Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

Dušica Vidović; Behrouz Shamsaei; Stephan C. Schürer; Phillip Kogan; Szymon Chojnacki; Michal Kouril; Mario Medvedovic; Wen Niu; Evren U. Azeloglu; Marc R. Birtwistle; Yibang Chen; Tong Chen; Jens Hansen; Bin Hu; Ravi Iyengar; Gomathi Jayaraman; Hong Li; Tong Liu; Eric A. Sobie; Yuguang Xiong; Matthew J. Berberich; Gary Bradshaw; Mirra Chung; Robert A. Everley; Ben Gaudio; Marc Hafner; Marian Kalocsay; Caitlin E. Mills; Maulik K. Nariya; Peter K. Sorger; Kartik Subramanian; Chiara Victor; Maria Banuelos; Victoria Dardov; Ronald Holewinski; Danica Mae Manalo; Berhan Mandefro; Andrea D. Matlock; Loren Ornelas; Dhruv Sareen; Clive N. Svendsen; Vineet Vaibhav; Jennifer E. Van Eyk; Vidya Venkatraman; Steve Finkbiener; Ernest Fraenkel; Jeffrey Rothstein; Leslie Thompson; Jacob Asiedu; Steven A. Carr; Karen E. Christianson; Desiree Davison; Deborah O. Dele-Oni; Katherine C. DeRuff; Shawn B. Egri; Alvaro Sebastian Vaca Jacome; Jacob D. Jaffe; Daniel Lam; Lev Litichevskiy; Xiaodong Lu; James Mullahoo; Adam Officer; Malvina Papanastasiou; Ryan Peckner; Caidin Toder; Joel Blanchard; Michael Bula; Tak Ko; Li Huei Tsai; Jennie Z. Young; Vagisha Sharma; Ajay Pillai; Jarek Meller; Michael J. MacCoss

doi:10.1016/j.mcpro.2025.100947

Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

Dušica Vidović
, Behrouz Shamsaei
, Stephan C. Schürer
, Phillip Kogan
, Szymon Chojnacki
, Michal Kouril
, Mario Medvedovic
, Wen Niu
, Evren U. Azeloglu
, Marc R. Birtwistle
, Yibang Chen
, Tong Chen
, Jens Hansen
, Bin Hu
, Ravi Iyengar
, Gomathi Jayaraman
, Hong Li
, Tong Liu
, Eric A. Sobie
, Yuguang Xiong

Matthew J. Berberich, Gary Bradshaw, Mirra Chung, Robert A. Everley, Ben Gaudio, Marc Hafner, Marian Kalocsay, Caitlin E. Mills, Maulik K. Nariya, Peter K. Sorger, Kartik Subramanian, Chiara Victor, Maria Banuelos, Victoria Dardov, Ronald Holewinski, Danica Mae Manalo, Berhan Mandefro, Andrea D. Matlock, Loren Ornelas, Dhruv Sareen, Clive N. Svendsen, Vineet Vaibhav, Jennifer E. Van Eyk, Vidya Venkatraman, Steve Finkbiener, Ernest Fraenkel, Jeffrey Rothstein, Leslie Thompson, Jacob Asiedu, Steven A. Carr, Karen E. Christianson, Desiree Davison, Deborah O. Dele-Oni, Katherine C. DeRuff, Shawn B. Egri, Alvaro Sebastian Vaca Jacome, Jacob D. Jaffe, Daniel Lam, Lev Litichevskiy, Xiaodong Lu, James Mullahoo, Adam Officer, Malvina Papanastasiou, Ryan Peckner, Caidin Toder, Joel Blanchard, Michael Bula, Tak Ko, Li Huei Tsai, Jennie Z. Young, Vagisha Sharma, Ajay Pillai, Jarek Meller, Michael J. MacCoss

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.

