High-Throughput Comprehensive Analysis of Human Plasma Proteins: A Step toward Population Proteomics

Dobrin Nedelkov, Kemmons A. Tubbs, Eric E. Niederkofler, Urban A. Kiernan, Randall W. Nelson

Research output: Contribution to journalArticle

59 Citations (Scopus)

Abstract

A high-throughput (HT) comprehensive analysis approach was developed for assaying proteins directly from human plasma. Proteins were selectively retrieved, by utilizing antibodies immobilized within affinity pipet tips, and eluted onto enzymatically active mass spectrometer targets for subsequent digestion and structural characterization. Several parameters, including uniform parallel protein elution from 96 affinity pipet tips, proper buffering for on-target digestion, termination of the digestion, and MALDI matrix (re)introduction, were evaluated and optimized. The approach was validated via parallel, high-throughput analysis of transthyretin (TTR) and transferrin (TRFE) from 96 identical plasma samples. The 96 parallel analyses for each protein were completed in less than 90 min, measured from protein extraction to insertion in the mass spectrometer. Virtually identical mass spectra were obtained from the 96 TTR analyses, characterized by the presence of 14 tryptic fragments that allowed TTR sequence mapping with 100% coverage. Database search returned TTR as the best match for all 96 data sets. In regard to the TRFE analyses, database searching using data from the 96 spectra returned TRFE as the best match for all but 1 of the spectra. TRFE was mapped with 47-69% sequence coverage, with gaps in the sequence coverage corresponding to the carbohydrate-containing peptide fragments and large and small trypsin fragments that fell outside the window of mass analysis. Overall, the combined high-throughput affinity capture-protein digestion approach showed high reproducibility and speed and yielded an exceptional level of protein characterization, suggesting its use in future population proteomics endeavors.

Original languageEnglish (US)
Pages (from-to)1733-1737
Number of pages5
JournalAnalytical Chemistry
Volume76
Issue number6
DOIs
StatePublished - Mar 15 2004

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Staphylococcal Protein A
Blood Proteins
Throughput
Prealbumin
Transferrin
Proteins
Mass spectrometers
Immobilized Antibodies
Plasma (human)
Peptide Fragments
Proteomics
Trypsin
Carbohydrates
Plasmas

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Nedelkov, D., Tubbs, K. A., Niederkofler, E. E., Kiernan, U. A., & Nelson, R. W. (2004). High-Throughput Comprehensive Analysis of Human Plasma Proteins: A Step toward Population Proteomics. Analytical Chemistry, 76(6), 1733-1737. https://doi.org/10.1021/ac035105+

High-Throughput Comprehensive Analysis of Human Plasma Proteins : A Step toward Population Proteomics. / Nedelkov, Dobrin; Tubbs, Kemmons A.; Niederkofler, Eric E.; Kiernan, Urban A.; Nelson, Randall W.

In: Analytical Chemistry, Vol. 76, No. 6, 15.03.2004, p. 1733-1737.

Research output: Contribution to journalArticle

Nedelkov, D, Tubbs, KA, Niederkofler, EE, Kiernan, UA & Nelson, RW 2004, 'High-Throughput Comprehensive Analysis of Human Plasma Proteins: A Step toward Population Proteomics', Analytical Chemistry, vol. 76, no. 6, pp. 1733-1737. https://doi.org/10.1021/ac035105+
Nedelkov, Dobrin ; Tubbs, Kemmons A. ; Niederkofler, Eric E. ; Kiernan, Urban A. ; Nelson, Randall W. / High-Throughput Comprehensive Analysis of Human Plasma Proteins : A Step toward Population Proteomics. In: Analytical Chemistry. 2004 ; Vol. 76, No. 6. pp. 1733-1737.
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