The emerging landscape of single-molecule protein sequencing technologies

Javier Antonio Alfaro; Peggy Bohländer; Mingjie Dai; Mike Filius; Cecil J. Howard; Xander F. van Kooten; Shilo Ohayon; Adam Pomorski; Sonja Schmid; Aleksei Aksimentiev; Eric V. Anslyn; Georges Bedran; Chan Cao; Mauro Chinappi; Etienne Coyaud; Cees Dekker; Gunnar Dittmar; Nicholas Drachman; Rienk Eelkema; David Goodlett; Sébastien Hentz; Umesh Kalathiya; Neil L. Kelleher; Ryan T. Kelly; Zvi Kelman; Sung Hyun Kim; Bernhard Kuster; David Rodriguez-Larrea; Stuart Lindsay; Giovanni Maglia; Edward M. Marcotte; John P. Marino; Christophe Masselon; Michael Mayer; Patroklos Samaras; Kumar Sarthak; Lusia Sepiashvili; Derek Stein; Meni Wanunu; Mathias Wilhelm; Peng Yin; Amit Meller; Chirlmin Joo

doi:10.1038/s41592-021-01143-1

The emerging landscape of single-molecule protein sequencing technologies

Javier Antonio Alfaro^*
, Peggy Bohländer
, Mingjie Dai
, Mike Filius
, Cecil J. Howard
, Xander F. van Kooten
, Shilo Ohayon
, Adam Pomorski
, Sonja Schmid
, Aleksei Aksimentiev
, Eric V. Anslyn
, Georges Bedran
, Chan Cao
, Mauro Chinappi
, Etienne Coyaud
, Cees Dekker
, Gunnar Dittmar
, Nicholas Drachman
, Rienk Eelkema
, David Goodlett

Sébastien Hentz, Umesh Kalathiya, Neil L. Kelleher, Ryan T. Kelly, Zvi Kelman, Sung Hyun Kim, Bernhard Kuster, David Rodriguez-Larrea, Stuart Lindsay, Giovanni Maglia, Edward M. Marcotte, John P. Marino, Christophe Masselon, Michael Mayer, Patroklos Samaras, Kumar Sarthak, Lusia Sepiashvili, Derek Stein, Meni Wanunu, Mathias Wilhelm, Peng Yin, Amit Meller, Chirlmin Joo

^*Corresponding author for this work

Proteomics of Cellular Signaling

Research output: Contribution to journal › Review article › peer-review

287 Citations (Scopus)

Abstract

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

Original language	English
Pages (from-to)	604-617
Number of pages	14
Journal	Nature Methods
Volume	18
Issue number	6
DOIs	https://doi.org/10.1038/s41592-021-01143-1
Publication status	Published - Jun 2021

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10.1038/s41592-021-01143-1

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Alfaro, J. A., Bohländer, P., Dai, M., Filius, M., Howard, C. J., van Kooten, X. F., Ohayon, S., Pomorski, A., Schmid, S., Aksimentiev, A., Anslyn, E. V., Bedran, G., Cao, C., Chinappi, M., Coyaud, E., Dekker, C., Dittmar, G., Drachman, N., Eelkema, R., ... Joo, C. (2021). The emerging landscape of single-molecule protein sequencing technologies. Nature Methods, 18(6), 604-617. https://doi.org/10.1038/s41592-021-01143-1

