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Matrix Science mascot search engine matrix version 2.6.0
Mascot Search Engine Matrix Version 2.6.0, supplied by Matrix Science, 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/mascot+2%2E6%2E0/mascot+search+algorithm/pmc10882324__ERJ___01228___2023__Supplement-95-7-10
Average 90 stars, based on 1 article reviews
mascot search engine matrix version 2.6.0 - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

Generated:

Article Title: A common gene signature of the right ventricle in failing rat and human hearts
Article Snippet: Data analysis was performed using Proteome Discoverer version 2.4.1.15 (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Sciences).

Article Title: Integrative gene regulatory network analysis discloses key driver genes of fibromuscular dysplasia.
Article Snippet: Valentina d’Escamard, Daniella Kadian-Dodov, Lijiang Ma, Sizhao Lu , Annette King, Yang Xu , Shouneng Peng , Bhargravi V′Gangula, Yu Zhou, Allison Thomas, Katherine C. Michelis, Emir Bander, Rihab Bouchareb, Adrien Georges , Aya Nomura-Kitabayashi , Robert J. Wiener , Kevin D. Costa, Elena Chepurko, Vadim Chepurko, Marika Fava, Temo Barwari , Anelechi Anyanwu, Farzan Filsoufi, Sander Florman, Nabila Bouatia-Naji , Lukas E. Schmidt , Manuel Mayr, Michael G. Katz, Ke Hao , Mary C. M. Weiser-Evans , Johan L. M. Björkegren , Jeffrey W. Olin & Jason C. Kovacic

Article Title: Integrated metabolomics and proteomics analyses to reveal anticancer mechanism of hemp oil extract in colorectal cancer.
Article Snippet: The protein search and quantification were generated in Proteome Discoverer 2.1 software (Thermo Scientific), and Mascot 2.6.0 (Matrix Science).

Article Title: Phosphosites of the yeast centrosome component Spc110 contribute to cell cycle progression and mitotic exit
Article Snippet: Peak lists were generated in Proteome Discoverer 2.3 software (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Science) and concatenated forward/decoy Saccharomyces cerevisiae database (7939 entries).

Article Title: Single molecule characterization of individual extracellular vesicles from pancreatic cancer
Article Snippet: Mass spectra were searched using Proteome Discoverer 2.2 (Thermo Fisher Scientific) and Mascot 2.6.0 (Matrix Science) against a SwissProt/UniprotKB Homo sapiens database (downloaded Jan 2017), allowing for tryptic rules and up to 2 missed cleavages, fixed cysteine carbamidomethylation, variable methionine oxidation, and N-terminal acetylation.


Article Title: SEPN1-related myopathy depends on the oxidoreductase ERO1A and is druggable with the chemical chaperone TUDCA
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Enriched functional analysis EnrichR https://maayanlab.cloud/Enrichr/ STRING analysis API (version 12) STRING consortium database https://string-db.org/ Mascot 2.6.0 Matrix Science N/A Proteome Discoverer 1.4 Thermo Scientific N/A Scaffold 4.11.1 Proteome Software Inc., Portland, OR https://support.proteomesoftware. com/hc/en-us GraphPad Prism 9 GraphPad Prism https://graphpad.com ImageJ ImageJ https://imagej.nih.gov/ij/ ‘‘Quantification 1’’ and ‘‘Quantification 2’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins ‘‘VolumeJ’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins GIMP Open Source https://www.gimp.org/ DESeq2 (v.1.36.0) Publication51 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RStudio (v. 2023.06.0 + 421) Posit.co https://posit.co/download/rstudio-desktop/ edgeR (v.3.38.4) Publication52 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Limma (v.3.52.2) Publication53 https://bioconductor.org/packages/ release/bioc/html/limma.html Bash (v. 5.0.17(1)-release (x86_64-pc-linux-gnu) [Ubuntu 20.04.6 LTS]) Bash Ubuntu (Linux) https://help.ubuntu.com/community/ Beginners/BashScripting bcl2fastq (v. 2.20.0.422) Illumina https://support.illumina.com/content/dam/ illumina-support/documents/documentation/ software_documentation/bcl2fastq/bcl2fastq2v2-20-software-guide-15051736-03.pdf STAR (v. 2.7.9a) Publication54 https://github.com/alexdobin/STAR SMASH – semi-automatic muscle analysis Smith LR, Barton ER.

