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Supplementary Dataset 12 - Alkyne-2PCA clicked to biotin-DADPS-azide enrichment with E coli proteome derived peptide libraries

ABSTRACT: Alkyne-2PCA clicked to biotin-DADPS-azide enrichment with E coli proteome derived peptide libraries

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Escherichia Coli (ncbitaxon:562)

SUBMITTER: Amy Weeks

PROVIDER: MSV000091258 | MassIVE | Sat Feb 11 17:40:00 GMT 2023

SECONDARY ACCESSION(S): PXD040055

REPOSITORIES: MassIVE

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Supplementary Dataset 10 - Alkyne-2PCA clicked to biotin-azide enrichment with E coli proteome-derived peptide libraries

Project description:Alkyne-2PCA clicked to biotin-azide enrichment with E coli proteome-derived peptide libraries

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Supplementary Dataset 11 - Alkyne-2PCA clicked to biotin-disulfide-azide enrichment with E coli proteome derived peptide libraries

Project description:Alkyne-2PCA clicked to biotin-disulfide-azide enrichment with E coli proteome derived peptide libraries

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Supplementary Dataset 14 - Alkyne-2PCA clicked to biotin-Diazo-azide enrichment with E coli proteome derived peptide libraries

Project description:Alkyne-2PCA clicked to biotin-Diazo-azide enrichment with E coli proteome derived peptide libraries

2023-02-11 | MSV000091260 | MassIVE

Supplementary Dataset 13 - Alkyne-2PCA clicked to biotin-Dde-azide enrichment with E coli proteome derived peptide libraries

Project description:Alkyne-2PCA clicked to biotin-Dde-azide enrichment with E coli proteome derived peptide libraries

2023-02-11 | MSV000091259 | MassIVE

Supplementary Dataset 7 - Human proteome-derived peptide library generated with trypsin; treated with 10 mM alkyne-2PCA for 20 h at 37C; clicked with biotin azide

Project description:Human proteome-derived peptide library generated with trypsin; treated with 10 mM alkyne-2PCA for 20 h at 37C; clicked with biotin azide

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Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomics Studies

Project description:We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major by-product under widely used bioorthogonal protein labelling “click” conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by high reactivity of cysteine free thiols yielding thiotriazole protein conjugates. The reaction by-products generate false positive protein hits in “functional” proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide-tags and cell lysates reveals formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by MS-based proteomics. The produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to improved experimental design. Here, we present modified CuAAC conditions, which avoids the undesired product formation and diminishes the background.

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Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition.

Project description:The azide-alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide-alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na(2)S(2)O(4), 2% HOCH(2)CH(2)SH, 10% HCO(2)H, 95% CF(3)CO(2)H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO(2)H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies.

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Supplementary Dataset 6 - Human proteome-derived peptide library generated with trypsin; treated with 10 mM alkyne-2PCA for 20 h at 37C

Project description:Human proteome-derived peptide library generated with trypsin; treated with 10 mM alkyne-2PCA for 20 h at 37C

2023-02-11 | MSV000091251 | MassIVE

Ecoli W3110_0.01 M sodium azide treatment vs untreated, timecourse

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