PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)

Anderson, Lindsey N; Sarkar, Snigdha; Van Fossen, Elise M M; Li, Xiaolu; Zhang, Tong; Feng, Song; Prozapas, Victoria N; Shouaib, Abdullah D; Hutchinson-Bunch, Chelsea M; Waters, Katrina M; Bohutskyi, Pavlo; Melchior, John T

doi:10.25584/PPI/2574396

Title: PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)

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Abstract

The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus cell lysates using three complementary mass spectrometry (MS) techniques using limited proteolysis (LiP-MS), thermal proteome profiling (TPP-MS), and redox enrichment (Redox-MS) in evaluating alterations solvent accessibility and structural stability caused by light perturbation at the molecular level. Experimentally processed sample data for LiP and TPP proteomic datasets were derived from the same cell culture stock, prepared simultaneously in parallel, and acquired by mass spectrometry. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files, computed outputs, and supporting metadata materials. Experimental samples processed for LiP-MS label-free quantification (LFQ) or TPP-MS tandem mass tag (TMT) 10-plex were acquired using a Q-Exactive HF-X mass spectrometer and processed/compiled using either MSGF+ (v2024.03.26) or PlexedPiper for proteome evaluation. Additional software supporting downstream proteomic analysis include FragPipe (v.4.0), MSFragger (v.22.1), and an adapted Microbial Isolate LiP Analysis Workflow (located at Zenodo). Processed proteomic data downloads include a sample naming key, normalized quantification results files, and processed protein annotated abundance files.

Authors:

;

; Shouaib, Abdullah D;

;

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Publication Date:: Thu Jul 31 04:00:00 UTC 2025

Other Number(s):: PPI-JM-PB-DP3
MSV000098676; MSV000098675; MSV000096184; MSV000098679

DOE Contract Number:: AC05-76RL01830

Research Org.:: PNNL (PNNL2)

Sponsoring Org.:: Predictive Phenomics Initiative (PPI), Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Cyanobacteria; Light Fluctuation; Limited Proteolysis; Post-Translational Modifi; Redox Proteomics; Structural Proteomics; Synechococcus elongatus PCC 7942; Thermal Proteome Profiling; Thiol Oxidation

OSTI Identifier:: 2574396

DOI:: https://doi.org/10.25584/PPI/2574396

Citation Formats


                    Anderson, Lindsey N, Sarkar, Snigdha, Van Fossen, Elise M M, Li, Xiaolu, Zhang, Tong, Feng, Song, Prozapas, Victoria N, Shouaib, Abdullah D, Hutchinson-Bunch, Chelsea M, Waters, Katrina M, Bohutskyi, Pavlo, and Melchior, John T. PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3).  United States: N. p., 2025. 
        Web.  doi:10.25584/PPI/2574396.

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                    Anderson, Lindsey N, Sarkar, Snigdha, Van Fossen, Elise M M, Li, Xiaolu, Zhang, Tong, Feng, Song, Prozapas, Victoria N, Shouaib, Abdullah D, Hutchinson-Bunch, Chelsea M, Waters, Katrina M, Bohutskyi, Pavlo, & Melchior, John T. PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3).  United States.  doi:https://doi.org/10.25584/PPI/2574396

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                    Anderson, Lindsey N, Sarkar, Snigdha, Van Fossen, Elise M M, Li, Xiaolu, Zhang, Tong, Feng, Song, Prozapas, Victoria N, Shouaib, Abdullah D, Hutchinson-Bunch, Chelsea M, Waters, Katrina M, Bohutskyi, Pavlo, and Melchior, John T. 2025.  
"PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)".  United States.  doi:https://doi.org/10.25584/PPI/2574396.  https://www.osti.gov/servlets/purl/2574396. Pub date:Thu Jul 31 04:00:00 UTC 2025

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@article{osti_2574396,

  title        = {PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)},

  author       = {Anderson, Lindsey N and Sarkar, Snigdha and Van Fossen, Elise M M and Li, Xiaolu and Zhang, Tong and Feng, Song and Prozapas, Victoria N and Shouaib, Abdullah D and Hutchinson-Bunch, Chelsea M and Waters, Katrina M and Bohutskyi, Pavlo and Melchior, John T},

  abstractNote = {The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus cell lysates using three complementary mass spectrometry (MS) techniques using limited proteolysis (LiP-MS), thermal proteome profiling (TPP-MS), and redox enrichment (Redox-MS) in evaluating alterations solvent accessibility and structural stability caused by light perturbation at the molecular level. Experimentally processed sample data for LiP and TPP proteomic datasets were derived from the same cell culture stock, prepared simultaneously in parallel, and acquired by mass spectrometry. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files, computed outputs, and supporting metadata materials. Experimental samples processed for LiP-MS label-free quantification (LFQ) or TPP-MS tandem mass tag (TMT) 10-plex were acquired using a Q-Exactive HF-X mass spectrometer and processed/compiled using either MSGF+ (v2024.03.26) or PlexedPiper for proteome evaluation. Additional software supporting downstream proteomic analysis include FragPipe (v.4.0), MSFragger (v.22.1), and an adapted Microbial Isolate LiP Analysis Workflow (located at Zenodo). Processed proteomic data downloads include a sample naming key, normalized quantification results files, and processed protein annotated abundance files.},

  doi          = {10.25584/PPI/2574396},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Thu Jul 31 04:00:00 UTC 2025},

  month        = {Thu Jul 31 04:00:00 UTC 2025}

}

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DOI: https://doi.org/10.25584/PPI/2574396

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