Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding Article Swipe
David Feldman
,
Jeremiah Nelson Sims
,
Xinting Li
,
Richard E. Johnson
,
Stacey Gerben
,
David E. Kim
,
Christian Richardson
,
Brian Koepnik
,
Helen E. Eisenach
,
Derrick R. Hicks
,
Erin C. Yang
,
Basile I. M. Wicky
,
Lukas F. Milles
,
Asim K. Bera
,
Evans Brackenbrough
,
Emily Joyce
,
Banumathi Sankaran
,
Joshua M. Lubner
,
Inna Goreshnik
,
Dionne Vafeados
,
Aza Allen
,
Lance Stewart
,
Michael J. MacCoss
,
Bingxu Liu
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.02.24.639402
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.02.24.639402
Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecules by DNA sequencing. However, the solution properties of individual protein molecules cannot be probed using such approaches because they are completely altered by DNA attachment. Mass spectrometry enables parallel evaluation of protein properties amenable to physical fractionation such as solubility and oligomeric state, but current approaches are limited to libraries of 1,000 or fewer proteins. Here, we improved mass spectrometry barcoding by co-synthesizing proteins with barcodes optimized to be highly multiplexable and minimally perturbative, scaling to libraries of >5,000 proteins. We use these barcodes together with mass spectrometry to assay the solution behavior of libraries of de novo -designed monomeric scaffolds, oligomers, binding proteins and nanocages, rapidly identifying design failure modes and successes.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.02.24.639402
- https://www.biorxiv.org/content/biorxiv/early/2025/02/28/2025.02.24.639402.full.pdf
- OA Status
- green
- Cited By
- 2
- References
- 38
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4408058763
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4408058763Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2025.02.24.639402Digital Object Identifier
- Title
-
Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcodingWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-02-28Full publication date if available
- Authors
-
David Feldman, Jeremiah Nelson Sims, Xinting Li, Richard E. Johnson, Stacey Gerben, David E. Kim, Christian Richardson, Brian Koepnik, Helen E. Eisenach, Derrick R. Hicks, Erin C. Yang, Basile I. M. Wicky, Lukas F. Milles, Asim K. Bera, Evans Brackenbrough, Emily Joyce, Banumathi Sankaran, Joshua M. Lubner, Inna Goreshnik, Dionne Vafeados, Aza Allen, Lance Stewart, Michael J. MacCoss, Bingxu LiuList of authors in order
- Landing page
-
https://doi.org/10.1101/2025.02.24.639402Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2025/02/28/2025.02.24.639402.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2025/02/28/2025.02.24.639402.full.pdfDirect OA link when available
- Concepts
-
Mass spectrometry, Peptide, Massive parallel sequencing, Massively parallel, Chemistry, DNA barcoding, Chromatography, Computer science, Computational biology, Parallel computing, Biology, DNA, Biochemistry, DNA sequencing, Evolutionary biologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 2Per-year citation counts (last 5 years)
- References (count)
-
38Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.are | 52, 79 |
| abstract_inverted_index.but | 76 |
| abstract_inverted_index.can | 6 |
| abstract_inverted_index.the | 8, 37, 123 |
| abstract_inverted_index.use | 114 |
| abstract_inverted_index.Mass | 58 |
| abstract_inverted_index.link | 21 |
| abstract_inverted_index.mass | 91, 119 |
| abstract_inverted_index.novo | 130 |
| abstract_inverted_index.such | 48, 70 |
| abstract_inverted_index.they | 51 |
| abstract_inverted_index.with | 97, 118 |
| abstract_inverted_index.1,000 | 84 |
| abstract_inverted_index.Here, | 88 |
| abstract_inverted_index.assay | 122 |
| abstract_inverted_index.fewer | 86 |
| abstract_inverted_index.given | 18 |
| abstract_inverted_index.large | 15 |
| abstract_inverted_index.modes | 143 |
| abstract_inverted_index.these | 115 |
| abstract_inverted_index.using | 47 |
| abstract_inverted_index.which | 27 |
| abstract_inverted_index.cannot | 44 |
| abstract_inverted_index.design | 141 |
| abstract_inverted_index.highly | 102 |
| abstract_inverted_index.probed | 46 |
| abstract_inverted_index.state, | 75 |
| abstract_inverted_index.Library | 1 |
| abstract_inverted_index.altered | 54 |
| abstract_inverted_index.because | 50 |
| abstract_inverted_index.between | 22 |
| abstract_inverted_index.binding | 9, 135 |
| abstract_inverted_index.current | 77 |
| abstract_inverted_index.enables | 28, 60 |
| abstract_inverted_index.failure | 142 |
| abstract_inverted_index.limited | 80 |
| abstract_inverted_index.members | 13 |
| abstract_inverted_index.methods | 5 |
| abstract_inverted_index.protein | 16, 23, 42, 64 |
| abstract_inverted_index.rapidly | 139 |
| abstract_inverted_index.scaling | 107 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.However, | 36 |
| abstract_inverted_index.amenable | 66 |
| abstract_inverted_index.barcodes | 98, 116 |
| abstract_inverted_index.behavior | 125 |
| abstract_inverted_index.improved | 90 |
| abstract_inverted_index.parallel | 61 |
| abstract_inverted_index.physical | 20, 68 |
| abstract_inverted_index.proteins | 96, 136 |
| abstract_inverted_index.solution | 38, 124 |
| abstract_inverted_index.together | 117 |
| abstract_inverted_index.>5,000 | 111 |
| abstract_inverted_index.-designed | 131 |
| abstract_inverted_index.barcoding | 93 |
| abstract_inverted_index.determine | 7 |
| abstract_inverted_index.libraries | 17, 82, 109, 127 |
| abstract_inverted_index.minimally | 105 |
| abstract_inverted_index.molecules | 32, 43 |
| abstract_inverted_index.monomeric | 132 |
| abstract_inverted_index.optimized | 99 |
| abstract_inverted_index.proteins. | 87, 112 |
| abstract_inverted_index.screening | 2 |
| abstract_inverted_index.selection | 4 |
| abstract_inverted_index.sequence, | 26 |
| abstract_inverted_index.activities | 10 |
| abstract_inverted_index.approaches | 49, 78 |
| abstract_inverted_index.completely | 53 |
| abstract_inverted_index.evaluation | 62 |
| abstract_inverted_index.functional | 31 |
| abstract_inverted_index.individual | 12, 41 |
| abstract_inverted_index.nanocages, | 138 |
| abstract_inverted_index.nucleotide | 25 |
| abstract_inverted_index.oligomeric | 74 |
| abstract_inverted_index.oligomers, | 134 |
| abstract_inverted_index.properties | 39, 65 |
| abstract_inverted_index.scaffolds, | 133 |
| abstract_inverted_index.solubility | 72 |
| abstract_inverted_index.successes. | 145 |
| abstract_inverted_index.attachment. | 57 |
| abstract_inverted_index.identifying | 140 |
| abstract_inverted_index.sequencing. | 35 |
| abstract_inverted_index.spectrometry | 59, 92, 120 |
| abstract_inverted_index.fractionation | 69 |
| abstract_inverted_index.multiplexable | 103 |
| abstract_inverted_index.perturbative, | 106 |
| abstract_inverted_index.identification | 29 |
| abstract_inverted_index.co-synthesizing | 95 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 95 |
| corresponding_author_ids | https://openalex.org/A5049784548 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 24 |
| corresponding_institution_ids | https://openalex.org/I201448701 |
| citation_normalized_percentile.value | 0.86596005 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |