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TranscriptomicsRNA-sequencing using SLAM-sequencing protocol of human iPSC-derived lower motor neurons treated with BDNF for 1, 2, 6 h
SLAM-sequencing was performed on i3 LMNs following protocols adapted from Herzog et al. (2017). Three biological replicates of i3 LMNs were treated with 100 µM 4sU (Control) + labelling medium or 100 µM 4sU + BDNF (BDNF condition) labelling medium on Day 7 for 1h, 2h, and 6h. Cells were washed with ...
ORGANISM(S): Homo sapiens 
2025-05-30 | E-MTAB-14537 | biostudies-arrayexpress
ProteomicsDifferential alkylation of PHLPP2
To determine the accessibility of cysteines in purified PHLPP2, we assessed their reactivity with iodoacetamide under native conditions. After denaturing with urea and reducing potential disulfide bridges with TCEP, the remaining free cysteines were modified with methyl methanethiosulfonate. This 2-...
ORGANISM(S): Homo sapiens (Human) 
2025-03-13 | PXD052551 | Pride
Differential alkylation Free thiols 
ProteomicsProteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress, PART 2
Reactive oxygen species (ROS) are increasingly recognised as important regulators of cellular biology through the oxidative modification of protein cysteine residues. Comprehensive identification of redox-regulated proteins and cellular pathways are crucial to understand ROS-mediated events. Here, w...
ORGANISM(S): Mus musculus (Mouse) 
2018-03-06 | PXD006372 | Pride
Oxidative stress High ph fractionation Proteome Orbitrap hf Ros Mouse kidney tissue fumarate hydratase (fh) deficient Dimethyl labeling Primary immortalised kidney epithelial cells fumarate hydratase (fh) deficient Cysteine oxidation quantitation 
ProteomicsProteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress, PART 3
Reactive oxygen species (ROS) are increasingly recognised as important regulators of cellular biology through the oxidative modification of protein cysteine residues. Comprehensive identification of redox-regulated proteins and cellular pathways are crucial to understand ROS-mediated events. Here, w...
ORGANISM(S): Mus musculus (Mouse) 
2018-03-06 | PXD006373 | Pride
Oxidative stress High ph fractionation Proteome Orbitrap hf Ros Mouse kidney tissue fumarate hydratase (fh) deficient Dimethyl labeling Primary immortalised kidney epithelial cells fumarate hydratase (fh) deficient Cysteine oxidation quantitation 
UnknownEvaluation and optimization of reduction and alkylation methods to maximize peptide identification with MS-based proteomics.
Not available
S-EPMC5698164 | biostudies-literature
ProteomicsThe impact of commonly used alkylating agents on artefactual peptide modification
Iodoacetamide is by far the most commonly used agent for alkylation of cysteine during sample preparation for proteomics. An alternative, 2-chloroacetamide, has been recently suggested to reduce the alkylation of residues other than cysteine, such as the N-terminus, Asp, Glu, Lys, Ser, Thr and Tyr....
ORGANISM(S): Rattus norvegicus (Rat) 
2017-08-16 | PXD007071 | Pride
Post-translational modification Cysteine alkylation Artefact N-terminal alkylation Alkylation 
OtherZFP36L2 orchestrates stress-adaptive plasticity in intestinal regeneration and colorectal cancer metastasis (SLAMseq)
Thiol-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) was used to measure genome-wide mRNA half-lives in patient-derived colorectal cancer (CRC) liver metastasis organoids (MSK107Li). Organoids expressing a doxycycline-inducible short hairpin RNA targeting ZFP36L2 (shZFP36L2) or a n...
ORGANISM(S): Homo sapiens 
2026-07-20 | GSE336417 | GEO
ProteomicsPitfalls and Solutions in Mass Spectrometry-based Identification of Protein Glycation
Protein glycation is a type of post-translational modification (PTM) involving complex non-enzymatic reactions of reducing sugars or reactive dicarbonyls with proteins, generating a heterogeneous group of advanced glycation end-products (AGEs) such as carboxymethyllysine (CML). In bottom-up proteomi...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2023-01-24 | PXD032235 | Pride
Cam Post-translational modification Human Iaa N-isopropylcarbamidoethylation Nipam Cm Cml Cell line Q-exactive N-isopropylacrylamide Hela 2-iodoacetamide Orbitrap Carboxymethylation Escherichia coli E. coli Ptm Kidney Protein glycation Hek293 Carboxymethyllysine Lc-ms/ms Age Nipcae Carbamidomethylation Advanced glycation end-product 
ProteomicspChem_benchmarking_dataset_QTRP_diff_ratios
Data sets are used for benchmarking, pChem, a modification-centric, blind-search tool to provide a streamlined pipeline for unbiased assessing of the performance of chemoproteomic probes. Data were produced from the IPM-based QTRP (quantitative thiol reactivity profiling) experiments where light and...
ORGANISM(S): Homo sapiens (Human) 
2022-12-16 | PXD027762 | Pride
Ipm diff_ratios pchem 
UnknownOne-pot copper-catalyzed three-component reaction: a modular approach to functionalized 2-quinolones.
Not available
S-EPMC9049946 | biostudies-literature
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