New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry

Henrique Dos Santos Seckler, Hae Min Park, Cameron M. Lloyd-Jones, Rafael D. Melani, Jeannie M. Camarillo, John T. Wilkins, Philip D. Compton, Neil L. Kelleher*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Different proteoform products of the same gene can exhibit differing associations with health and disease, and their patterns of modifications may offer more precise markers of phenotypic differences between individuals. However, currently employed protein-biomarker discovery and quantification tools, such as bottom-up proteomics and ELISAs, are mostly proteoform-unaware. Moreover, the current throughput for proteoform-level analyses by liquid chromatography mass spectrometry (LCMS) for quantitative top-down proteomics is incompatible with population-level biomarker surveys requiring robust, faster proteoform analysis. To this end, we developed immunoprecipitation coupled to SampleStream mass spectrometry (IP-SampleStream-MS) as a high-Throughput, automated technique for the targeted quantification of proteoforms. We applied IP-SampleStream-MS to serum samples of 25 individuals to assess the proteoform abundances of apolipoproteins A-I (ApoA-I) and C-III (ApoC-III). The results for ApoA-I were compared to those of LCMS for these individuals, with IP-SampleStream-MS showing a >7-fold higher throughput with >50% better analytical variation. Proteoform abundances measured by IP-SampleStream-MS correlated strongly to LCMS-based values (R2 = 0.6-0.9) and produced convergent proteoform-To-phenotype associations, namely, the abundance of canonical ApoA-I was associated with lower HDL-C (R = 0.5) and glycated ApoA-I with higher fasting glucose (R = 0.6). We also observed proteoform-To-phenotype associations for ApoC-III, 22 glycoproteoforms of which were characterized in this study. The abundance of ApoC-III modified by a single N-Acetyl hexosamine (HexNAc) was associated with indices of obesity, such as BMI, weight, and waist circumference (R ∼0.7). These data show IP-SampleStream-MS to be a robust, scalable workflow for high-Throughput associations of proteoforms to phenotypes.

Original languageEnglish (US)
Pages (from-to)1659-1670
Number of pages12
JournalJournal of the American Society for Mass Spectrometry
Issue number7
StatePublished - Jul 7 2021

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy


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