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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 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PAe000116 | Human Erythroleukemia K562 cell line,Q | Human huamn erythroleukemia K5632 cell line I think... | Human | K562 (erythroleukemia) | LTQ | K562 grown in suspension. | Proteins in the pooled fractions were alkylated with iodoacetamide, desalted into 100 mM NH₄HCO₃, digested, lyophilized, and processed in the same manner as sample 1 (referring PSM1018) and sample 2 (referring PSM1019). | Cells were washed twice by centrifugation, and pellets were flash frozen in liquid nitrogen. Cell pellets were suspended in lysis buffer (140mM potassium phosphate, pH 7.4, 150mM NaF, 1mM Na₃VO₄, 6mM EDTA, 6mM EGTA, 250mM NaCl, 4mM DTT) containing 40µg/mL leupeptin, 5µg/mL pepstatin A, 4mM benzamidine, and 20mM PMSF and sonicated 4 × 15 s at 4°C (Branson, microtip probe). Lysates were centrifuged at 200000g for 30 min at 4°C and soluble proteins recovered in the supernatant. Typically 10⁸ cells yielded ~15mg of protein. | Proteins were homogenized in lysis buffer on a gel filtration column (Sephacryl HR300 (26/60), Amersham) equilibrated in lysis buffer. The column was run at 1.3 mL/min, collecting 8-mL fractions over the included volume. | PMID:15228325 | |
| PAe000115 | Human Erythroleukemia K562 cell line, PLC | Human Erythroleukemia K562 cell line huamn erythroleukemia K5632 cell line I think... | Human | K562 (erythroleukemia) | LTQ | K562 grown in suspension. | Proteins were alkylated with 14 mM iodoacetamide (Aldrich, Milwaukee, WI) for 30 min in the dark at room temperature. Reactions were quenched by adding 3 mM DTT, and proteins were immediately desalted on a PD10 column (Amersham, Piscataway, NJ) equilibrated with 100 mM NH₄HCO₃, followed by trypsinization at 37°C with 3% (w/w) trypsin (Wako, Richmond, VA, Catalog No. 20709891) added in 1% aliquots at t = 0, 4, and 12 h. The NH₄HCO₃ was removed by repeated lyophilization and resuspension in water (usually 3 times) until the conductivity after dilution of 10 µL of sample into 3 mL of water was less than 0.004 Ω⁻¹/cm. | Cells were washed twice by centrifugation, and pellets were flash frozen in liquid nitrogen. Cell pellets were suspended in lysis buffer (140mM potassium phosphate, pH 7.4, 150mM NaF, 1mM Na₃VO₄, 6mM EDTA, 6mM EGTA, 250mM NaCl, 4mM DTT) containing 40µg/mL leupeptin, 5µg/mL pepstatin A, 4mM benzamidine, and 20mM PMSF and sonicated 4 × 15 s at 4°C (Branson, microtip probe). Lysates were centrifuged at 200000g for 30 min at 4°C and soluble proteins recovered in the supernatant. Typically 10⁸ cells yielded ~15mg of protein. | Lyophilized peptides were dissolved in buffer A (5 mM K₂HPO₄, 5% acetonitrile pH 2.5) and fractionated by HPLC using a SCX column (PolySulfoethyl A, 2.1 mm i.d. × 200 mm, Poly LC), equilibrated in buffer A, and eluted using a gradient of increasing 0.5 M KCl in buffer A. | PMID:15228325 | |
| PAe000007 | Human prostate cancer cell lines, nuclear, ICAT | Human prostate cancer cell lines: LNCaP, CL-1, nuclear. Labeled with old ICAT. nuclear fraction comparison with ICAT | Human | Human prostate cancer cell lines LNCaP, CL-1. | LTQ | LNCaP and CL1 cells were grown as described by Tso et al. Cancer J Sci Am 2000, 6: 220–33. | Procedures based on Han et al., Nat Biotechnol 2001; 19: 946–51. | Fractionation of cells into cytosolic, microsomal, and nuclear fractions according to Han et al., Nat Biotechnol 2001; 19: 946–51. | Procedures based on Han et al., Nat Biotechnol 2001; 19: 946–51. | PMID:15833837 | |
| PAe000334 | human serum fractionation/depletion methods, 20_cys | 20_cys | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Cysteinyl-peptide enrichment Briefly, the reduced tryptic digest of human serum protein was incubated with Thiopropyl Sepharose 6B thiol-affinity resin (100µL; Amersham Biosciences, Piscataway, NJ) for 1 h at room temperature and washed. The captured cysteinyl peptides were released with 100µL of 20 mM DTT (in washing buffer) followed by 100µL of 80% ACN. The pH was adjusted to 8.0 and peptides were alkylated with 80 mM IAM for 30 min at room temperature in the dark. The eluted cysteinyl peptides were desalted with a SPE C18 column and lyophilized. | PMID:17269739 | ||