@article{a86a2f20d39d4397b129b942995e323f,

title = "The emerging landscape of single-molecule protein sequencing technologies",

abstract = "Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.",

author = "Alfaro, \{Javier Antonio\} and Peggy Bohl{\"a}nder and Mingjie Dai and Mike Filius and Howard, \{Cecil J.\} and \{van Kooten\}, \{Xander F.\} and Shilo Ohayon and Adam Pomorski and Sonja Schmid and Aleksei Aksimentiev and Anslyn, \{Eric V.\} and Georges Bedran and Chan Cao and Mauro Chinappi and Etienne Coyaud and Cees Dekker and Gunnar Dittmar and Nicholas Drachman and Rienk Eelkema and David Goodlett and S{\'e}bastien Hentz and Umesh Kalathiya and Kelleher, \{Neil L.\} and Kelly, \{Ryan T.\} and Zvi Kelman and Kim, \{Sung Hyun\} and Bernhard Kuster and David Rodriguez-Larrea and Stuart Lindsay and Giovanni Maglia and Marcotte, \{Edward M.\} and Marino, \{John P.\} and Christophe Masselon and Michael Mayer and Patroklos Samaras and Kumar Sarthak and Lusia Sepiashvili and Derek Stein and Meni Wanunu and Mathias Wilhelm and Peng Yin and Amit Meller and Chirlmin Joo",

note = "Funding Information: We thank all the presenting delegates of the 2019 Single-Molecule Protein Sequencing conference (Jerusalem). We thank the PL-Grid and CI-TASK Infrastructure, Poland, for providing their hardware and software resources. S.S. acknowledges Postdoc Mobility fellowship no. P400PB 180889 from the Swiss National Science Foundation. E.M.M. and E.V.A. acknowledge funding from the NIH (R35 GM122480 and R01 DK110520 to E.M.M.), Welch Foundation (F1515 to E.M.M. and F-0046 to E.V.A.), Army Research Office grant W911NF-12-1-0390 and Erisyon. E.M.M. and E.V.A. are co-founders and shareholders of Erisyon. R.T.K. acknowledges funding from NIGMS (R01 GM138931). P.Y. acknowledges funding from an NIH Director{\textquoteright}s New Innovator Award (1DP2OD007292), an NIH Transformative Research Award (1R01EB018659), an NIH Pioneer Award (1DP1GM133052), and the Molecular Robotics Initiative fund at the Wyss Institute for Biologically Inspired Engineering. M.D. acknowledges funding from a Systems Biology Department Fellowship from Harvard Medical School and a Technology Development Fellowship from Wyss Institute for Biologically Inspired Engineering. C.C. acknowledges the Peter and Traudl Engelhorn Foundation. C.D. acknowledges the ERC Advanced Grant Looping DNA (no. 883684) and the NWO programs NanoFront and Basyc. E.M.M., E.V.A. and C.J.H. are co-inventors on patents relevant to this work. S.O. acknowledges the support of the Azrieli fellowship foundation. N.L.K. acknowledges funding from the Paul G. Allen Frontiers Program (11715), the NIH HuBMAP program (UH3 CA246635) and NIGMS (P41 GM108569). J.P.M. and Z.K. acknowledge internal funding from NIST and are co-inventors on patents relevant to this work. M. Wanunu acknowledges funding from the NIH (HG009186). K.S. and A.A. acknowledge funding from the NSF (PHY-1430124). C.J., C.D. and R.E. acknowledge funding from NWO-I (SMPS). C.J. acknowledges funding from HFSP (RGP0026/2019). A.P. acknowledges Bekker fellowship no. PPN/BEK/2018/1/00296 from the Polish National Agency for Academic Exchange. C.M. and S.H. acknowledge funding from the European Research Council (ERC {\textquoteleft}Enlightened{\textquoteright}, GA 616251) and the CEA Transverse Program {\textquoteleft}Instrumentation and Detection{\textquoteright} (PTC-ID VIRIONEMS). Support from the Proteomics French Infrastructure (PROFI) is also gratefully acknowledged. G.D. acknowledges funding from FNR (C17/BM/11642138). M.M. acknowledges funding from the Adolphe Merkle Foundation, the Michael J. Fox Foundation for Parkinson{\textquoteright}s Research (grant 17924) and the Swiss National Science Foundation (grant no. 200021-169304). A.M. acknowledges funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme under grant agreement no. 833399-ERC NanoProt-ID and ISF award 3485/19. M.C. acknowledges computational resources from CINECA (NATWE project) and the Swiss National Super-Computing Centre (CSCS), under projects sm11 and s865. E.C. acknowledges funding from I-Site Lille, R{\'e}gion Hauts-de-France, and the European Union{\textquoteright}s Horizon 2020 Marie Sk{\l}odowska-Curie no. 843052. The study was supported by the project {\textquoteleft}International Centre for Cancer Vaccine Science{\textquoteright} that is carried out within the International Agendas Programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund. D.G. thanks Genome Canada and Genome British Columbia for financial support for Genomics Technology Platforms (GTP) funding for operations and technology development (264PRO). We thank V. Globyte for critical reading. Publisher Copyright: {\textcopyright} 2021, Springer Nature America, Inc.",

