Dataset Information

Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons

ABSTRACT: Supporting TMT MS data for paper (doi: 10.1016/j.neuron.2021.12.029) by Goldsmith J. et al., titled "Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons". Index of RAW files uploaded: AO3068-3079: Fractionated (12 fractions) Autophagosome Proteome Profiling (Unimod: 35; 737; 4)). Five replicates of autophagosome prep treated or not with Proteinase K. TMT: 126 (G3_01); 127n (G3+PK_01); 127c (G3_02); 128n (G3+PK_02); 128c (G3_03); 129n (G3+PK_03); 129c (G3_04); 130n (G3+PK_04); 130c (G3_05); 131n (G3+PK_05).

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Alban Ordureau

PROVIDER: MSV000092565 | MassIVE | Tue Aug 01 10:14:00 BST 2023

REPOSITORIES: MassIVE

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Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons.

Goldsmith Juliet J Ordureau Alban A Harper J Wade JW Holzbaur Erika L F ELF

Neuron 20220119 6

Neurons depend on autophagy to maintain cellular homeostasis, and defects in autophagy are pathological hallmarks of neurodegenerative disease. To probe the role of basal autophagy in the maintenance of neuronal health, we isolated autophagic vesicles from mouse brain tissue and used proteomics to identify the major cargos engulfed within autophagosomes, validating our findings in rodent primary and human iPSC-derived neurons. Mitochondrial proteins were identified as a major cargo in the absenc ...[more]