| PAe000337 | human serum fractionation/depletion methods, 21_unfract | 21_unfract | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Unfractionated | PMID:17269739 | ||
| PAe000114 | Human erythroleukemia K562 cell line A8_IP | Human Erythroleukemia K562 cell line huamn erythroleukemia K5632 cell line I think... | Human | K562 (erythroleukemia) | LTQ | K562 grown in suspension. | Proteins were alkylated with 14 mM iodoacetamide (Aldrich, Milwaukee, WI) for 30 min in the dark at room temperature. Reactions were quenched by adding 3 mM DTT, and proteins were immediately desalted on a PD10 column (Amersham, Piscataway, NJ) equilibrated with 100 mM NH₄HCO₃, followed by trypsinization at 37°C with 3% (w/w) trypsin (Wako, Richmond, VA, Catalog No. 20709891) added in 1% aliquots at t = 0, 4, and 12 h. The NH₄HCO₃ was removed by repeated lyophilization and resuspension in water (usually 3 times) until the conductivity after dilution of 10 µL of sample into 3 mL of water was less than 0.004 Ω⁻¹/cm. | Cells were washed twice by centrifugation, and pellets were flash frozen in liquid nitrogen. Cell pellets were suspended in lysis buffer (140mM potassium phosphate, pH 7.4, 150mM NaF, 1mM Na₃VO₄, 6mM EDTA, 6mM EGTA, 250mM NaCl, 4mM DTT) containing 40µg/mL leupeptin, 5µg/mL pepstatin A, 4mM benzamidine, and 20mM PMSF and sonicated 4 × 15 s at 4°C (Branson, microtip probe). Lysates were centrifuged at 200000g for 30 min at 4°C and soluble proteins recovered in the supernatant. Typically 10⁸ cells yielded ~15mg of protein. | Lyophilized peptides were dissolved in buffer A (5 mM K₂HPO₄, 5% acetonitrile pH 2.5) and fractionated by HPLC using a SCX column (PolySulfoethyl A, 2.1 mm i.d. × 200 mm, Poly LC), equilibrated in buffer A, and eluted using a gradient of increasing 0.5 M KCl in buffer A. | PMID:15228325 | |
| PAe000333 | human serum fractionation/depletion methods, 19_proteinag | 19_proteinag | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Protein A/G depletion Immunoglobulins were depleted by using a 2 mL pre-packed immobilized Protein A/G column (Pierce, Rockford, IL) per the manufacturer's instructions. Briefly, 50 mL of human serum sample was diluted 1:5 with binding buffer and centrifuged at 10 000×g for 20 min. The supernatant was applied to a Protein A/G column that was preequilibrated with 5 mL of binding buffer. 15 mL of binding buffer was added to wash the column, and the flow-through fraction was collected. Sample was then dialyzed against 50 mM ammonium bicarbonate and lyophilized. | PMID:17269739 | ||
| PAe000330 | human serum fractionation/depletion methods, 01_glyco | 01_glyco | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | N-linked glycopeptide enrichment Briefly, 0.6 mL human serum was oxidized and coupled to 4 mL of Affi-Gel Hz Hydrazide Gel (50% slurry) (Bio-Rad, Hercules, CA). N-linked glycopeptides were released from the resin by adding 3µL PNGase F (glycerol free) (New England Biolabs, Inc., Beverly, MA) in 2 mL of 0.1 M freshly prepared NH₄HCO₃.The cleavage reaction was performed at 37°C with mixing overnight followed by washing with 2×2 mL of 80% ACN. The released glycopeptides were dried and resuspended in 0.4% acetic acid. | PMID:17269739 | ||
| PAe000331 | human serum fractionation/depletion methods, 15_clinprot_c3 | 15_clinprot_c3 | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Bruker ClinProt C3 magnetic beads ClinProt purification reagent sets were obtained from Bruker Daltonics (Billerica, MA). The magnetic beads were shaken 20 times to achieve a homogeneous suspension. MB-HIC binding solution (10µL) and 5µL of human serum were mixed in a thin wall PCR tube. Magnetic beads (5µL) were added to the mixture. After 1 min, the tube was placed in a magnetic bead separator (MBS) for 20 s to separate the beads from the supernatant. The beads were washed with 100µL washing solution three times. For elution, 5µL 50% ACN was added to the beads and mixed thoroughly. After 1 min, the tube was placed in a MBS and the beads were separated from the elution solution at the wall of the tubes. | PMID:17269739 | ||
