Literature DB >> 29945450

Transformative Opportunities for Single-Cell Proteomics.

Harrison Specht1, Nikolai Slavov1,2.   

Abstract

Many pressing medical challenges, such as diagnosing disease, enhancing directed stem-cell differentiation, and classifying cancers, have long been hindered by limitations in our ability to quantify proteins in single cells. Mass spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thousands of proteins and proteoforms across many thousands of single cells. We outline specific technological developments and ideas that can increase the sensitivity and throughput of single-cell MS by orders of magnitude and usher in this new age. These advances will transform medicine and ultimately contribute to understanding biological systems on an entirely new level.

Entities:  

Keywords:  Simpson’s paradox; causal inference; counting noise; disease diagnosis; network inference; sample preparation; single-cell analysis; single-cell mass-spectrometry; systems biology; ultrasensitive proteomics

Mesh:

Substances:

Year:  2018        PMID: 29945450      PMCID: PMC6089608          DOI: 10.1021/acs.jproteome.8b00257

Source DB:  PubMed          Journal:  J Proteome Res        ISSN: 1535-3893            Impact factor:   4.466


  38 in total

1.  Metabolic cycling without cell division cycling in respiring yeast.

Authors:  Nikolai Slavov; Joanna Macinskas; Amy Caudy; David Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-07       Impact factor: 11.205

2.  Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device.

Authors:  Florian Meier; Scarlet Beck; Niklas Grassl; Markus Lubeck; Melvin A Park; Oliver Raether; Matthias Mann
Journal:  J Proteome Res       Date:  2015-11-13       Impact factor: 4.466

3.  Core transcriptional regulatory circuitry in human embryonic stem cells.

Authors:  Laurie A Boyer; Tong Ihn Lee; Megan F Cole; Sarah E Johnstone; Stuart S Levine; Jacob P Zucker; Matthew G Guenther; Roshan M Kumar; Heather L Murray; Richard G Jenner; David K Gifford; Douglas A Melton; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2005-09-23       Impact factor: 41.582

4.  Measuring and managing ratio compression for accurate iTRAQ/TMT quantification.

Authors:  Mikhail M Savitski; Toby Mathieson; Nico Zinn; Gavain Sweetman; Carola Doce; Isabelle Becher; Fiona Pachl; Bernhard Kuster; Marcus Bantscheff
Journal:  J Proteome Res       Date:  2013-07-02       Impact factor: 4.466

Review 5.  Exploring the new world of the genome with DNA microarrays.

Authors:  P O Brown; D Botstein
Journal:  Nat Genet       Date:  1999-01       Impact factor: 38.330

6.  Green fluorescent protein as a marker for gene expression.

Authors:  M Chalfie; Y Tu; G Euskirchen; W W Ward; D C Prasher
Journal:  Science       Date:  1994-02-11       Impact factor: 47.728

7.  Proteogenomic characterization of human colon and rectal cancer.

Authors:  Bing Zhang; Jing Wang; Xiaojing Wang; Jing Zhu; Qi Liu; Zhiao Shi; Matthew C Chambers; Lisa J Zimmerman; Kent F Shaddox; Sangtae Kim; Sherri R Davies; Sean Wang; Pei Wang; Christopher R Kinsinger; Robert C Rivers; Henry Rodriguez; R Reid Townsend; Matthew J C Ellis; Steven A Carr; David L Tabb; Robert J Coffey; Robbert J C Slebos; Daniel C Liebler
Journal:  Nature       Date:  2014-07-20       Impact factor: 49.962

Review 8.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

9.  Single Cell Proteomics Using Frog (Xenopus laevis) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content.

Authors:  Liangliang Sun; Kyle M Dubiak; Elizabeth H Peuchen; Zhenbin Zhang; Guijie Zhu; Paul W Huber; Norman J Dovichi
Journal:  Anal Chem       Date:  2016-06-22       Impact factor: 6.986

10.  Post-transcriptional regulation across human tissues.

Authors:  Alexander Franks; Edoardo Airoldi; Nikolai Slavov
Journal:  PLoS Comput Biol       Date:  2017-05-08       Impact factor: 4.475

