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PeptideAtlas provides a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments collected for human, mouse, yeast, and several other organisms.
(last updated: Nov 28, 2017)
Data or Model Molecule| Accession | Sample Title | Summary | Organism | Characteristics | Instrument | Treatment | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PAe000138 | Peroximal cleavable ICAT | peroximal_clICAT This is the 3rd of 3 ICAT experiments in Marrelli et al., JCB 2004 | Yeast | BY4743 (MATa/MATα his3D1/his3D1 leu2D0/leu2D0 lys2D0/ + met15D0/ + ura3D0/ura3D0) | LTQ | Strains were grown in YEPD (1% yeast extract, 2% peptone, and 2% glucose), YPB (0.5% KPi, pH 6.0, 0.3% yeast extract, and 0.5% peptone) containing 2% glucose (YPBD), 2% glycerol (YPBG), 2% acetate (YPBA), 0.2% Tween 40, 0.15% oleic acid (YPBO), or 0.15% oleic acid, 0.075 g lauric acid /L (YPBO/L), and synthetic minimal medium (SM) supplemented with the necessary amino acids or nucleotides at 30°C unless otherwise stated. For peroxisome isolation, yeast cells were induced for 16 h in SCIM medium (0.7% yeast nitrogen base, 0.5% yeast extract, 0.5% peptone, 0.5% Tween 40, 0.79 g of complete synthetic medium [Qbiogene]/L, 0.5% (NH4)2SO4, 0.1% glucose, and 0.15% oleic acid). For growth assays, yeast mutants were grown in YEPD at 25°C and spotted onto YPBD, YPBG, YPBA, and YPBO/L. Cells were incubated at 25°C and images captured after 2–3 d in YPBD, 4 d on the nonfermentable carbon sources (YPBA and YPBG), and after 7 d in YPBO/L. For slowly growing strains, cells were incubated for extended periods in nonfermentable carbon sources (8 d) and 20 d in YPBO/L. | Trypsin digestion. | Subcellular fractionation and organelle extractions were performed as described in Smith et al., 2002, J. Cell Biol. 158: 259–271. Peak peroxisome and mitochondrial fractions were isolated from oleic acid-induced BY4743 cells, and organelles were extracted with Ti8 buffer (10mM Tris, pH 8.0, and 1mM EDTA) containing PINS (0.2mM PMSF, 2µg leupeptin/ml, 2µg aprotinin/ml, and 0.4µg pepstatin A/ml). Membrane fractions from peroxisomal (Ti8PP) and mitochondrial (Ti8PM) fractions were collected by centrifugation, and the pellets were solubilized in 0.1% SDS. For the affinity purification of peroxisomal membranes, peroxisomes were isolated from a heterozygous diploid yeast strain synthesizing Pex11p fused to protein A (Pex11p-pA) by isopycnic density gradient centrifugation. Fractions enriched for peroxisomes were diluted fivefold in MS buffer (0.65M sorbitol and 5mM MES, pH 5.5) containing PINS, and organelles were collected by centrifugation at 20,000g at 4°C. The resulting pellet was resuspended in Ti8 buffer containing 50mM KPi and PINS. Pex11p-pA–containing membranes were isolated from 500µg of Ti8PP by affinity chromatography using IgG- coupled magnetic beads (Dynal) for 8 h at 4°C. Bound material was washed with Ti8 buffer containing 50 mM KPi and PINS, and eluted with 0.1% SDS to generate a fraction of affinity-purified peroxisomal membranes. | PMID:15596542 | ||
| PAe000128 | perixisomal fraction vs mitochondrial fraction | Yeast: identification of peroxisomal proteins with subcellular fractionation and tandem mass spectrometry. ICAT labeled peptides. dataset included in Marelli et al., JCB 2004; perixisomal fraction vs mitochondrial fraction | Yeast | BY4743 (MATa/MATα his3D1/his3D1 leu2D0/leu2D0 lys2D0/ + met15D0/ + ura3D0/ura3D0) | LTQ | Strains were grown in YEPD (1% yeast extract, 2% peptone, and 2% glucose), YPB (0.5% KPi, pH 6.0, 0.3% yeast extract, and 0.5% peptone) containing 2% glucose (YPBD), 2% glycerol (YPBG), 2% acetate (YPBA), 0.2% Tween 40, 0.15% oleic acid (YPBO), or 0.15% oleic acid, 0.075 g lauric acid /L (YPBO/L), and synthetic minimal medium (SM) supplemented with the necessary amino acids or nucleotides at 30°C unless otherwise stated. For peroxisome isolation, yeast cells were induced for 16 h in SCIM medium (0.7% yeast nitrogen base, 0.5% yeast extract, 0.5% peptone, 0.5% Tween 40, 0.79 g of complete synthetic medium [Qbiogene]/L, 0.5% (NH4)2SO4, 0.1% glucose, and 0.15% oleic