Proteomics

Dataset Information

0

Cysteine alkylating methods in shotgun proteomics and their possible effects on methionine residues

ABSTRACT: Neatly every proteomic protocol has a Cysteine reduction and alkylation step in it preceding the trypsin digestion. It needs to be done in order to remove the s-s bonds and prevent proteins from folding, thus, provide better access for trypsin. Among various reagents used for alkylation, iodoacetamide (IAM) seems to be the most common. Although, it has been shown that IAM can cause some undesired side reactions [Chernobrovkin et al., 2015; Muller et al., 2017]. In this work, we have compared the effect of four alkylating agents: iodoacetamide (IAM), 4-vinylpyridine (4-VP), chloroacetamide (CAM) and S-Methyl methanethiosulfonate (MMTS). In addition, we tried to check whether post-treatment with DTT (p-red) is reasonable in the case of irreversible alkylation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Irina Ilina  

LAB HEAD: Sergei A. Moshkovskii

PROVIDER: PXD015889 | Pride | 2024-02-14

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
60_1.mgf Mgf
60_1.raw Raw
60_1_full.pep.xml Pepxml
60_2.mgf Mgf
60_2.raw Raw
Items per page:
1 - 5 of 213
altmetric image

Publications

Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues.

Kuznetsova Ksenia G KG   Levitsky Lev I LI   Pyatnitskiy Mikhail A MA   Ilina Irina Y IY   Bubis Julia A JA   Solovyeva Elizaveta M EM   Zgoda Victor G VG   Gorshkov Mikhail V MV   Moshkovskii Sergei A SA  

Journal of proteomics 20201020

In order to optimize sample preparation for shotgun proteomics, we compared four cysteine alkylating agents: iodoacetamide, chloroacetamide, 4-vinylpyridine and methyl methanethiosulfonate, and estimated their effects on the results of proteome analysis. Because alkylation may result in methionine modification in vitro, proteomics data were searched for methionine to isothreonine conversions, which may mimic genomic methionine to threonine substitutions found in proteogenomic analyses. We found  ...[more]

Similar Datasets

Proteomics Cysteine alkylating methods in shotgun proteomics and their possible effects on methionine residues
2020-10-28 | PXD013973 | Pride
Transcriptomics SlamSeq of subcellular compartments in mouse primary cortical neurons
2023-07-12 | E-MTAB-12888 | biostudies-arrayexpress
Transcriptomics Transcription profiling of chromosome 22 genes in human peripheral blood mononuclear cells after stimulation with HIV-gag and env peptides
2008-10-31 | E-TABM-571 | biostudies-arrayexpress
Transcriptomics Transcription profiling of stress treated fission yeast (stressors: compound: heavy metal, oxidation, alkylation and osmosis
2004-10-31 | E-MEXP-29 | biostudies-arrayexpress
Transcriptomics The global expression profile of Bacillus subtilis to the toxic carbonyls methylglyoxal (MG) and formaldehyde (FA)
2010-05-15 | E-GEOD-13925 | biostudies-arrayexpress
Transcriptomics Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and mutants
2013-08-03 | E-GEOD-49530 | biostudies-arrayexpress
Transcriptomics Comparative transcriptional analysis of Desulfovibrio alaskensis G20 and regulator proteins mutants
2013-08-03 | E-GEOD-49529 | biostudies-arrayexpress
Transcriptomics Distinct chromatin signatures in plant male germline cells - RNA-seq
2022-12-02 | E-MTAB-10965 | biostudies-arrayexpress
Transcriptomics Comparative transcriptional analysis of Desulfovibrio alaskensis G20, a choline utilization regulator and LysX
2013-08-03 | E-GEOD-49528 | biostudies-arrayexpress
Proteomics Developmental profile of core postsynaptic density protein complexes integrates signaling components of brain disorders
2017-08-22 | PXD006277 | Pride