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  37 in total

1.  Embracing Systems Toxicology at Single-Cell Resolution.

Authors:  Qiang Zhang; W Michael Caudle; Jingbo Pi; Sudin Bhattacharya; Melvin E Andersen; Norbert E Kaminski; Rory B Conolly
Journal:  Curr Opin Toxicol       Date:  2019-04-19

Review 2.  The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

Authors:  Deanne M Taylor; Bruce J Aronow; Kai Tan; Kathrin Bernt; Nathan Salomonis; Casey S Greene; Alina Frolova; Sarah E Henrickson; Andrew Wells; Liming Pei; Jyoti K Jaiswal; Jeffrey Whitsett; Kathryn E Hamilton; Sonya A MacParland; Judith Kelsen; Robert O Heuckeroth; S Steven Potter; Laura A Vella; Natalie A Terry; Louis R Ghanem; Benjamin C Kennedy; Ingo Helbig; Kathleen E Sullivan; Leslie Castelo-Soccio; Arnold Kreigstein; Florian Herse; Martijn C Nawijn; Gerard H Koppelman; Melissa Haendel; Nomi L Harris; Jo Lynne Rokita; Yuanchao Zhang; Aviv Regev; Orit Rozenblatt-Rosen; Jennifer E Rood; Timothy L Tickle; Roser Vento-Tormo; Saif Alimohamed; Monkol Lek; Jessica C Mar; Kathleen M Loomes; David M Barrett; Prech Uapinyoying; Alan H Beggs; Pankaj B Agrawal; Yi-Wen Chen; Amanda B Muir; Lana X Garmire; Scott B Snapper; Javad Nazarian; Steven H Seeholzer; Hossein Fazelinia; Larry N Singh; Robert B Faryabi; Pichai Raman; Noor Dawany; Hongbo Michael Xie; Batsal Devkota; Sharon J Diskin; Stewart A Anderson; Eric F Rappaport; William Peranteau; Kathryn A Wikenheiser-Brokamp; Sarah Teichmann; Douglas Wallace; Tao Peng; Yang-Yang Ding; Man S Kim; Yi Xing; Sek Won Kong; Carsten G Bönnemann; Kenneth D Mandl; Peter S White
Journal:  Dev Cell       Date:  2019-03-28       Impact factor: 12.270

Review 3.  A systems approach to clinical oncology uses deep phenotyping to deliver personalized care.

Authors:  James T Yurkovich; Qiang Tian; Nathan D Price; Leroy Hood
Journal:  Nat Rev Clin Oncol       Date:  2019-10-16       Impact factor: 66.675

Review 4.  The quest of cell surface markers for stem cell therapy.

Authors:  Anna Meyfour; Sara Pahlavan; Mehdi Mirzaei; Jeroen Krijgsveld; Hossein Baharvand; Ghasem Hosseini Salekdeh
Journal:  Cell Mol Life Sci       Date:  2020-07-24       Impact factor: 9.261

Review 5.  Proteomic Approaches to Decipher Mechanisms Underlying Pathogenesis in Multiple Sclerosis Patients.

Authors:  Vaibhav Singh; Ajai Tripathi; Ranjan Dutta
Journal:  Proteomics       Date:  2019-06-21       Impact factor: 3.984

6.  Unpicking the proteome in single cells.

Authors:  Nikolai Slavov
Journal:  Science       Date:  2020-01-31       Impact factor: 47.728

Review 7.  Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies.

Authors:  Liwei Yang; Justin George; Jun Wang
Journal:  Proteomics       Date:  2019-12-02       Impact factor: 3.984

Review 8.  Single cell protein analysis for systems biology.

Authors:  Ezra Levy; Nikolai Slavov
Journal:  Essays Biochem       Date:  2018-10-26       Impact factor: 8.000

9.  Deciphering Metabolic Heterogeneity by Single-Cell Analysis.

Authors:  Tom M J Evers; Mazène Hochane; Sander J Tans; Ron M A Heeren; Stefan Semrau; Peter Nemes; Alireza Mashaghi
Journal:  Anal Chem       Date:  2019-10-08       Impact factor: 6.986

10.  Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers.

Authors:  Harrison Specht; Nikolai Slavov
Journal:  J Proteome Res       Date:  2020-11-14       Impact factor: 4.466

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