Article Title: CETSA interaction proteomics define specific RNA-modification pathways as key components of fluorouracil-based cancer drug cytotoxicity.
Article Snippet: Article CETSA interaction proteomics define specific RNA- modification pathways as key components of fluorouracil-based cancer drug cytotoxicity

Software:

Article Title: A common gene signature of the right ventricle in failing rat and human hearts
Article Snippet: Data analysis was performed using Proteome Discoverer version 2.4.1.15 (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Sciences).

Article Title: Integrative gene regulatory network analysis discloses key driver genes of fibromuscular dysplasia.
Article Snippet: Valentina d’Escamard, Daniella Kadian-Dodov, Lijiang Ma, Sizhao Lu , Annette King, Yang Xu , Shouneng Peng , Bhargravi V′Gangula, Yu Zhou, Allison Thomas, Katherine C. Michelis, Emir Bander, Rihab Bouchareb, Adrien Georges , Aya Nomura-Kitabayashi , Robert J. Wiener , Kevin D. Costa, Elena Chepurko, Vadim Chepurko, Marika Fava, Temo Barwari , Anelechi Anyanwu, Farzan Filsoufi, Sander Florman, Nabila Bouatia-Naji , Lukas E. Schmidt , Manuel Mayr, Michael G. Katz, Ke Hao , Mary C. M. Weiser-Evans , Johan L. M. Björkegren , Jeffrey W. Olin & Jason C. Kovacic

Article Title: Integrated metabolomics and proteomics analyses to reveal anticancer mechanism of hemp oil extract in colorectal cancer.
Article Snippet: The protein search and quantification were generated in Proteome Discoverer 2.1 software (Thermo Scientific), and Mascot 2.6.0 (Matrix Science).

Article Title: Phosphosites of the yeast centrosome component Spc110 contribute to cell cycle progression and mitotic exit
Article Snippet: Peak lists were generated in Proteome Discoverer 2.3 software (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Science) and concatenated forward/decoy Saccharomyces cerevisiae database (7939 entries).

Article Title: Single molecule characterization of individual extracellular vesicles from pancreatic cancer
Article Snippet: Mass spectra were searched using Proteome Discoverer 2.2 (Thermo Fisher Scientific) and Mascot 2.6.0 (Matrix Science) against a SwissProt/UniprotKB Homo sapiens database (downloaded Jan 2017), allowing for tryptic rules and up to 2 missed cleavages, fixed cysteine carbamidomethylation, variable methionine oxidation, and N-terminal acetylation.


Article Title: SEPN1-related myopathy depends on the oxidoreductase ERO1A and is druggable with the chemical chaperone TUDCA
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Enriched functional analysis EnrichR https://maayanlab.cloud/Enrichr/ STRING analysis API (version 12) STRING consortium database https://string-db.org/ Mascot 2.6.0 Matrix Science N/A Proteome Discoverer 1.4 Thermo Scientific N/A Scaffold 4.11.1 Proteome Software Inc., Portland, OR https://support.proteomesoftware. com/hc/en-us GraphPad Prism 9 GraphPad Prism https://graphpad.com ImageJ ImageJ https://imagej.nih.gov/ij/ ‘‘Quantification 1’’ and ‘‘Quantification 2’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins ‘‘VolumeJ’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins GIMP Open Source https://www.gimp.org/ DESeq2 (v.1.36.0) Publication51 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RStudio (v. 2023.06.0 + 421) Posit.co https://posit.co/download/rstudio-desktop/ edgeR (v.3.38.4) Publication52 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Limma (v.3.52.2) Publication53 https://bioconductor.org/packages/ release/bioc/html/limma.html Bash (v. 5.0.17(1)-release (x86_64-pc-linux-gnu) [Ubuntu 20.04.6 LTS]) Bash Ubuntu (Linux) https://help.ubuntu.com/community/ Beginners/BashScripting bcl2fastq (v. 2.20.0.422) Illumina https://support.illumina.com/content/dam/ illumina-support/documents/documentation/ software_documentation/bcl2fastq/bcl2fastq2v2-20-software-guide-15051736-03.pdf STAR (v. 2.7.9a) Publication54 https://github.com/alexdobin/STAR SMASH – semi-automatic muscle analysis Smith LR, Barton ER.

