Institute of Animal Physiology and Genetics LAPA - SWATH NSC Skyline

Institute of Animal Physiology and Genetics LAPA - SWATH NSC Skyline
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NV0001_Mouse-Skin_mProphet_Panorama_2024-03-09_19-20-18.sky.zip2024-03-10 20:30:291,6595,7905,79028,90434
XW0008_Cas9Myc_DIAassayLIB_OmBcells_17Nov2023_2024-02-24_08-51-18.sky.zip2024-02-24 12:56:485,20383,67483,675605,04024
XW0009_DIAassayLIB_OmBcells_17Nov2023_2024-02-23_18-35-50.sky.zip2024-02-23 22:06:575,20383,64583,647604,72019
AutoQC-lumos-SysS-MouAD-PFC-C2-B5-B7.sky.zip2024-02-20 07:53:561889414
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B07.sky.zip2024-02-18 11:31:099,778127,624127,624966,34712
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B06.sky.zip2024-02-18 10:45:259,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B05.sky.zip2024-02-18 09:51:569,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B04.sky.zip2024-02-18 01:14:219,778127,624127,624966,34716
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Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B21.sky.zip2024-02-17 09:01:129,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B20.sky.zip2024-02-17 01:24:329,778127,624127,624966,34716
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Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B13.sky.zip2024-02-16 17:05:369,778127,624127,624966,34716
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XW0008-Myc248_DIAassayLIB_OmBcells_17Nov2023_2024-02-16_10-02-13.sky.zip2024-02-16 15:02:065,20383,67483,675605,04024
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B11.sky.zip2024-02-16 11:03:589,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B10.sky.zip2024-02-16 10:07:519,778127,624127,624966,34716
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Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B08.sky.zip2024-02-16 08:20:059,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B07.sky.zip2024-02-16 01:08:409,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B06.sky.zip2024-02-16 00:17:379,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B05.sky.zip2024-02-15 23:29:389,778127,624127,624966,34716
XW0008_nanos3_DIAassayLIB_OmBcells_17Nov2023_2024-02-15_17-02-46.sky.zip2024-02-15 21:13:165,20383,67483,675605,04024
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B04.sky.zip2024-02-15 16:37:369,778127,624127,624966,34716
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B03.sky.zip2024-02-15 14:42:299,778127,624127,624966,34716
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Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B01.sky.zip2024-02-15 12:45:409,778127,624127,624966,34716
AutoQC-lumos-PCs-MouAD-PFC-C2-B5-B7.sky.zip2024-02-14 16:42:502141417344
AutoQC-lumos-PCs-MouAD-PFC-C2-B1-B4.sky.zip2024-02-14 16:42:332141417364
AutoQC-lumos-PCs-MouAD-PFC-C1-B9-B12.sky.zip2024-02-14 16:42:152141417364
AutoQC-lumos-PCs-MouAD-PFC-C1-B4-B8.sky.zip2024-02-14 16:42:002141417380
AutoQC-lumos-PCs-MouAD-PFC-C1-B25-B28.sky.zip2024-02-14 16:41:372141417354
AutoQC-lumos-PCs-MouAD-PFC-C1-B21-B24.sky.zip2024-02-14 16:41:002141417364
AutoQC-lumos-PCs-MouAD-PFC-C1-B17-B20.sky.zip2024-02-14 16:40:442141417365
AutoQC-lumos-PCs-MouAD-PFC-C1-B13-B16.sky.zip2024-02-14 16:40:282141417364
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AutoQC-lumos-SysS-MouAD-PFC-C1-B9-B12.sky.zip2024-02-14 16:06:251889416
AutoQC-lumos-SysS-MouAD-PFC-C1-B4-B8.sky.zip2024-02-14 16:02:231889422
AutoQC-lumos-SysS-MouAD-PFC-C1-B1-B3.sky.zip2024-02-14 15:59:501889418
AutoQC-lumos-SysS-MouAD-PFC-C1-B17-B20.sky.zip2024-02-14 14:48:381889410
ZipChip_HR_Metabolomics_2024Protocol_2024-02-05_17-24-05.sky.zip2024-02-05 14:24:28100821594
22AminoAcids_Fully13CLabeled_2024-01-29_14-30-52.sky.zip2024-01-29 11:32:1410444936