Original language	English
Article number	100947
Journal	Molecular and Cellular Proteomics
Volume	24
Issue number	7
DOIs	https://doi.org/10.1016/j.mcpro.2025.100947
State	Published - Jul 2025

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10.1016/j.mcpro.2025.100947

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Vidović, D., Shamsaei, B., Schürer, S. C., Kogan, P., Chojnacki, S., Kouril, M., Medvedovic, M., Niu, W., Azeloglu, E. U., Birtwistle, M. R., Chen, Y., Chen, T., Hansen, J., Hu, B., Iyengar, R., Jayaraman, G., Li, H., Liu, T., Sobie, E. A., ... MacCoss, M. J. (2025). Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data. Molecular and Cellular Proteomics, 24(7), Article 100947. https://doi.org/10.1016/j.mcpro.2025.100947

@article{41afdb1ab6724b5b8990b0501a98b5ba,

title = "Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data",

abstract = "The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.",

author = "Du{\v s}ica Vidovi{\'c} and Behrouz Shamsaei and Sch{\"u}rer, \{Stephan C.\} and Phillip Kogan and Szymon Chojnacki and Michal Kouril and Mario Medvedovic and Wen Niu and Azeloglu, \{Evren U.\} and Birtwistle, \{Marc R.\} and Yibang Chen and Tong Chen and Jens Hansen and Bin Hu and Ravi Iyengar and Gomathi Jayaraman and Hong Li and Tong Liu and Sobie, \{Eric A.\} and Yuguang Xiong and Berberich, \{Matthew J.\} and Gary Bradshaw and Mirra Chung and Everley, \{Robert A.\} and Ben Gaudio and Marc Hafner and Marian Kalocsay and Mills, \{Caitlin E.\} and Nariya, \{Maulik K.\} and Sorger, \{Peter K.\} and Kartik Subramanian and Chiara Victor and Maria Banuelos and Victoria Dardov and Ronald Holewinski and Manalo, \{Danica Mae\} and Berhan Mandefro and Matlock, \{Andrea D.\} and Loren Ornelas and Dhruv Sareen and Svendsen, \{Clive N.\} and Vineet Vaibhav and \{Van Eyk\}, \{Jennifer E.\} and Vidya Venkatraman and Steve Finkbiener and Ernest Fraenkel and Jeffrey Rothstein and Leslie Thompson and Jacob Asiedu and Carr, \{Steven A.\} and Christianson, \{Karen E.\} and Desiree Davison and Dele-Oni, \{Deborah O.\} and DeRuff, \{Katherine C.\} and Egri, \{Shawn B.\} and Jacome, \{Alvaro Sebastian Vaca\} and Jaffe, \{Jacob D.\} and Daniel Lam and Lev Litichevskiy and Xiaodong Lu and James Mullahoo and Adam Officer and Malvina Papanastasiou and Ryan Peckner and Caidin Toder and Joel Blanchard and Michael Bula and Tak Ko and Tsai, \{Li Huei\} and Young, \{Jennie Z.\} and Vagisha Sharma and Ajay Pillai and Jarek Meller and MacCoss, \{Michael J.\}",

note = "Publisher Copyright: {\textcopyright} 2025 THE AUTHORS.",

year = "2025",

month = jul,

doi = "10.1016/j.mcpro.2025.100947",

language = "English",

volume = "24",

journal = "Molecular and Cellular Proteomics",

issn = "1535-9476",

publisher = "American Society for Biochemistry and Molecular Biology Inc.",

number = "7",

}

Vidović, D, Shamsaei, B, Schürer, SC, Kogan, P, Chojnacki, S, Kouril, M, Medvedovic, M, Niu, W, Azeloglu, EU, Birtwistle, MR, Chen, Y, Chen, T, Hansen, J, Hu, B, Iyengar, R, Jayaraman, G, Li, H, Liu, T, Sobie, EA, Xiong, Y, Berberich, MJ, Bradshaw, G, Chung, M, Everley, RA, Gaudio, B, Hafner, M, Kalocsay, M, Mills, CE, Nariya, MK, Sorger, PK, Subramanian, K, Victor, C, Banuelos, M, Dardov, V, Holewinski, R, Manalo, DM, Mandefro, B, Matlock, AD, Ornelas, L, Sareen, D, Svendsen, CN, Vaibhav, V, Van Eyk, JE, Venkatraman, V, Finkbiener, S, Fraenkel, E, Rothstein, J, Thompson, L, Asiedu, J, Carr, SA, Christianson, KE, Davison, D, Dele-Oni, DO, DeRuff, KC, Egri, SB, Jacome, ASV, Jaffe, JD, Lam, D, Litichevskiy, L, Lu, X, Mullahoo, J, Officer, A, Papanastasiou, M, Peckner, R, Toder, C, Blanchard, J, Bula, M, Ko, T, Tsai, LH, Young, JZ, Sharma, V, Pillai, A, Meller, J & MacCoss, MJ 2025, 'Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data', Molecular and Cellular Proteomics, vol. 24, no. 7, 100947. https://doi.org/10.1016/j.mcpro.2025.100947

