-MS based proteomics

Rubinfeld, Bonnee; Anex, Deon; Strout, Cheryl; Lyman, Matt

doi:10.1016/j.ijms.2023.117104

Developing a peptide concatemer (PepCon) as a process control for LC-MS based proteomics

Journal Article · Tue Jul 25 00:00:00 EDT 2023 · International Journal of Mass Spectrometry

DOI:https://doi.org/10.1016/j.ijms.2023.117104· OSTI ID:2246704

Rubinfeld, Bonnee ^[1]; Anex, Deon ^[1]; Strout, Cheryl ^[1]; Lyman, Matt ^[1]

Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Quantitative concatenated peptide (QconCAT) technology is currently used for the absolute quantification of proteins of interest in a biological sample. It relies on artificially created proteins that are concatenations of different, isotopically labeled peptides. Because these isotopically labeled peptides are at a 1:1 ratio and correspond to naturally occurring peptides in the biological sample, each peptide can be used as a standard for the absolute quantitation of all proteins of interest at once. Although the QconCAT technology has utility for quantitation of known peptides in a mixture, it is not helpful for scientists who need a proteomics standard (1) that can be spiked into a protein mixture at an extremely low level, (2) that can be co-purified during sample fractionation, and (3) that is optimized for ESI used in mass spectrometry. Thus, there exists a need for an ideal standard protein that is large enough to behave as a protein but consists of multiple, concatenated copies of the same peptide, which, upon digestion, amplifies (e.g., >10-fold) into a detectable peptide species. Here, this technical report describes the development of “PepCon”, a peptide concatemer that fulfills this unmet need.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 2246704

Report Number(s):: LLNL--JRNL-857789; 1086551

Journal Information:: International Journal of Mass Spectrometry, Journal Name: International Journal of Mass Spectrometry Vol. 492; ISSN 1387-3806

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (13)

QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification Simpson, Deborah M.; Beynon, Robert J. Analytical and Bioanalytical Chemistry, Vol. 404, Issue 4 https://doi.org/10.1007/s00216-012-6230-1	journal	July 2012
Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events Oliveira, Pedro H.; Prather, Kristala Jones; Prazeres, Duarte M. F. Applied Microbiology and Biotechnology, Vol. 87, Issue 6 https://doi.org/10.1007/s00253-010-2671-7	journal	May 2010
Instability of repeated DNAs during transformation in Escherichia coli Hashem, Vera I.; Klysik, Elzbieta A.; Rosche, William A. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 502, Issue 1-2 https://doi.org/10.1016/S0027-5107(02)00027-1	journal	May 2002
Amino Acid Contribution to Protein Solubility: Asp, Glu, and Ser Contribute more Favorably than the other Hydrophilic Amino Acids in RNase Sa Trevino, Saul R.; Scholtz, J. Martin; Pace, C. Nick Journal of Molecular Biology, Vol. 366, Issue 2 https://doi.org/10.1016/j.jmb.2006.10.026	journal	February 2007
Design and expression of a QconCAT protein to validate Hi3 protein quantification of influenza vaccine antigens Smith, Daryl G. S.; Gingras, Geneviève; Aubin, Yves Journal of Proteomics, Vol. 146 https://doi.org/10.1016/j.jprot.2016.06.024	journal	September 2016
MALDI versus ESI: The Impact of the Ion Source on Peptide Identification Nadler, Wiebke Maria; Waidelich, Dietmar; Kerner, Alexander Journal of Proteome Research, Vol. 16, Issue 3 https://doi.org/10.1021/acs.jproteome.6b00805	journal	February 2017
Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics Swaney, Danielle L.; Wenger, Craig D.; Coon, Joshua J. Journal of Proteome Research, Vol. 9, Issue 3 https://doi.org/10.1021/pr900863u	journal	March 2010
Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides Beynon, Robert J.; Doherty, Mary K.; Pratt, Julie M. Nature Methods, Vol. 2, Issue 8 https://doi.org/10.1038/nmeth774	journal	July 2005
Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes Pratt, Julie M.; Simpson, Deborah M.; Doherty, Mary K. Nature Protocols, Vol. 1, Issue 2 https://doi.org/10.1038/nprot.2006.129	journal	August 2006
Detergent binding explains anomalous SDS-PAGE migration of membrane proteins Rath, Arianna; Glibowicka, Mira; Nadeau, Vincent G. Proceedings of the National Academy of Sciences, Vol. 106, Issue 6 https://doi.org/10.1073/pnas.0813167106	journal	January 2009
Instability of repetitive DNA sequences: The role of replication in multiple mechanisms Bzymek, M.; Lovett, S. T. Proceedings of the National Academy of Sciences, Vol. 98, Issue 15 https://doi.org/10.1073/pnas.111008398	journal	July 2001
Absolute Multiplexed Quantitative Analysis of Protein Expression during Muscle Development Using QconCAT Rivers, Jenny; Simpson, Deborah M.; Robertson, Duncan H. L. Molecular & Cellular Proteomics, Vol. 6, Issue 8 https://doi.org/10.1074/mcp.M600456-MCP200	journal	August 2007
Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins Johnson, James; Harman, Victoria M.; Franco, Catarina BMC Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s12915-021-01135-9	journal	September 2021

Similar Records

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS

Book · Thu Feb 11 23:00:00 EST 2016 · OSTI ID:1240224

A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments

Journal Article · Thu Jan 31 23:00:00 EST 2013 · Proteomics, 13(3-4):493-503 · OSTI ID:1072870

The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS

Journal Article · Tue Jan 01 23:00:00 EST 2008 · Journal of Proteome Research, 7(1):164-169 · OSTI ID:924662

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES

Developing a peptide concatemer (PepCon) as a process control for LC-MS based proteomics

Citation Formats

References (13)

Similar Records

Related Subjects