Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics

Fredrik Edfors, Björn Forsström, Helian Vunk, David Kotol, Claudia Fredolini, Gianluca Maddalo, Anne Sophie Svensson, Tove Boström, Hanna Tegel, Peter Nilsson, Jochen M. Schwenk, Mathias Uhlén

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.
Original languageEnglish
JournalJournal of Proteome Research
Volume18
Issue number7
Pages (from-to)2706-2718
ISSN1535-3893
DOIs
Publication statusPublished - 2019

Cite this

Edfors, Fredrik ; Forsström, Björn ; Vunk, Helian ; Kotol, David ; Fredolini, Claudia ; Maddalo, Gianluca ; Svensson, Anne Sophie ; Boström, Tove ; Tegel, Hanna ; Nilsson, Peter ; Schwenk, Jochen M. ; Uhlén, Mathias. / Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. In: Journal of Proteome Research. 2019 ; Vol. 18, No. 7. pp. 2706-2718.
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abstract = "The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.",
author = "Fredrik Edfors and Bj{\"o}rn Forsstr{\"o}m and Helian Vunk and David Kotol and Claudia Fredolini and Gianluca Maddalo and Svensson, {Anne Sophie} and Tove Bostr{\"o}m and Hanna Tegel and Peter Nilsson and Schwenk, {Jochen M.} and Mathias Uhl{\'e}n",
year = "2019",
doi = "10.1021/acs.jproteome.8b00924",
language = "English",
volume = "18",
pages = "2706--2718",
journal = "Journal of Proteome Research",
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Edfors, F, Forsström, B, Vunk, H, Kotol, D, Fredolini, C, Maddalo, G, Svensson, AS, Boström, T, Tegel, H, Nilsson, P, Schwenk, JM & Uhlén, M 2019, 'Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics', Journal of Proteome Research, vol. 18, no. 7, pp. 2706-2718. https://doi.org/10.1021/acs.jproteome.8b00924

Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. / Edfors, Fredrik; Forsström, Björn; Vunk, Helian; Kotol, David; Fredolini, Claudia; Maddalo, Gianluca; Svensson, Anne Sophie; Boström, Tove; Tegel, Hanna; Nilsson, Peter; Schwenk, Jochen M.; Uhlén, Mathias.

In: Journal of Proteome Research, Vol. 18, No. 7, 2019, p. 2706-2718.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics

AU - Edfors, Fredrik

AU - Forsström, Björn

AU - Vunk, Helian

AU - Kotol, David

AU - Fredolini, Claudia

AU - Maddalo, Gianluca

AU - Svensson, Anne Sophie

AU - Boström, Tove

AU - Tegel, Hanna

AU - Nilsson, Peter

AU - Schwenk, Jochen M.

AU - Uhlén, Mathias

PY - 2019

Y1 - 2019

N2 - The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.

AB - The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.

U2 - 10.1021/acs.jproteome.8b00924

DO - 10.1021/acs.jproteome.8b00924

M3 - Journal article

C2 - 31094526

VL - 18

SP - 2706

EP - 2718

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 7

ER -