TY - JOUR

T1 - Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

AU - Vidović, Dušica

AU - Shamsaei, Behrouz

AU - Schürer, Stephan C.

AU - Kogan, Phillip

AU - Chojnacki, Szymon

AU - Kouril, Michal

AU - Medvedovic, Mario

AU - Niu, Wen

AU - Azeloglu, Evren U.

AU - Birtwistle, Marc R.

AU - Chen, Yibang

AU - Chen, Tong

AU - Hansen, Jens

AU - Hu, Bin

AU - Iyengar, Ravi

AU - Jayaraman, Gomathi

AU - Li, Hong

AU - Liu, Tong

AU - Sobie, Eric A.

AU - Xiong, Yuguang

AU - Berberich, Matthew J.

AU - Bradshaw, Gary

AU - Chung, Mirra

AU - Everley, Robert A.

AU - Gaudio, Ben

AU - Hafner, Marc

AU - Kalocsay, Marian

AU - Mills, Caitlin E.

AU - Nariya, Maulik K.

AU - Sorger, Peter K.

AU - Subramanian, Kartik

AU - Victor, Chiara

AU - Banuelos, Maria

AU - Dardov, Victoria

AU - Holewinski, Ronald

AU - Manalo, Danica Mae

AU - Mandefro, Berhan

AU - Matlock, Andrea D.

AU - Ornelas, Loren

AU - Sareen, Dhruv

AU - Svendsen, Clive N.

AU - Vaibhav, Vineet

AU - Van Eyk, Jennifer E.

AU - Venkatraman, Vidya

AU - Finkbiener, Steve

AU - Fraenkel, Ernest

AU - Rothstein, Jeffrey

AU - Thompson, Leslie

AU - Asiedu, Jacob

AU - Carr, Steven A.

AU - Christianson, Karen E.

AU - Davison, Desiree

AU - Dele-Oni, Deborah O.

AU - DeRuff, Katherine C.

AU - Egri, Shawn B.

AU - Jacome, Alvaro Sebastian Vaca

AU - Jaffe, Jacob D.

AU - Lam, Daniel

AU - Litichevskiy, Lev

AU - Lu, Xiaodong

AU - Mullahoo, James

AU - Officer, Adam

AU - Papanastasiou, Malvina

AU - Peckner, Ryan

AU - Toder, Caidin

AU - Blanchard, Joel

AU - Bula, Michael

AU - Ko, Tak

AU - Tsai, Li Huei

AU - Young, Jennie Z.

AU - Sharma, Vagisha

AU - Pillai, Ajay

AU - Meller, Jarek

AU - MacCoss, Michael J.

PY - 2025/7

Y1 - 2025/7

N2 - The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.

AB - The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and their modifications to the response of specific cellular perturbations, four of the six LINCS centers have included significant proteomics efforts in the characterization of the resulting phenotype. This manuscript aims to describe this effort and the data harmonization and integration of the LINCS proteomics data discussed in recent LINCS papers.

UR - https://www.scopus.com/pages/publications/105012968889

U2 - 10.1016/j.mcpro.2025.100947

DO - 10.1016/j.mcpro.2025.100947

M3 - Article

C2 - 40089066

AN - SCOPUS:105012968889

SN - 1535-9476

VL - 24

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

IS - 7

M1 - 100947

ER -

Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

Abstract

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