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maxquant andromeda search engine  (Biostatistical Consulting)

 
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    Biostatistical Consulting maxquant andromeda search engine
    LC-MS/MS analysis of FFPE, bulk frozen tissues, and GSCs highlights subgroup-specific proteomic differences. (A) We profiled bulk frozen (n = 15) and macrodissected FFPE glioma tissues (n = 15) using Q Exactive LC-MS/MS. GSCs (n = 3), grown in duplicate, were profiled in the presence and absence of EGF/FGF (n = 12). (B) Raw MS datasets searched in <t>Maxquant</t> Andromeda search engine yielded on average ∼2,900, ∼2,400, and ∼2,950, quantified proteins per frozen, FFPE, and tissue culture samples, respectively. Bar graph illustrates quantified peptides/protein and Venn diagram illustrates overlaps of identified protein IDs, with 2,130 proteins measured across all three datasets. Venn diagram on the right indicates the overlap between our tissue datasets with previously published MS-based proteome characterizations. (C) DAVID analysis of the three datasets demonstrate an overall similarity in percentage of proteins localized to particular cellular components and involved in indicated biological processes. (D) Clustering based on global Pearson correlation coefficients demonstrate clustering of primary tumor samples largely based on WHO grade classification (grade I-IV) and IDH mutation status. Macrodissected FFPE tumors demonstrate slightly improved segregation of tumors according to IDH.
    Maxquant Andromeda Search Engine, supplied by Biostatistical Consulting, 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/result/maxquant andromeda search engine/product/Biostatistical Consulting
    Average 90 stars, based on 1 article reviews
    maxquant andromeda search engine - by Bioz Stars, 2026-03
    90/100 stars

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    1) Product Images from "Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry * "

    Article Title: Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry *

    Journal: Molecular & Cellular Proteomics : MCP

    doi: 10.1074/mcp.RA119.001521

    LC-MS/MS analysis of FFPE, bulk frozen tissues, and GSCs highlights subgroup-specific proteomic differences. (A) We profiled bulk frozen (n = 15) and macrodissected FFPE glioma tissues (n = 15) using Q Exactive LC-MS/MS. GSCs (n = 3), grown in duplicate, were profiled in the presence and absence of EGF/FGF (n = 12). (B) Raw MS datasets searched in Maxquant Andromeda search engine yielded on average ∼2,900, ∼2,400, and ∼2,950, quantified proteins per frozen, FFPE, and tissue culture samples, respectively. Bar graph illustrates quantified peptides/protein and Venn diagram illustrates overlaps of identified protein IDs, with 2,130 proteins measured across all three datasets. Venn diagram on the right indicates the overlap between our tissue datasets with previously published MS-based proteome characterizations. (C) DAVID analysis of the three datasets demonstrate an overall similarity in percentage of proteins localized to particular cellular components and involved in indicated biological processes. (D) Clustering based on global Pearson correlation coefficients demonstrate clustering of primary tumor samples largely based on WHO grade classification (grade I-IV) and IDH mutation status. Macrodissected FFPE tumors demonstrate slightly improved segregation of tumors according to IDH.
    Figure Legend Snippet: LC-MS/MS analysis of FFPE, bulk frozen tissues, and GSCs highlights subgroup-specific proteomic differences. (A) We profiled bulk frozen (n = 15) and macrodissected FFPE glioma tissues (n = 15) using Q Exactive LC-MS/MS. GSCs (n = 3), grown in duplicate, were profiled in the presence and absence of EGF/FGF (n = 12). (B) Raw MS datasets searched in Maxquant Andromeda search engine yielded on average ∼2,900, ∼2,400, and ∼2,950, quantified proteins per frozen, FFPE, and tissue culture samples, respectively. Bar graph illustrates quantified peptides/protein and Venn diagram illustrates overlaps of identified protein IDs, with 2,130 proteins measured across all three datasets. Venn diagram on the right indicates the overlap between our tissue datasets with previously published MS-based proteome characterizations. (C) DAVID analysis of the three datasets demonstrate an overall similarity in percentage of proteins localized to particular cellular components and involved in indicated biological processes. (D) Clustering based on global Pearson correlation coefficients demonstrate clustering of primary tumor samples largely based on WHO grade classification (grade I-IV) and IDH mutation status. Macrodissected FFPE tumors demonstrate slightly improved segregation of tumors according to IDH.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mutagenesis