acid). For growth assays, yeast mutants were grown in YEPD at 25°C and spotted onto YPBD, YPBG, YPBA, and YPBO/L. Cells were incubated at 25°C and images captured after 2–3 d in YPBD, 4 d on the nonfermentable carbon sources (YPBA and YPBG), and after 7 d in YPBO/L. For slowly growing strains, cells were incubated for extended periods in nonfermentable carbon sources (8 d) and 20 d in YPBO/L. | Trypsin digestion. | Subcellular fractionation and organelle extractions were performed as described in Smith et al., 2002, J. Cell Biol. 158: 259–271. Peak peroxisome and mitochondrial fractions were isolated from oleic acid-induced BY4743 cells, and organelles were extracted with Ti8 buffer (10mM Tris, pH 8.0, and 1mM EDTA) containing PINS (0.2mM PMSF, 2µg leupeptin/ml, 2µg aprotinin/ml, and 0.4µg pepstatin A/ml). Membrane fractions from peroxisomal (Ti8PP) and mitochondrial (Ti8PM) fractions were collected by centrifugation, and the pellets were solubilized in 0.1% SDS. For the affinity purification of peroxisomal membranes, peroxisomes were isolated from a heterozygous diploid yeast strain synthesizing Pex11p fused to protein A (Pex11p-pA) by isopycnic density gradient centrifugation. Fractions enriched for peroxisomes were diluted fivefold in MS buffer (0.65M sorbitol and 5mM MES, pH 5.5) containing PINS, and organelles were collected by centrifugation at 20,000g at 4°C. The resulting pellet was resuspended in Ti8 buffer containing 50mM KPi and PINS. Pex11p-pA–containing membranes were isolated from 500µg of Ti8PP by affinity chromatography using IgG- coupled magnetic beads (Dynal) for 8 h at 4°C. Bound material was washed with Ti8 buffer containing 50 mM KPi and PINS, and eluted with 0.1% SDS to generate a fraction of affinity-purified peroxisomal membranes. | PMID:15596542 | ||
| PAe000150 | peroximalPrep0702 | peroximalPrep0702 This is the 2nd of 3 ICAT experiments in Marrelli et al., JCB 2004 | Yeast | BY4743 (MATa/MATα his3D1/his3D1 leu2D0/leu2D0 lys2D0/ + met15D0/ + ura3D0/ura3D0) | LTQ | Strains were grown in YEPD (1% yeast extract, 2% peptone, and 2% glucose), YPB (0.5% KPi, pH 6.0, 0.3% yeast extract, and 0.5% peptone) containing 2% glucose (YPBD), 2% glycerol (YPBG), 2% acetate (YPBA), 0.2% Tween 40, 0.15% oleic acid (YPBO), or 0.15% oleic acid, 0.075 g lauric acid /L (YPBO/L), and synthetic minimal medium (SM) supplemented with the necessary amino acids or nucleotides at 30°C unless otherwise stated. For peroxisome isolation, yeast cells were induced for 16 h in SCIM medium (0.7% yeast nitrogen base, 0.5% yeast extract, 0.5% peptone, 0.5% Tween 40, 0.79 g of complete synthetic medium [Qbiogene]/L, 0.5% (NH4)2SO4, 0.1% glucose, and 0.15% oleic acid). For growth assays, yeast mutants were grown in YEPD at 25°C and spotted onto YPBD, YPBG, YPBA, and YPBO/L. Cells were incubated at 25°C and images captured after 2–3 d in YPBD, 4 d on the nonfermentable carbon sources (YPBA and YPBG), and after 7 d in YPBO/L. For slowly growing strains, cells were incubated for extended periods in nonfermentable carbon sources (8 d) and 20 d in YPBO/L. | Trypsin digestion. | Subcellular fractionation and organelle extractions were performed as described in Smith et al., 2002, J. Cell Biol. 158: 259–271. Peak peroxisome and mitochondrial fractions were isolated from oleic acid-induced BY4743 cells, and organelles were extracted with Ti8 buffer (10mM Tris, pH 8.0, and 1mM EDTA) containing PINS (0.2mM PMSF, 2µg leupeptin/ml, 2µg aprotinin/ml, and 0.4µg pepstatin A/ml). Membrane fractions from peroxisomal (Ti8PP) and mitochondrial (Ti8PM) fractions were collected by centrifugation, and the pellets were solubilized in 0.1% SDS. For the affinity purification of peroxisomal membranes, peroxisomes were isolated from a heterozygous diploid yeast strain synthesizing Pex11p fused to protein A (Pex11p-pA) by isopycnic density gradient centrifugation. Fractions enriched for peroxisomes were diluted fivefold in MS buffer (0.65M sorbitol and 5mM MES, pH 5.5) containing PINS, and organelles were collected by centrifugation at 20,000g at 4°C. The resulting pellet was resuspended in Ti8 buffer containing 50mM KPi and PINS. Pex11p-pA–containing membranes were isolated from 500µg of Ti8PP by affinity chromatography using IgG- coupled magnetic beads (Dynal) for 8 h at 4°C. Bound material was washed with Ti8 buffer containing 50 mM KPi and PINS, and eluted with 0.1% SDS to generate a fraction of affinity-purified peroxisomal membranes. | PMID:15596542 | ||