Article Title: CETSA interaction proteomics define specific RNA-modification pathways as key components of fluorouracil-based cancer drug cytotoxicity.
Article Snippet: Article CETSA interaction proteomics define specific RNA- modification pathways as key components of fluorouracil-based cancer drug cytotoxicity

Functional Assay:

Article Title: A common gene signature of the right ventricle in failing rat and human hearts
Article Snippet: Data analysis was performed using Proteome Discoverer version 2.4.1.15 (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Sciences).

Article Title: Integrative gene regulatory network analysis discloses key driver genes of fibromuscular dysplasia.
Article Snippet: Valentina d’Escamard, Daniella Kadian-Dodov, Lijiang Ma, Sizhao Lu , Annette King, Yang Xu , Shouneng Peng , Bhargravi V′Gangula, Yu Zhou, Allison Thomas, Katherine C. Michelis, Emir Bander, Rihab Bouchareb, Adrien Georges , Aya Nomura-Kitabayashi , Robert J. Wiener , Kevin D. Costa, Elena Chepurko, Vadim Chepurko, Marika Fava, Temo Barwari , Anelechi Anyanwu, Farzan Filsoufi, Sander Florman, Nabila Bouatia-Naji , Lukas E. Schmidt , Manuel Mayr, Michael G. Katz, Ke Hao , Mary C. M. Weiser-Evans , Johan L. M. Björkegren , Jeffrey W. Olin & Jason C. Kovacic

Article Title: Integrated metabolomics and proteomics analyses to reveal anticancer mechanism of hemp oil extract in colorectal cancer.
Article Snippet: The protein search and quantification were generated in Proteome Discoverer 2.1 software (Thermo Scientific), and Mascot 2.6.0 (Matrix Science).

Article Title: Phosphosites of the yeast centrosome component Spc110 contribute to cell cycle progression and mitotic exit
Article Snippet: Peak lists were generated in Proteome Discoverer 2.3 software (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Science) and concatenated forward/decoy Saccharomyces cerevisiae database (7939 entries).

Article Title: Single molecule characterization of individual extracellular vesicles from pancreatic cancer
Article Snippet: Mass spectra were searched using Proteome Discoverer 2.2 (Thermo Fisher Scientific) and Mascot 2.6.0 (Matrix Science) against a SwissProt/UniprotKB Homo sapiens database (downloaded Jan 2017), allowing for tryptic rules and up to 2 missed cleavages, fixed cysteine carbamidomethylation, variable methionine oxidation, and N-terminal acetylation.


Article Title: SEPN1-related myopathy depends on the oxidoreductase ERO1A and is druggable with the chemical chaperone TUDCA
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Enriched functional analysis EnrichR https://maayanlab.cloud/Enrichr/ STRING analysis API (version 12) STRING consortium database https://string-db.org/ Mascot 2.6.0 Matrix Science N/A Proteome Discoverer 1.4 Thermo Scientific N/A Scaffold 4.11.1 Proteome Software Inc., Portland, OR https://support.proteomesoftware. com/hc/en-us GraphPad Prism 9 GraphPad Prism https://graphpad.com ImageJ ImageJ https://imagej.nih.gov/ij/ ‘‘Quantification 1’’ and ‘‘Quantification 2’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins ‘‘VolumeJ’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins GIMP Open Source https://www.gimp.org/ DESeq2 (v.1.36.0) Publication51 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RStudio (v. 2023.06.0 + 421) Posit.co https://posit.co/download/rstudio-desktop/ edgeR (v.3.38.4) Publication52 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Limma (v.3.52.2) Publication53 https://bioconductor.org/packages/ release/bioc/html/limma.html Bash (v. 5.0.17(1)-release (x86_64-pc-linux-gnu) [Ubuntu 20.04.6 LTS]) Bash Ubuntu (Linux) https://help.ubuntu.com/community/ Beginners/BashScripting bcl2fastq (v. 2.20.0.422) Illumina https://support.illumina.com/content/dam/ illumina-support/documents/documentation/ software_documentation/bcl2fastq/bcl2fastq2v2-20-software-guide-15051736-03.pdf STAR (v. 2.7.9a) Publication54 https://github.com/alexdobin/STAR SMASH – semi-automatic muscle analysis Smith LR, Barton ER.

Article Title: CETSA interaction proteomics define specific RNA-modification pathways as key components of fluorouracil-based cancer drug cytotoxicity.
Article Snippet: Article CETSA interaction proteomics define specific RNA- modification pathways as key components of fluorouracil-based cancer drug cytotoxicity

Sequencing:

Article Title: A common gene signature of the right ventricle in failing rat and human hearts
Article Snippet: Data analysis was performed using Proteome Discoverer version 2.4.1.15 (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Sciences).

