Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer
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Over the past decade, developments in high resolution mass spectrometry have enabled the high throughput analysis of intact proteins from complex proteomes, leading to the identification of thousands of proteoforms. Several previous reports on top-down proteomics (TDP) relied on hybrid ion trap-Fourier transform mass spectrometers combined with data-dependent acquisition strategies. To further reduce TDP to practice, we use a quadrupole-Orbitrap instrument coupled with software for proteoform-dependent data acquisition to identify and characterize nearly 2000 proteoforms at a 1% false discovery rate from human fibroblasts. By combining a 3 m/z isolation window with short transients to improve specificity and signal-to-noise for proteoforms >30 kDa, we demonstrate improving proteome coverage by capturing 439 proteoforms in the 30-60 kDa range. Three different data acquisition strategies were compared and resulted in the identification of many proteoforms not observed in replicate data-dependent experiments. Notably, the data set is reported with updated metrics and tools including a new viewer and assignment of permanent proteoform record identifiers for inclusion of highly characterized proteoforms (i.e., those with C-scores >40) in a repository curated by the Consortium for Top-Down Proteomics.
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Benchtop Orbitrap mass spectrometers are the most common instrument for proteomics, bypass cryogenic cooling, and offer high resolution and faster acquisition.
“Currently, benchtop Orbitrap mass spectrometers are the most common instrument for proteomics as they bypass the need for cryogenic cooling (which is needed for the magnets of FTICR instruments) while still offering high-resolution and faster acquisition speeds [98,99].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [98]
Tuning Orbitrap instrument parameters by the Brodbelt and Kelleher group increased its scope for targeted and global analysis of larger proteoforms.
“Work by the Brodbelt and Kelleher group in tuning the Orbitrap instrument parameters has increased its scope for targeted and global analysis of larger proteoforms [98,102].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [98]
HCD was used when the med/hi strategy was originally developed to investigate 30-60 kDa proteoforms because it was the only ion activation technique available on a Q Exactive mass spectrometer.
“HCD was used when the med/hi strategy was originally developed to investigate 30–60 kDa proteoforms as it was the only ion activation technique available on a Q Exactive mass spectrometer.23”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [23]
The medium/high DDA method collects MS1 spectra by averaging 10-15 short transients before Fourier transform, improving S/N at the cost of resolving power and yielding average rather than monoisotopic proteoform masses.
“broadband spectra (MS1) are collected by averaging a large number (i.e., 10–15) of short time-domain transients (i.e., microscans) prior to Fourier transform. In this way, the S/N of MS1 spectra is substantially improved at the expense of resolving power, with the resulting non-isotopically resolved spectra leading to the determination of an average proteoform mass rather than the monoisotopic one”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [23]
The 850-900 m/z window center was chosen because previous experimental data showed that the highest intensity charge states for most nanoflow electrospray-ionized proteins localize in that m/z region.
“The 850–900 m/z window center was selected for tPTCR runs based on the analysis of experimental data from previous studies23 that showed that the highest intensity charge states for most proteins ionized by nanoflow electrospray were localized in that m/z region.”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [23]
SIM cannot serve as a gas-phase fractionation method for large proteins because only one to three charge states per proteoform fall within a narrow SIM window, and determining charge from isotope spacing would require high resolution and reintroduce S/N problems; it also does not reduce overlap from coeluted analytes.
“Selected ion monitoring (SIM) cannot be applied as a GPF method for characterizing large proteins, because only a few charge states (typically 1 to 3, depending on SIM window width and protein mass) of each proteoform can be detected within a narrow SIM window: if charge states (and hence mass) cannot be determined using a charge state envelope, high resolution would be needed (to determine charge”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [23]
The medium/high DDA approach yielded hundreds of identifications of large proteoforms in the 30-60 kDa range from human fibroblasts.
“The medium/high data acquisition brought the identification of hundreds of large proteoforms (between 30 and 60 kDa) from human fibroblasts.23”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [23]
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Self-citation
- Authors
- Fornelli, L., Durbin, K. R., Fellers, R. T., Early, B. P., Greer, J. B., LeDuc, R. D., Compton, P. D., & Kelleher, N. L.
- Affiliations
- Northwestern University (US)
- Corresponding author
- Kelleher, Neil L.
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-12-02
- Volume
- 16
- Issue
- 2
- Pages
- 609-618
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC5395285
- OpenAlex
- W2508035970
- Cited by
- 88
- References
- 46
- Citations by year
- 2026: 3 · 2025: 10 · 2024: 5 · 2023: 3 · 2022: 10 · 2021: 11 · 2020: 10 · 2019: 11 · 2018: 16 · 2017: 8 · 2015: 1
- FWCI
- 5.81
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- National Institute of General Medical Sciences (GM067193, P41 GM108569)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- top-down proteomics, proteoforms, human proteome, data-dependent acquisition, human fibroblasts, proteoform identification, C-score, false discovery rate
- MeSH terms
- Fibroblasts, Humans, Software, Mass Spectrometry, Proteome, Proteomics
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