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    maxquant andromeda search engine  (Biostatistical Consulting)
    90
    Biostatistical Consulting maxquant andromeda search engine
    LC-MS/MS analysis of FFPE, bulk frozen tissues, and GSCs highlights subgroup-specific proteomic differences. (A) We profiled bulk frozen (n = 15) and macrodissected FFPE glioma tissues (n = 15) using Q Exactive LC-MS/MS. GSCs (n = 3), grown in duplicate, were profiled in the presence and absence of EGF/FGF (n = 12). (B) Raw MS datasets searched in <t>Maxquant</t> Andromeda search engine yielded on average ∼2,900, ∼2,400, and ∼2,950, quantified proteins per frozen, FFPE, and tissue culture samples, respectively. Bar graph illustrates quantified peptides/protein and Venn diagram illustrates overlaps of identified protein IDs, with 2,130 proteins measured across all three datasets. Venn diagram on the right indicates the overlap between our tissue datasets with previously published MS-based proteome characterizations. (C) DAVID analysis of the three datasets demonstrate an overall similarity in percentage of proteins localized to particular cellular components and involved in indicated biological processes. (D) Clustering based on global Pearson correlation coefficients demonstrate clustering of primary tumor samples largely based on WHO grade classification (grade I-IV) and IDH mutation status. Macrodissected FFPE tumors demonstrate slightly improved segregation of tumors according to IDH.
    Maxquant Andromeda Search Engine, supplied by Biostatistical Consulting, 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/result/maxquant andromeda search engine/product/Biostatistical Consulting
    Average 90 stars, based on 1 article reviews
    maxquant andromeda search engine - by Bioz Stars, 2026-03
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    LC-MS/MS analysis of FFPE, bulk frozen tissues, and GSCs highlights subgroup-specific proteomic differences. (A) We profiled bulk frozen (n = 15) and macrodissected FFPE glioma tissues (n = 15) using Q Exactive LC-MS/MS. GSCs (n = 3), grown in duplicate, were profiled in the presence and absence of EGF/FGF (n = 12). (B) Raw MS datasets searched in Maxquant Andromeda search engine yielded on average ∼2,900, ∼2,400, and ∼2,950, quantified proteins per frozen, FFPE, and tissue culture samples, respectively. Bar graph illustrates quantified peptides/protein and Venn diagram illustrates overlaps of identified protein IDs, with 2,130 proteins measured across all three datasets. Venn diagram on the right indicates the overlap between our tissue datasets with previously published MS-based proteome characterizations. (C) DAVID analysis of the three datasets demonstrate an overall similarity in percentage of proteins localized to particular cellular components and involved in indicated biological processes. (D) Clustering based on global Pearson correlation coefficients demonstrate clustering of primary tumor samples largely based on WHO grade classification (grade I-IV) and IDH mutation status. Macrodissected FFPE tumors demonstrate slightly improved segregation of tumors according to IDH.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry *

    doi: 10.1074/mcp.RA119.001521

    Figure Lengend Snippet: LC-MS/MS analysis of FFPE, bulk frozen tissues, and GSCs highlights subgroup-specific proteomic differences. (A) We profiled bulk frozen (n = 15) and macrodissected FFPE glioma tissues (n = 15) using Q Exactive LC-MS/MS. GSCs (n = 3), grown in duplicate, were profiled in the presence and absence of EGF/FGF (n = 12). (B) Raw MS datasets searched in Maxquant Andromeda search engine yielded on average ∼2,900, ∼2,400, and ∼2,950, quantified proteins per frozen, FFPE, and tissue culture samples, respectively. Bar graph illustrates quantified peptides/protein and Venn diagram illustrates overlaps of identified protein IDs, with 2,130 proteins measured across all three datasets. Venn diagram on the right indicates the overlap between our tissue datasets with previously published MS-based proteome characterizations. (C) DAVID analysis of the three datasets demonstrate an overall similarity in percentage of proteins localized to particular cellular components and involved in indicated biological processes. (D) Clustering based on global Pearson correlation coefficients demonstrate clustering of primary tumor samples largely based on WHO grade classification (grade I-IV) and IDH mutation status. Macrodissected FFPE tumors demonstrate slightly improved segregation of tumors according to IDH.

    Article Snippet: The following MS method parameters were used: MS1 automatic gain control target was set to 3e6 with maximum injection time of 100 ms; MS2 automatic gain control was set to 5e4 with maximum injection time of 50 ms; isolation window was 1.6 Da; underfill ratio 2%; intensity threshold 2e4; normalized collision energy was set to 27; charge exclusion was set to fragment only 2+, 3+, and 4+ charge state ions; peptide match set to preferred; and dynamic exclusion set to 42 (for 90-min method) or 48 s (for 120-min method). . Biostatistical and Informatics Analysis Raw data files were searched using MaxQuant Andromeda search engine ( www.coxdocs.org ) against the Human Swiss-Prot protein database (July 2017 version) using match between runs algorithm.

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mutagenesis