| PAe000157 | peroxisomal proteomics | peroxisomal proteomics Yeast cells, unlike higher eukaryotes, have a conditional requirement for peroxisomes. In yeast peroxisomes are necessary to metabolize (and grow on) long chain fatty acids. On glucose yeast peroxisomes are repressed. Yeast cells, grown on long chain fatty acids as their sole carbon source induces the proliferation of peroxisomes. Cells grown in glycerol, de-represses peroxisome regulation. Here, peroxisomes were isolated from equal number of de-repressed (glycerol grown) and induced (fatty acid grown) yeast cells by Nycodenz gradient centrifugation. To reduce the complexity of the sample the peroxisomes were and lysed hypotonically to release abundant matrix components/enzymes. Proteins derived from the peroxisomal membranes from each sample were differentially labelled with the CL-ICAT reagent, where proteins from de-repressed samples were labeled with 'light' CL-ICAT; and those from induced cultures with the 'heavy' CL-ICAT. Light and heavy labeled protein samples were then mixed at a 1:2 (light:heavy) ratio and analysed by Quant/MS. d0-control sample d9-affinity purified peroxisomes | Yeast | BY4743 (MATa/MATα his3D1/his3D1 leu2D0/leu2D0 lys2D0/ + met15D0/ + ura3D0/ura3D0) | LTQ | Strains were grown in YEPD (1% yeast extract, 2% peptone, and 2% glucose), YPB (0.5% KPi, pH 6.0, 0.3% yeast extract, and 0.5% peptone) containing 2% glucose (YPBD), 2% glycerol (YPBG), 2% acetate (YPBA), 0.2% Tween 40, 0.15% oleic acid (YPBO), or 0.15% oleic acid, 0.075 g lauric acid /L (YPBO/L), and synthetic minimal medium (SM) supplemented with the necessary amino acids or nucleotides at 30°C unless otherwise stated. For peroxisome isolation, yeast cells were induced for 16 h in SCIM medium (0.7% yeast nitrogen base, 0.5% yeast extract, 0.5% peptone, 0.5% Tween 40, 0.79 g of complete synthetic medium [Qbiogene]/L, 0.5% (NH4)2SO4, 0.1% glucose, and 0.15% oleic acid). For growth assays, yeast mutants were grown in YEPD at 25°C and spotted onto YPBD, YPBG, YPBA, and YPBO/L. Cells were incubated at 25°C and images captured after 2–3 d in YPBD, 4 d on the nonfermentable carbon sources (YPBA and YPBG), and after 7 d in YPBO/L. For slowly growing strains, cells were incubated for extended periods in nonfermentable carbon sources (8 d) and 20 d in YPBO/L. | Trypsin digestion. | Subcellular fractionation and organelle extractions were performed as described in Smith et al., 2002, J. Cell Biol. 158: 259–271. Peak peroxisome and mitochondrial fractions were isolated from oleic acid-induced BY4743 cells, and organelles were extracted with Ti8 buffer (10mM Tris, pH 8.0, and 1mM EDTA) containing PINS (0.2mM PMSF, 2µg leupeptin/ml, 2µg aprotinin/ml, and 0.4µg pepstatin A/ml). Membrane fractions from peroxisomal (Ti8PP) and mitochondrial (Ti8PM) fractions were collected by centrifugation, and the pellets were solubilized in 0.1% SDS. For the affinity purification of peroxisomal membranes, peroxisomes were isolated from a heterozygous diploid yeast strain synthesizing Pex11p fused to protein A (Pex11p-pA) by isopycnic density gradient centrifugation. Fractions enriched for peroxisomes were diluted fivefold in MS buffer (0.65M sorbitol and 5mM MES, pH 5.5) containing PINS, and organelles were collected by centrifugation at 20,000g at 4°C. The resulting pellet was resuspended in Ti8 buffer containing 50mM KPi and PINS. Pex11p-pA–containing membranes were isolated from 500µg of Ti8PP by affinity chromatography using IgG- coupled magnetic beads (Dynal) for 8 h at 4°C. Bound material was washed with Ti8 buffer containing 50 mM KPi and PINS, and eluted with 0.1% SDS to generate a fraction of affinity-purified peroxisomal membranes. | PMID:15596542 |
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