RBD_M_Glyco_2024-01-25_15-29-41.sky.zip2024-01-26 17:23:2672923972,3829
20240104_Neg_FMT_MCBAs_isoRemove_Cleaned_Final_2024-01-25_21-40-19.sky.zip2024-01-26 16:43:471010030056
20231220_Neg_FMT_BA_Full_reduce_Res50_High_final_2024-01-04_15-44-59.sky.zip2024-01-26 16:43:47405112176
P179_UNCSet1_ACE_v0p3_2024-01-24_22-42-18.sky.zip2024-01-24 19:51:4423034963724
P179_UNCSet2_ACE_v0p3_2024-01-24_22-37-25.sky.zip2024-01-24 19:40:1117021336726
New_iRBD2024-01-15 23:30:5233474794292
Paired_CSF_Plasma_Serum2024-01-15 23:30:523347479460
Initial_Targeted_Proteomics2024-01-15 23:30:5233474794441
TPAD_VL_CSF_PRTC_APOA1_2024-01-07_23-01-46.sky.zip2024-01-07 23:08:493464642412
TPAD-CSF-SP3_1-5.sky.zip2024-01-05 06:03:432,90823,74323,743189,895396
173_peptides_iRTs_chromatogram_library_2023-12-22_00-47-19.sky.zip2023-12-22 01:06:36311833561,0822
Figure_8B_Freiburg_ALG1-CDG-Patients_Comparison_2023-12-22_02-34-55.sky.zip2023-12-22 01:06:2022691284006
Figures_4_5_6_7_8A_Heidelberg_CDG-Patients_2023-12-22_02-32-43.sky.zip2023-12-22 01:06:20206712439014
Figure_S5_Freiburg_ALG11_I-CDG_Natural_Variant_2023-12-22_01-59-41.sky.zip2023-12-22 01:06:2021112146
Figure_9_Freiburg_ALG11_I-CDG_Natural_Variant_2023-12-22_01-53-52.sky.zip2023-12-22 01:06:2021418404
Figures_3_and_S3_HEK_293T_Fibroblasts_HeLa_2023-12-22_01-03-03.sky.zip2023-12-22 01:06:2023701303989
20210301 Calibration Dev_DilutionOil_2023-12-11_10-57-35.sky.zip2023-12-20 00:34:263482654
20210607 Calibration Curve_DilutionDigest_2023-12-11_10-50-40.sky.zip2023-12-20 00:34:2634824108
20210212 Low range exploration 140K-fragmod_Pub_2023-12-08_16-04-13.sky.zip2023-12-20 00:34:263482456
HeatedOilSpike-LowTemp_HighTemp_Combined_Final_2022-05-26_12-00-47.sky.zip2023-12-20 00:34:26591548204
20200715_PeptideSpecificity_SignalRatio_2022-05-25_16-33-02.sky.zip2023-12-20 00:34:2611202212044
20200622_PeptideSpecificityTest_2022-05-25_16-30-20.sky.zip2023-12-20 00:34:2614252713545
20191112_Diff-TempConc_Oil-Spike_24pep_2022-05-25_14-24-35.sky.zip2023-12-20 00:34:2611242715040
20191007_HeatedOilSpike_Extraction_method_24pep_2022-05-25_14-16-21.sky.zip2023-12-20 00:34:2611242715032
20190904_Organic_Aqueous_Extraction_Oil_Spike_24pep_2022-05-25_14-12-26.sky.zip2023-12-20 00:34:2611242715636
September 21 Import V1 (Samples with IS) w Cal Curve_Blanks Deleted_2023-12-01_11-40-59.sky.zip2023-12-02 23:51:3320262687
September 21 Kaylie New Molecule Import v1 (Filtered)_2023-12-01_11-40-01.sky.zip2023-12-02 23:51:3310161698
September 21 Import V1 all samples (Neg mode only)_2023-12-01_11-35-34.sky.zip2023-12-02 23:51:338014514598
THP1_IFN_PRM_Skyline_2023-11-14_14-22-42.sky.zip2023-11-16 13:26:09711771771,5148
CCS_library_v2.sky.zip2023-11-15 14:36:301061,86361,8630
IdentExpression_2023-09-25_14-39-47.sky.zip2023-10-02 20:45:1381581941,16419
2DGel_II_2023-09-25_14-37-39.sky.zip2023-10-02 20:45:13897408805,28034
2DGel_I_2023-09-25_14-36-13.sky.zip2023-10-02 20:45:13252142321,39232
InGelDigest_Der_p_SEA_II_2023-09-18_10-01-52.sky.zip2023-09-21 11:03:445004,0584,42026,52051
InGelDigest_Der_p_SEA_I_2023-09-15_16-14-11.sky.zip2023-09-21 11:03:443272,3822,52115,12652
FASP_Der_p_SEA_2023-09-15_14-24-26.sky.zip2023-09-21 11:03:445504,2964,77128,6261
230504_Myllys_231247ff_2023-09-20_13-22-59.sky.zip2023-09-21 10:31:2410434398
230512MyllysUrea_231247ff_2023-09-21_15-27-13.sky.zip2023-09-21 10:31:24102292
230511Myllys231247ff_AA_Crea_2023-09-20_13-36-24.sky.zip2023-09-21 10:31:242044166126
AutoQC-lumos-SysS-MouAD-C2-B8-10.sky.zip2023-09-17 11:22:321889414
AutoQC-lumos-SysS-MouAD-C2-B5-B7.sky.zip2023-09-17 11:22:301889415
AutoQC-lumos-SysS-MouAD-C2-B1-B4.sky.zip2023-09-17 11:22:281889419
AutoQC-lumos-SysS-MouAD-C1-B9-B12.sky.zip2023-09-17 11:22:261889413
Proteomic characterization of human neural stem cells during in vitro differentiation