| PAe000332 | human serum fractionation/depletion methods, 17_wcx | 17_wcx | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Bruker WCX magnetic beads The WCX magnetic bead solution was mixed thoroughly for 1 min. MB-WCX binding solution (10µL) and 10µL MB-WCX beads were mixed in a thin wall PCR tube. 5µL serum was added to the solution and incubated for 5 min. The tube was placed into a MBS and the beads were collected at the wall of the tube for 1 min. The beads were washed two more times with 100µL MB-WCX wash solution. MB-WCX (5µL) elution solution was added, and the beads were collected at the tube wall for 2 min. The supernatant was collected. | PMID:17269739 | ||
| PAe000335 | human serum fractionation/depletion methods, 18_size | 18_size | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Size fractionation Human serum samples were diluted 1:5 in 50 mM ammonium bicarbonate/20% ACN (pH 8.0) and centrifuged at 16 000×g for 5 min at 4°C to pellet any precipitate. A Millipore filter unit with 30 kDa molecular weight cutoff was rinsed with 50 mM ammonium bicarbonate/20% ACN and centrifuged at 2000×g for 5 min. Diluted serum sample (400µL) was added to the washed filter unit and centrifuged at 5000×g at 4°C for 30 min. The flow-through aliquot was transferred to a siliconized sterile vial. Ammonium bicarbonate/20% ACN (200µL) was added to the remaining sample and centrifuged in the same way as in the previous step. This cycle was repeated three times. Coomassie protein assay (Pierce, Rockford, IL) was performed on the pooled flowthrough aliquot to verify protein concentration. The flow through aliquot was dried in a SpeedVac and stored at -80°C until analysis. | PMID:17269739 | ||
| PAe000336 | human serum fractionation/depletion methods, 22_mars | 22_mars | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Multiple Affinity Removal System (MARS) column depletion The human Multiple Affinity Removal System (MARS) was purchased from Agilent Technologies (Palo Alto, CA) to deplete albumin, transferrin, IgG, IgA, anti-trypsin, and haptoglobin from human serum. Briefly, 100µL human serum was diluted 5-fold with Buffer A, filtered (0.22µm filter), and injected on the MARS column connected to a BioCad Vision HPLC system (Applied Biosystems, Foster City, CA). The flow-through was collected for 6 min (about 1.5 mL), desalted, and resuspended in 50 mM ammonium bicarbonate. | PMID:17269739 | ||
| PAe000338 | human serum fractionation/depletion methods, 16_clinprot_c8 | 16_clinprot_c8 | Human | Male, Serum, Sigma-Aldrich, catalog #H4522, lot #043K0502 | LTQ | Ammonium bicarbonate (50 mM) was added to achieve a final methanol concentration of 20% and the samples were digested with Trypsin Gold (Promega, Madison, WI) at a protein to enzyme ratio of 50:1 (w/w) at 37°C for 6 h. The samples were dried in a SpeedVac and resuspended in 50 mM ammonium bicarbonate prior to LC-MS analysis. | Human serum samples were denatured and reduced with 60% methanol and 10 mM dithiothreitol (DTT) at 60°C for 1 h and alkylated with 50 mM iodoacetamide (IAM) at room temperature in the dark for 30 min. | Bruker ClinProt C8 magnetic beads ClinProt purification reagent sets were obtained from Bruker Daltonics (Billerica, MA). The magnetic beads were shaken 20 times to achieve a homogeneous suspension. MB-HIC binding solution (10µL) and 5µL of human serum were mixed in a thin wall PCR tube. Magnetic beads (5µL) were added to the mixture. After 1 min, the tube was placed in a magnetic bead separator (MBS) for 20 s to separate the beads from the supernatant. The beads were washed with 100µL washing solution three times. For elution, 5µL 50% ACN was added to the beads and mixed thoroughly. After 1 min, the tube was placed in a MBS and the beads were separated from the elution solution at the wall of the tubes. | PMID:17269739 |
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