Article Title: Integrative gene regulatory network analysis discloses key driver genes of fibromuscular dysplasia.
Article Snippet: Valentina d’Escamard, Daniella Kadian-Dodov, Lijiang Ma, Sizhao Lu , Annette King, Yang Xu , Shouneng Peng , Bhargravi V′Gangula, Yu Zhou, Allison Thomas, Katherine C. Michelis, Emir Bander, Rihab Bouchareb, Adrien Georges , Aya Nomura-Kitabayashi , Robert J. Wiener , Kevin D. Costa, Elena Chepurko, Vadim Chepurko, Marika Fava, Temo Barwari , Anelechi Anyanwu, Farzan Filsoufi, Sander Florman, Nabila Bouatia-Naji , Lukas E. Schmidt , Manuel Mayr, Michael G. Katz, Ke Hao , Mary C. M. Weiser-Evans , Johan L. M. Björkegren , Jeffrey W. Olin & Jason C. Kovacic

Article Title: Integrated metabolomics and proteomics analyses to reveal anticancer mechanism of hemp oil extract in colorectal cancer.
Article Snippet: The protein search and quantification were generated in Proteome Discoverer 2.1 software (Thermo Scientific), and Mascot 2.6.0 (Matrix Science).

Article Title: Phosphosites of the yeast centrosome component Spc110 contribute to cell cycle progression and mitotic exit
Article Snippet: Peak lists were generated in Proteome Discoverer 2.3 software (Thermo Fisher Scientific) with Mascot 2.6.0 (Matrix Science) and concatenated forward/decoy Saccharomyces cerevisiae database (7939 entries).

Article Title: Single molecule characterization of individual extracellular vesicles from pancreatic cancer
Article Snippet: Mass spectra were searched using Proteome Discoverer 2.2 (Thermo Fisher Scientific) and Mascot 2.6.0 (Matrix Science) against a SwissProt/UniprotKB Homo sapiens database (downloaded Jan 2017), allowing for tryptic rules and up to 2 missed cleavages, fixed cysteine carbamidomethylation, variable methionine oxidation, and N-terminal acetylation.


Article Title: SEPN1-related myopathy depends on the oxidoreductase ERO1A and is druggable with the chemical chaperone TUDCA
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Enriched functional analysis EnrichR https://maayanlab.cloud/Enrichr/ STRING analysis API (version 12) STRING consortium database https://string-db.org/ Mascot 2.6.0 Matrix Science N/A Proteome Discoverer 1.4 Thermo Scientific N/A Scaffold 4.11.1 Proteome Software Inc., Portland, OR https://support.proteomesoftware. com/hc/en-us GraphPad Prism 9 GraphPad Prism https://graphpad.com ImageJ ImageJ https://imagej.nih.gov/ij/ ‘‘Quantification 1’’ and ‘‘Quantification 2’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins ‘‘VolumeJ’’ plugin Tito Cali’s lab https://github.com/titocali1/ Quantification-Plugins GIMP Open Source https://www.gimp.org/ DESeq2 (v.1.36.0) Publication51 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RStudio (v. 2023.06.0 + 421) Posit.co https://posit.co/download/rstudio-desktop/ edgeR (v.3.38.4) Publication52 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Limma (v.3.52.2) Publication53 https://bioconductor.org/packages/ release/bioc/html/limma.html Bash (v. 5.0.17(1)-release (x86_64-pc-linux-gnu) [Ubuntu 20.04.6 LTS]) Bash Ubuntu (Linux) https://help.ubuntu.com/community/ Beginners/BashScripting bcl2fastq (v. 2.20.0.422) Illumina https://support.illumina.com/content/dam/ illumina-support/documents/documentation/ software_documentation/bcl2fastq/bcl2fastq2v2-20-software-guide-15051736-03.pdf STAR (v. 2.7.9a) Publication54 https://github.com/alexdobin/STAR SMASH – semi-automatic muscle analysis Smith LR, Barton ER.

Article Title: CETSA interaction proteomics define specific RNA-modification pathways as key components of fluorouracil-based cancer drug cytotoxicity.
Article Snippet: Article CETSA interaction proteomics define specific RNA- modification pathways as key components of fluorouracil-based cancer drug cytotoxicity



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