PMID: 35051374

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Project description:Supporting raw MS data for paper (doi: 10.1016/j.cell.2024.05.018) by Sinha N.K. et al, titled "The ribotoxic stress response drives UV-mediated cell death". Index of MS files and labels Table S1 - HaCaT Timecourse. 1-1 - Proteome (AO3604-3627 | Unimod:35; 2016; 4 | 126 -UT_01; 127n - UT_02; 127c - UT_03; 128n -1min_01; 128c - 1min_02; 129n - 1min_03; 129c - 1min_04; 130n - 5min_01; 130c - 5min_02; 131n - 5min_03; 131c - 15min_01; 132n - 15min_02; 132c - 15min_03; 133n - 30min_01; 133c - 30min_02; 134n - 30min_03) 1-2 - Phospho (AO3628-3651 | Unimod:35; 2016; 4; 21 | 126 -UT_01; 127n - UT_02; 127c - UT_03; 128n -1min_01; 128c - 1min_02; 129n - 1min_03; 129c - 1min_04; 130n - 5min_01; 130c - 5min_02; 131n - 5min_03; 131c - 15min_01; 132n - 15min_02; 132c - 15min_03; 133n - 30min_01; 133c - 30min_02; 134n - 30min_03) Table S2 - MCF10a KO and inhibitor (Set1 - ZAK & Set 2 - GCN2). 2-1-1 - Proteome (Set 1 - AO4019-4042 | Unimod:35; 2016; 4 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_ZAKi01; 128c - WT_UT_ZAKi02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_ZAKi01; 130c - WT_UV_ZAKi02; 131n - ZAK-KO_UT_DMSO01; 131c - ZAK-KO_UT_DMSO02; 132n - ZAK-KO_UT_ZAKi01; 132c - ZAK-KO_UT_ZAKi02; 133n - ZAK-KO_UV_DMSO01; 133c - ZAK-KO_UV_DMSO02; 134n - ZAK-KO_UV_ZAKi01; 134c -ZAK-KO_UV_ZAKi02) 2-1-2 - Proteome (Set 2 - AO4049-4072 | Unimod:35; 2016; 4 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_GCN2i01; 128c - WT_UT_GCN2i02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_GCN2i01; 130c - WT_UV_GCN2i02; 131n - GCN2-KO_UT_DMSO01; 131c - GCN2-KO_UT_DMSO02; 132n - GCN2-KO_UT_GCN2i01; 132c - GCN2-KO_UT_GCN2i02; 133n - GCN2-KO_UV_DMSO01; 133c - GCN2-KO_UV_DMSO02; 134n - GCN2-KO_UV_GCN2i01; 135n -GCN2-KO_UV_GCN2i02) 2-2-1 - Phospho (Set 1 - AO4013-4019 | Unimod:35; 2016; 4; 21 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_ZAKi01; 128c - WT_UT_ZAKi02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_ZAKi01; 130c - WT_UV_ZAKi02; 131n - ZAK-KO_UT_DMSO01; 131c - ZAK-KO_UT_DMSO02; 132n - ZAK-KO_UT_ZAKi01; 132c - ZAK-KO_UT_ZAKi02; 133n - ZAK-KO_UV_DMSO01; 133c - ZAK-KO_UV_DMSO02; 134n - ZAK-KO_UV_ZAKi01; 134c -ZAK-KO_UV_ZAKi02) 2-2-2 - Phospho (Set 2 - AO4043-4048 | Unimod:35; 2016; 4; 21 | 126 - WT_UT_DMSO01; 127c - WT_UT_DMSO02; 128n - WT_UT_GCN2i01; 128c - WT_UT_GCN2i02; 129n - WT_UV_DMSO01; 129c -WT_UV_DMSO02; 130n - WT_UV_GCN2i01; 130c - WT_UV_GCN2i02; 131n - GCN2-KO_UT_DMSO01; 131c - GCN2-KO_UT_DMSO02; 132n - GCN2-KO_UT_GCN2i01; 132c - GCN2-KO_UT_GCN2i02; 133n - GCN2-KO_UV_DMSO01; 133c - GCN2-KO_UV_DMSO02; 134n - GCN2-KO_UV_GCN2i01; 135n -GCN2-KO_UV_GCN2i02) Table S3 - HaCaT Kinase inhibitors (Set 1 & Set 2). 3-1-1 - Proteome (Set 1 - AO3766-3777 | Unimod:35; 2016; 4 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Nil)_UT01; 129n - ZAKi(Nil)_UT02; 129c - ZAKi(Nil)_UV01; 130n - ZAKi(Nil)_UV02; 130c - p38i_UT01; 131n - p38i_UT02; 131c - p38i_UV01; 132n - p38i_UV02; 132c - JNKi_UT01; 133n - JNKi_UT02; 133c - JNKi_UV01; 134n - JNKi_UV02) 3-1-2 - Proteome (Set 2 - AO3778-3789 | Unimod:35; 2016; 4 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Vem)_UT01; 129n - ZAKi(Vem)_UT02; 129c - ZAKi(Vem)_UV01; 130n - ZAKi(Vem)_UV02; 130c - GCN2i_UT01; 131n - GCN2i_UT02; 131c - GCN2i_UV01; 132n - GCN2i_UV02; 132c - ATRi_UT01; 133n - ATRi_UT02; 133c - ATRi_UV01; 134n - ATRi_UV02) 3-2-1 - Phospho (Set 1 - AO3754-3759 | Unimod:35; 2016; 4; 21 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Nil)_UT01; 129n - ZAKi(Nil)_UT02; 129c - ZAKi(Nil)_UV01; 130n - ZAKi(Nil)_UV02; 130c - p38i_UT01; 131n - p38i_UT02; 131c - p38i_UV01; 132n - p38i_UV02; 132c - JNKi_UT01; 133n - JNKi_UT02; 133c - JNKi_UV01; 134n - JNKi_UV02) 3-2-2 - Phospho (Set 2 - AO3760-3765 | Unimod:35; 2016; 4; 21 | 126 - DMSO_UT01; 127n - DMSO_UT02; 127c - DMSO_UV01; 128n - DMSO_UV02; 128c - ZAKi(Vem)_UT01; 129n - ZAKi(Vem)_UT02; 129c - ZAKi(Vem)_UV01; 130n - ZAKi(Vem)_UV02; 130c - GCN2i_UT01; 131n - GCN2i_UT02; 131c - GCN2i_UV01; 132n - GCN2i_UV02; 132c - ATRi_UT01; 133n - ATRi_UT02; 133c - ATRi_UV01; 134n - ATRi_UV02). Tabel S4 - ZAK affinity purification. 4-1 - Label-free ZAK pulldown (mNG-ZAK-WT labeled files | Unimod:35; 4| Untreated or ANS treated cells) Additional file: AO4072_GCN2_RSP10_tMS2: Targeted RPS10-Kgg search | Unimod:35; 2016; 4; 492 | TMT label as 2-1-2.