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

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Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data

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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, …

Molecular & cellular proteomics, Vol.24(7), p.100947

2025-07-01

DOI: https://doi.org/10.1016/j.mcpro.2025.100947

PMID: 40089066

Appears in Miller School of Medicine - Latest Publications

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.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.

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Collaboration types: Domestic collaboration
Citation topics: 2 Chemistry; 2.211 Mass Spectrometry; 2.211.497 Proteomics Mass Spectrometry
Web Of Science research areas: Biochemical Research Methods
ESI research areas: Molecular Biology & Genetics

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Title: Comprehensive proteomics metadata and integrative web portals facilitate sharing and integration of LINCS multiomics data
Creators: Dušica Vidović - University of Miami
Behrouz Shamsaei - University of Cincinnati
Stephan C Schürer - Sylvester Comprehensive Cancer Center
Phillip Kogan - University of Cincinnati
Szymon Chojnacki - University of Cincinnati
Michal Kouril - University of Cincinnati
Mario Medvedovic - University of Cincinnati
Wen Niu - University of Cincinnati
Evren U Azeloglu - Icahn School of Medicine at Mount Sinai
Marc R Birtwistle - Icahn School of Medicine at Mount Sinai
Yibang Chen - Icahn School of Medicine at Mount Sinai
Tong Chen - Rutgers, The State University of New Jersey
Jens Hansen - Icahn School of Medicine at Mount Sinai
Bin Hu - Icahn School of Medicine at Mount Sinai
Ravi Iyengar - Icahn School of Medicine at Mount Sinai
Gomathi Jayaraman - Icahn School of Medicine at Mount Sinai
Hong Li - Rutgers, The State University of New Jersey
Tong Liu - Rutgers, The State University of New Jersey
Eric A Sobie - Icahn School of Medicine at Mount Sinai
Yuguang Xiong - Icahn School of Medicine at Mount Sinai
Matthew J Berberich - Center for Systems Biology
Gary Bradshaw - Center for Systems Biology
Mirra Chung - Center for Systems Biology
Robert A Everley - Center for Systems Biology
Ben Gaudio
Marc Hafner - Center for Systems Biology
Marian Kalocsay - Center for Systems Biology
Caitlin E Mills - Center for Systems Biology
Maulik K Nariya - Center for Systems Biology
Peter K Sorger - Center for Systems Biology
Kartik Subramanian - Center for Systems Biology
Chiara Victor - Center for Systems Biology
Maria Banuelos - Cedars-Sinai Medical Center
Victoria Dardov - Cedars-Sinai Medical Center
Ronald Holewinski - Cedars-Sinai Medical Center
Danica-Mae Manalo - Cedars-Sinai Medical Center
Berhan Mandefro - Cedars-Sinai Medical Center
Andrea D Matlock - Cedars-Sinai Medical Center
Loren Ornelas - Cedars-Sinai Medical Center
Dhruv Sareen - Cedars-Sinai Medical Center
Clive N Svendsen - Cedars-Sinai Medical Center
Vineet Vaibhav - Cedars-Sinai Medical Center
Jennifer E Van Eyk - Cedars-Sinai Medical Center
Vidya Venkatraman - Cedars-Sinai Medical Center
Steve Finkbiener - Gladstone Institutes
Ernest Fraenkel
Jeffrey Rothstein - Johns Hopkins University
Leslie Thompson - University of California, Irvine
Jacob Asiedu - Broad Institute
Steven A Carr - Broad Institute
Karen E Christianson - Broad Institute
Desiree Davison - Broad Institute
Deborah O Dele-Oni - Broad Institute
Katherine C DeRuff - Broad Institute
Shawn B Egri - Broad Institute
Alvaro Sebastian Vaca Jacome - Broad Institute
Jacob D Jaffe - Broad Institute
Daniel Lam - Broad Institute
Lev Litichevskiy - Broad Institute
Xiaodong Lu - Broad Institute
James Mullahoo - Broad Institute
Adam Officer - Broad Institute
Malvina Papanastasiou - Broad Institute
Ryan Peckner - Broad Institute
Caidin Toder - Broad Institute
Joel Blanchard - Massachusetts Institute of Technology
Michael Bula - Massachusetts Institute of Technology
Tak Ko - Massachusetts Institute of Technology
Li-Huei Tsai
Jennie Z Young - Massachusetts Institute of Technology
Vagisha Sharma - University of Washington
Ajay Pillai - National Institutes of Health
Jarek Meller - University of Cincinnati
Michael J MacCoss - University of Washington
Publication Details: Molecular & cellular proteomics, Vol.24(7), p.100947
Publisher: ELSEVIER; AMSTERDAM
Number of pages: 12
Grant note: National Institutes of Health (NIH): U54HL127624, U54HG008098, S10OD025047, U54HL127365, U54NS091046, U54HG008097 National Library of Medicine (NLM): U01LM012630 National Center for Advancing Translational Sciences (NCATS) award: U24TR002278 National Human Genome Research Institute (NHGRI) award: U24HG012674
This work was supported by the National Institutes of Health (NIH) [U54HL127624: BD2K-LINCS DCIC; U54HG008098 and S10OD025047: DToxS; U54HL127365: HMS LINCS; U54NS091046: NeuroLINCS; U54HG008097: PCCSE] ; National Library of Medicine (NLM) [U01LM012630: BD2K, Enhancing the efficiency and effectiveness of digital curation for biomedical 'big data'] . DV and SCS are also grateful for the National Center for Advancing Translational Sciences (NCATS) award [U24TR002278: Illuminating the Druggable Genome Resource Dissemination and Outreach Center, IDGRDOC] and National Human Genome Research Institute (NHGRI) award [U24HG012674: Molecular Phenotypes of Null Alleles in Cells (MorPhiC) Data Resource and Administrative Coordinating Center (DRACC)].
Academic Unit: Miller School of Medicine; Molecular and Cellular Pharmacology Research
Language: English
Resource Type: Journal article
PMID: 40089066
Record Identifier: 991032596325902976