High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

Shen, Yufeng; Tolic, Nikola; Piehowski, Paul D.; Shukla, Anil K.; Kim, Sangtae; Zhao, Rui; Qu, Yi; Robinson, E. W.; Smith, Richard D.; Pasa-Tolic, Ljiljana

doi:10.1016/j.chroma.2017.01.008

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics

Journal Article · Mon May 01 00:00:00 EDT 2017 · Journal of Chromatography

DOI:https://doi.org/10.1016/j.chroma.2017.01.008· OSTI ID:1364003

Shen, Yufeng; Tolic, Nikola; Piehowski, Paul D.; Shukla, Anil K.; Kim, Sangtae; Zhao, Rui; Qu, Yi; Robinson, E. W.; Smith, Richard D.; Pasa-Tolic, Ljiljana

We report development of an approach providing high-resolution RPLC of proteins and its utility for mass spectrometry-based top-down proteomics. A chromatographic peak capacity of ~450 was achieved for proteins and large polypeptides having MWs up to 43 kDa in the context of proteomics applications. RPLC column lengths from 20 to 200 cm, particle sizes from 1.5 to 5 m, bonding alkyl chains from C1 to C2, C4, C8, and C18, and particle surface structures that spanned porous, superficially porous (porous shell, core-shell), and nonporous were investigated at pressures up to14K psi. Column length was found as the most important factor for >20 kDa proteins in gradient RPLC, and shortening column length degraded RPLC resolution and sensitivity regardless of the size and surface structure of the packing particles used. The alkyl chains bonded to the silica particle surface significantly affected the RPLC recovery and efficiency, and short alkyl C1-C4 phases provided higher sensitivity and resolution than C8 and C18 phases. Long gradient separations (e.g., >10 hours) with long columns (e.g., 100 cm) were particularly effective in conjunction with use of high accuracy mass spectrometers (e.g., the Orbitrap Elite) for top-down proteomics with improved proteoform coverage by allowing multiple HCD, CID, and ETD dissociation modes. It was also found that HCD produced small fragments useful for proteoform identification, while low energy CID and ETD often complemented HCD by providing large fragments.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1364003

Report Number(s):: PNNL-SA-104738; 47418; KP1601010

Journal Information:: Journal of Chromatography, Journal Name: Journal of Chromatography Journal Issue: C Vol. 1498; ISSN 0021-9673

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

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