Data License: CC BY 4.0 | ProteomeXchange: PXD021860
  • Organism: Homo sapiens
  • Instrument: TripleTOF 5600+
  • SpikeIn: No
  • Keywords: NSCs, neural differentiation, SWATH-MS
  • Lab head: Petr Vodička Submitter: Jirina Tyleckova
Abstract
One of the promising approaches to slow down or treat neurodegenerative diseases or spinal cord injuries represent cell therapies. The grafted cells could either integrate into the damaged tissue to replace dead or damaged cells or by secretion of different factors modulate inflammatory reaction, reduce tissue damage and support neuronal survival. However, due to the heterogeneity of in vitro cultured cells, comprehensive characterization of such cells is absolutely crucial to prevent safety risks. Here, we performed SWATH-MS analysis to characterize changes in proteome of human neural stem cells (NSCs) during their differentiation either spontaneously by withdrawal of EGF and FGF2 in cell culture media or by trophic support of BDNF/GDNF growth factors. We quantified about 2800 proteins over the 28 days of differentiation and showed that changes in cellular proteomes are caused mostly by differentiation time course, rather than type of differentiation itself and that the major changes in protein expression occurred between day 0 and day 7 of both differentiations.
Experiment Description
Human neural stem cells (NSCs) derived from NIH approved H9 human embryonic stem cells were cultivated on polyornithine/laminine coated dishes in the KnockOut Dulbecco’s modified Eagle’s medium/F-12, 2 mM GlutaMA, 1% penicillin-streptomycin, 2% StemPro Neural Supplement, and supplemented with 20 ng/mL human recombinant EGF and 20 ng/mL human recombinant FGF2 and differentiated either spontaneously (S) by withdrawal of EGF and FGF2 growth factors from the cell culture media or by trophic support of BDNF and GDNF growth factors (B/G). The cells were differentiated for 0, 7, 14, 21 and 28 days, harvested manually and SWATH-MS analysis was performed to reveal changes in cellular proteome during both differentiation protocols.
Sample Description
Proteomic sample preparation: Cells on culture dishes were washed with PBS and harvested mechanically. Cells were then lysed with 8 M urea and 5 mM EDTA in 50 mM ammonium bicarbonate and homogenized. Protein concentration was determined by Pierce 660 nm protein assay. Each protein lysate sample was then treated with ProteaseMAX surfactant, reduced and alkylated, followed by enzymatic digestion with endoproteinase LysC and trypsin. The digestion was stopped with formic acid (FA); the resulting peptide mixtures were desalted on C18 spin columns. The eluted peptides were vacuum centrifuged to dryness and resuspended in aqueous solution with 2% ACN and 0.5% FA. The peptide concentration was determined by measuring absorbance at 280 nm and the peptide samples were diluted to a final concentration of 0.5 µg/µl with 1:30 (v/v) of spiked-in indexed Retention Time Biognosys peptides. The peptide mixtures in randomized order were loaded and separated on C18 columns in a trap-elute mode using the Eksigent nano-LC 425 (Sciex) on-line connected to 5600+ TripleTOF (Sciex) on a linear gradient of 5-35% acetonitrile in 0.1% FA over 120 min and 35-50% acetonitrile in 0.1% FA over 10 minutes at a flow rate of 200 nL/min. For DDA, the top 30 precursors with accumulation time 300 ms and mass range 400-1250 in high sensitivity mode were fragmented (MS/MS accumulation time 150 ms and mass range 170-1500 Da) in each cycle. For SWATH-MS were monitored 35 variable windows calculated with SWATH Variable window calculator (Sciex) with 150 ms accumulation time in MS and 100 ms accumulation tome in MS/MS with mass range 400-1250 Da, respectively 170-2000 Da, cycle time 3.5 s.
Created on 10/6/20, 11:03 AM