year = "2021",

month = jun,

doi = "10.1038/s41592-021-01143-1",

language = "English",

volume = "18",

pages = "604--617",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "6",

}

Alfaro, JA, Bohländer, P, Dai, M, Filius, M, Howard, CJ, van Kooten, XF, Ohayon, S, Pomorski, A, Schmid, S, Aksimentiev, A, Anslyn, EV, Bedran, G, Cao, C, Chinappi, M, Coyaud, E, Dekker, C, Dittmar, G, Drachman, N, Eelkema, R, Goodlett, D, Hentz, S, Kalathiya, U, Kelleher, NL, Kelly, RT, Kelman, Z, Kim, SH, Kuster, B, Rodriguez-Larrea, D, Lindsay, S, Maglia, G, Marcotte, EM, Marino, JP, Masselon, C, Mayer, M, Samaras, P, Sarthak, K, Sepiashvili, L, Stein, D, Wanunu, M, Wilhelm, M, Yin, P, Meller, A & Joo, C 2021, 'The emerging landscape of single-molecule protein sequencing technologies', Nature Methods, vol. 18, no. 6, pp. 604-617. https://doi.org/10.1038/s41592-021-01143-1

TY - JOUR

T1 - The emerging landscape of single-molecule protein sequencing technologies

AU - Alfaro, Javier Antonio

AU - Bohländer, Peggy

AU - Dai, Mingjie

AU - Filius, Mike

AU - Howard, Cecil J.

AU - van Kooten, Xander F.

AU - Ohayon, Shilo

AU - Pomorski, Adam

AU - Schmid, Sonja

AU - Aksimentiev, Aleksei

AU - Anslyn, Eric V.

AU - Bedran, Georges

AU - Cao, Chan

AU - Chinappi, Mauro

AU - Coyaud, Etienne

AU - Dekker, Cees

AU - Dittmar, Gunnar

AU - Drachman, Nicholas

AU - Eelkema, Rienk

AU - Goodlett, David

AU - Hentz, Sébastien

AU - Kalathiya, Umesh

AU - Kelleher, Neil L.

AU - Kelly, Ryan T.

AU - Kelman, Zvi

AU - Kim, Sung Hyun

AU - Kuster, Bernhard

AU - Rodriguez-Larrea, David

AU - Lindsay, Stuart

AU - Maglia, Giovanni

AU - Marcotte, Edward M.

AU - Marino, John P.

