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ptmscan method  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc ptmscan method
    Ptmscan Method, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ptmscan+method/ptmscan+method/pm40627385-246-5-9
    Average 90 stars, based on 1 article reviews
    ptmscan method - by Bioz Stars, 2026-09
    90/100 stars

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    Mass Spectrometry:

    Article Title: USP22 Functions as an Oncogenic Driver in Prostate Cancer by Regulating Cell Proliferation and DNA Repair
    Article Snippet: Samples were analyzed using the Cell Signaling Technology PTMScan method as described previously (Cell Signaling Technology; refs. 20–22).

    Article Title: The WWP1-JARID1B axis sustains acute myeloid leukemia chemoresistance.
    Article Snippet: Samples were analyzed using the PTMScan method provided by Cell Signaling Technology as previously described (25, 48).

    Article Title: Heat Stress and Thermal Ablation Induce Local Expression of Nerve Growth Factor Inducible (VGF) in Hepatocytes and Hepatocellular Carcinoma: Preclinical and Clinical Studies
    Article Snippet: Quantitative Mass Spectrometry (LC-MS/MS) and Phosphoproteomic Pathway Analysis Per Cell Signaling Technology (CST; Danvers, MA, USA) protocol, samples were analyzed using the PTMScan method as previously described 25–27 .

    Article Title: Heat Stress and Thermal Ablation Induce Local Expression of Nerve Growth Factor Inducible (VGF) in Hepatocytes and Hepatocellular Carcinoma: Preclinical and Clinical Studies
    Article Snippet: Treatment temperature was monitored using an Omega HH41 digital thermometer (Omega Engineering, Stamford, CT, USA) and maintained to within ±0.05°C.

    Article Title: Heat Stress and Thermal Ablation Induce Local Expression of Nerve Growth Factor Inducible (VGF) in Hepatocytes and Hepatocellular Carcinoma: Preclinical and Clinical Studies
    Article Snippet: Per Cell Signaling Technology (CST; Danvers, MA, USA) protocol, samples were analyzed using the PTMScan method as previously described 25–27 .

    Article Title: Heat stress induced, ligand-independent MET and EGFR signaling in hepatocellular carcinoma.
    Article Snippet: Quantitative Mass Spectrometry (LC-MS/MS) and Phosphoproteomic Pathway Analysis Per Cell Signaling Technology (CST; Danvers, MA) protocol, samples were analyzed using the PTMScan method as previously described [ 26 , 27 , 28 ].



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    a Experimental workflow for <t>in-depth</t> <t>diGly</t> peptide library construction (upper panel) and our single-run data-independent acquisition (DIA)-based workflow (lower panel). Protein digestion and peptide extraction are followed by basic reversed-phase (bRP) fractionation and diGly peptide enrichment. For library construction, samples were measured by data-dependent acquisition <t>(DDA)</t> and computationally processed (Spectronaut Pulsar). Individual samples are measured by our DIA workflow, including matching against a library for identification (Spectronaut software). b Number of identified diGly peptides in three different spectral libraries (MG132 treated HEK293 library—green, MG132 treated U2OS library—violet, U2OS library—light violet, all diGly peptides—gray). c Commonly and exclusively identified diGly peptides for different libraries (MG132 treated HEK293 library—green, MG132 treated U2OS library—violet, U2OS library—light violet). d Identified diGly sites (mean ± SEM) of MG132 treated HEK293 cells using different DIA library search strategies ( n = 6, three workflow replicates measured in analytical duplicates). Source data are provided as a Source data file.
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    a Experimental workflow for in-depth diGly peptide library construction (upper panel) and our single-run data-independent acquisition (DIA)-based workflow (lower panel). Protein digestion and peptide extraction are followed by basic reversed-phase (bRP) fractionation and diGly peptide enrichment. For library construction, samples were measured by data-dependent acquisition (DDA) and computationally processed (Spectronaut Pulsar). Individual samples are measured by our DIA workflow, including matching against a library for identification (Spectronaut software). b Number of identified diGly peptides in three different spectral libraries (MG132 treated HEK293 library—green, MG132 treated U2OS library—violet, U2OS library—light violet, all diGly peptides—gray). c Commonly and exclusively identified diGly peptides for different libraries (MG132 treated HEK293 library—green, MG132 treated U2OS library—violet, U2OS library—light violet). d Identified diGly sites (mean ± SEM) of MG132 treated HEK293 cells using different DIA library search strategies ( n = 6, three workflow replicates measured in analytical duplicates). Source data are provided as a Source data file.

    Journal: Nature Communications

    Article Title: Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

    doi: 10.1038/s41467-020-20509-1

    Figure Lengend Snippet: a Experimental workflow for in-depth diGly peptide library construction (upper panel) and our single-run data-independent acquisition (DIA)-based workflow (lower panel). Protein digestion and peptide extraction are followed by basic reversed-phase (bRP) fractionation and diGly peptide enrichment. For library construction, samples were measured by data-dependent acquisition (DDA) and computationally processed (Spectronaut Pulsar). Individual samples are measured by our DIA workflow, including matching against a library for identification (Spectronaut software). b Number of identified diGly peptides in three different spectral libraries (MG132 treated HEK293 library—green, MG132 treated U2OS library—violet, U2OS library—light violet, all diGly peptides—gray). c Commonly and exclusively identified diGly peptides for different libraries (MG132 treated HEK293 library—green, MG132 treated U2OS library—violet, U2OS library—light violet). d Identified diGly sites (mean ± SEM) of MG132 treated HEK293 cells using different DIA library search strategies ( n = 6, three workflow replicates measured in analytical duplicates). Source data are provided as a Source data file.

