Recombinant:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Mass Spectrometry:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Sequencing:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Modification:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Transfection:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Staining:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Protease Inhibitor:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Bicinchoninic Acid Protein Assay:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Magnesium Assay:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Mutagenesis:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Polymerase Chain Reaction:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Labeling:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Plasmid Preparation:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
Software:Article Title: High-throughput identification of calcium-regulated proteins across diverse proteomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-FLAG-Tag Cell Signaling Technologies 86861 Anti-His-Tag Cell Signaling Technologies 2365 Chemicals, peptides, and recombinant proteins TMTpro 16plex Label Reagent Set Thermo Scientific A44520 Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode No. 4987481427648 Sequencing Grade Modified Trypsin Promega V5113 Iodoacetamide Millipore Sigma I1149-25G Oregon Green TM 488 BAPTA-6F, Hexapotassium Salt, Cell impermeant Invitrogen 023990 Fluo-4, Pentapotassium Salt, cell impermeant Invitrogen F14200 X-tremeGENE 9 DNA Transfection Reagent Sigma-Aldrich 6365787001 SYPRO Ruby Protein Gel Stain Invitrogen S12000 HisPur Ni-NTA resin Thermo Scientific 88221 DL-Dithiothreitol Millipore Sigma D0632-10G cOmpleteTM Protease Inhibitor Cocktail Roche 4693116001 SpeedBeads magnetic carboxylate modified particles GE GE65152105050250, GE45152105050250 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Scientific 23227 Magnesium Assay Kit LSBio LS-K220 Buffer Kit for Calibration of Fluorescent Ca2 Indicators Biotium 59100 QuickChange Lightning Mutagenesis Kit Agilent 210518 Genlantis MyoScope PCR Detection Kit VWR 10497–508 His-Tag labeling Kit RED-tris-NTA 2ND Generation Nanotemper MO-L018 Deposited data All proteomics data ProteomeXchange (https://www.proteomexchange.org/) ProteomeXchange: PXD048653 Experimental models: Cell lines HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse Livers: C57BL/6J (mitochondria were pooled from male and female mice) The Jackson Laboratory Strain #:000664 Yeast: Saccharomyces cerevisiae BY4742 (MATa his3D1 leu2D0 lys2D0 ura3D0) – N/A Recombinant DNA pLJM1 Addgene 19319 EPS15-GFP-His Addgene 170860 DECR1 cDNA DNASU Plasmid Repository GenBank: BC105080.1 Software and algorithms R The R Project https://www.r-project.org; RRID: SCR_001905 ShinyGO Ge et al.36 http://bioinformatics.sdstate. edu/go/; RRID:SCR_019213 (Continued on next page) 18 Cell Reports 43, 114879, November 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism GraphPad RRID:SCR_002798 MO.Affinity Analysis Software Nanotemper MO-S001A MSigDB Liberson et al.90 RRID:SCR_016863 clusterProfiler Yu et al.91 RRID:SCR_016884 ComBat Johnson et al.92 RRID:SCR_010974 Other Waters 100mg Sep-Pak Waters WAT036820 Zorbax 300 Extend C18 column Agilent 770995–902 1260 Infinity II LC System Agilent N/A Orbitrap Eclipse Tribrid Mass Spectrometer Thermo Fisher FSN04-10000 MST Regular Capillaries Nanotemper MO-K022 MST Premium Capillaries Nanotemper MO-K025 Monolith Nano-RED Nanotemper N/A
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