AU - Masselon, Christophe

AU - Mayer, Michael

AU - Samaras, Patroklos

AU - Sarthak, Kumar

AU - Sepiashvili, Lusia

AU - Stein, Derek

AU - Wanunu, Meni

AU - Wilhelm, Mathias

AU - Yin, Peng

AU - Meller, Amit

AU - Joo, Chirlmin

N1 - Funding Information: We thank all the presenting delegates of the 2019 Single-Molecule Protein Sequencing conference (Jerusalem). We thank the PL-Grid and CI-TASK Infrastructure, Poland, for providing their hardware and software resources. S.S. acknowledges Postdoc Mobility fellowship no. P400PB 180889 from the Swiss National Science Foundation. E.M.M. and E.V.A. acknowledge funding from the NIH (R35 GM122480 and R01 DK110520 to E.M.M.), Welch Foundation (F1515 to E.M.M. and F-0046 to E.V.A.), Army Research Office grant W911NF-12-1-0390 and Erisyon. E.M.M. and E.V.A. are co-founders and shareholders of Erisyon. R.T.K. acknowledges funding from NIGMS (R01 GM138931). P.Y. acknowledges funding from an NIH Director’s New Innovator Award (1DP2OD007292), an NIH Transformative Research Award (1R01EB018659), an NIH Pioneer Award (1DP1GM133052), and the Molecular Robotics Initiative fund at the Wyss Institute for Biologically Inspired Engineering. M.D. acknowledges funding from a Systems Biology Department Fellowship from Harvard Medical School and a Technology Development Fellowship from Wyss Institute for Biologically Inspired Engineering. C.C. acknowledges the Peter and Traudl Engelhorn Foundation. C.D. acknowledges the ERC Advanced Grant Looping DNA (no. 883684) and the NWO programs NanoFront and Basyc. E.M.M., E.V.A. and C.J.H. are co-inventors on patents relevant to this work. S.O. acknowledges the support of the Azrieli fellowship foundation. N.L.K. acknowledges funding from the Paul G. Allen Frontiers Program (11715), the NIH HuBMAP program (UH3 CA246635) and NIGMS (P41 GM108569). J.P.M. and Z.K. acknowledge internal funding from NIST and are co-inventors on patents relevant to this work. M. Wanunu acknowledges funding from the NIH (HG009186). K.S. and A.A. acknowledge funding from the NSF (PHY-1430124). C.J., C.D. and R.E. acknowledge funding from NWO-I (SMPS). C.J. acknowledges funding from HFSP (RGP0026/2019). A.P. acknowledges Bekker fellowship no. PPN/BEK/2018/1/00296 from the Polish National Agency for Academic Exchange. C.M. and S.H. acknowledge funding from the European Research Council (ERC ‘Enlightened’, GA 616251) and the CEA Transverse Program ‘Instrumentation and Detection’ (PTC-ID VIRIONEMS). Support from the Proteomics French Infrastructure (PROFI) is also gratefully acknowledged. G.D. acknowledges funding from FNR (C17/BM/11642138). M.M. acknowledges funding from the Adolphe Merkle Foundation, the Michael J. Fox Foundation for Parkinson’s Research (grant 17924) and the Swiss National Science Foundation (grant no. 200021-169304). A.M. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 833399-ERC NanoProt-ID and ISF award 3485/19. M.C. acknowledges computational resources from CINECA (NATWE project) and the Swiss National Super-Computing Centre (CSCS), under projects sm11 and s865. E.C. acknowledges funding from I-Site Lille, Région Hauts-de-France, and the European Union’s Horizon 2020 Marie Skłodowska-Curie no. 843052. The study was supported by the project ‘International Centre for Cancer Vaccine Science’ that is carried out within the International Agendas Programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund. D.G. thanks Genome Canada and Genome British Columbia for financial support for Genomics Technology Platforms (GTP) funding for operations and technology development (264PRO). We thank V. Globyte for critical reading. Publisher Copyright: © 2021, Springer Nature America, Inc.

PY - 2021/6

Y1 - 2021/6

N2 - Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

AB - Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

UR - https://www.scopus.com/pages/publications/85107573284

U2 - 10.1038/s41592-021-01143-1

DO - 10.1038/s41592-021-01143-1

M3 - Review article

C2 - 34099939

AN - SCOPUS:85107573284

SN - 1548-7091

VL - 18

SP - 604

EP - 617

JO - Nature Methods

JF - Nature Methods

IS - 6

ER -

The emerging landscape of single-molecule protein sequencing technologies

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