    Article Snippet: The resulting nine pooled fractions were enriched for diGly peptides, which were separately analyzed using a DDA method (PTMScan Ubiquitin Remnant Motif (K-ε-GG) Kit, CST) (Fig. and Supplementary Fig. ).

    Techniques: Ubiquitin Proteomics, Data-independent acquisition, Extraction, Fractionation, Data-dependent acquisition, Software

    a Number of identified diGly peptides (mean, n = 2) for data-independent acquisition (DIA, blue, HEK293 hybrid library) and data-dependent acquisition (DDA, red) strategies ( n = 6, three workflow replicates measured in analytical duplicates). Venn diagram depicts the proportion of shared and exclusively identified diGly sites between DIA and DDA approaches. b Coefficient of variation (CV) value distribution for DIA and DDA approaches. Solid and dotted lines denote median and 1st or 3rd quantile, respectively. c Fractions of CV values below 50% and 20% are shown with solid and dotted lines, respectively. d Dilution series of diGly enriched sample. Plots show individual ubiquitin-chain linkage type peptides measured via DIA (blue) or DDA (red) ( n = 3). Top panels depict CV values of replicate measurements. Bottom panels show individual measurements compared to the expected dilution depicted as dotted line. R 2 values describe the goodness-of-fit of measured values to the expected dilution series (dotted line). Source data are provided as a Source data file.

    Journal: Nature Communications

    Article Title: Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

    doi: 10.1038/s41467-020-20509-1

    Figure Lengend Snippet: a Number of identified diGly peptides (mean, n = 2) for data-independent acquisition (DIA, blue, HEK293 hybrid library) and data-dependent acquisition (DDA, red) strategies ( n = 6, three workflow replicates measured in analytical duplicates). Venn diagram depicts the proportion of shared and exclusively identified diGly sites between DIA and DDA approaches. b Coefficient of variation (CV) value distribution for DIA and DDA approaches. Solid and dotted lines denote median and 1st or 3rd quantile, respectively. c Fractions of CV values below 50% and 20% are shown with solid and dotted lines, respectively. d Dilution series of diGly enriched sample. Plots show individual ubiquitin-chain linkage type peptides measured via DIA (blue) or DDA (red) ( n = 3). Top panels depict CV values of replicate measurements. Bottom panels show individual measurements compared to the expected dilution depicted as dotted line. R 2 values describe the goodness-of-fit of measured values to the expected dilution series (dotted line). Source data are provided as a Source data file.

    Article Snippet: The resulting nine pooled fractions were enriched for diGly peptides, which were separately analyzed using a DDA method (PTMScan Ubiquitin Remnant Motif (K-ε-GG) Kit, CST) (Fig. and Supplementary Fig. ).

    Techniques: Ubiquitin Proteomics, Data-independent acquisition, Data-dependent acquisition

    a Workflow for ubiquitinome analysis in tumor necrosis factor (TNF) signaling. b Identified diGly sites (±SD) for TNF treated (100 ng/ml for 10 min) and control U2OS cells in data-independent acquisition (DIA, blue) and data-dependent acquisition (DDA, red) experiments ( n = 6, three workflow replicates measured in analytical duplicates). c Volcano plot of significantly regulated diGly sites at 5% false discovery rate (FDR) (FDR controlled, two-sided t -test, randomizations = 250, s0 = 0.1) (lower line) and 1% (upper line) for DIA (blue) and DDA (red) and overlaps of significantly upregulated diGly sites for 1 and 5% FDR cutoffs ( t -test, s0 = 0.1). d Overrepresentation analysis of gene ontology biological process (GOBP) terms filtered for 5% corrected FDR (Fisher’s Exact test). e Cytoscape network of proteins with significantly upregulated diGly sites in DIA that are associated with NFκB signaling (GO 0043122; GO 0051092; 5% FDR). Upregulated diGly sites also captured by DDA are marked in red (5% FDR). Source data are provided as a Source data file.

    Journal: Nature Communications

    Article Title: Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

    doi: 10.1038/s41467-020-20509-1

    Figure Lengend Snippet: a Workflow for ubiquitinome analysis in tumor necrosis factor (TNF) signaling. b Identified diGly sites (±SD) for TNF treated (100 ng/ml for 10 min) and control U2OS cells in data-independent acquisition (DIA, blue) and data-dependent acquisition (DDA, red) experiments ( n = 6, three workflow replicates measured in analytical duplicates). c Volcano plot of significantly regulated diGly sites at 5% false discovery rate (FDR) (FDR controlled, two-sided t -test, randomizations = 250, s0 = 0.1) (lower line) and 1% (upper line) for DIA (blue) and DDA (red) and overlaps of significantly upregulated diGly sites for 1 and 5% FDR cutoffs ( t -test, s0 = 0.1). d Overrepresentation analysis of gene ontology biological process (GOBP) terms filtered for 5% corrected FDR (Fisher’s Exact test). e Cytoscape network of proteins with significantly upregulated diGly sites in DIA that are associated with NFκB signaling (GO 0043122; GO 0051092; 5% FDR). Upregulated diGly sites also captured by DDA are marked in red (5% FDR). Source data are provided as a Source data file.

    Article Snippet: The resulting nine pooled fractions were enriched for diGly peptides, which were separately analyzed using a DDA method (PTMScan Ubiquitin Remnant Motif (K-ε-GG) Kit, CST) (Fig. and Supplementary Fig. ).

    Techniques: Ubiquitin Proteomics, Control, Data-independent acquisition, Data-dependent acquisition