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BioWorks Inc bioworks 3.3.1 software
Bioworks 3.3.1 Software, supplied by BioWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bioworks 3.3.1 software - by Bioz Stars, 2026-10
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Tandem Mass Spectroscopy:

Article Title: Proteomics-based network analysis characterizes biological processes and pathways activated by preconditioned mesenchymal stem cells in cardiac repair mechanisms.
Article Snippet: BACKGROUND: We have demonstrated that intramyocardial delivery of human mesenchymal stem cells preconditioned with a hyaluronan mixed ester of butyric and retinoic acid (MSCp) is more effective in preventing the decay of regional myocardial contractility in a swine model of myocardial infarction (MI).. However, the understanding of the role of MSCp in proteomic remodeling of cardiac infarcted tissue is not complete.. We therefore sought to perform a comprehensive analysis of the proteome of infarct remote (RZ) and border zone (BZ) of pigs treated with MSCp or unconditioned stem cells.

Article Title: Shotgun protein profile of human adipose tissue and its changes in relation to systemic amyloidoses.
Article Snippet: In systemic amyloidosis, accumulation of misfolded proteins as extracellular amyloid fibrils in tissues causes severe organ dysfunction, but the molecular events of tissue damage related to amyloid deposition are still largely unknown.. Through the use of the MudPIT proteomic approach, comprehensive protein profiles of human amyloid-affected adipose tissue from patients and its control (non-amyloid-affected) counterpart were acquired.. Label-free comparison between patients and controls made it possible to highlight differences related to the presence of amyloid, by describing upand down-represented proteins, connected into interacting networks.

Article Title: Quantitative Gingival Crevicular Fluid Proteome in Health and Periodontal Disease Using Stable-Isotope Chemistries and Mass Spectrometry
Article Snippet: Database search and protein/peptide identification and quantification All MS/MS spectra from LC-ESI-MS/MS were searched against the human database, Uniprot (Universal Protein Resource, Version 9.0), which combines the data from Swiss-Prot (Version 51), TreMBL (Version 34) and PIR using Bioworks 3.3.1 software and SEQUEST search engine ( Eng et al., 1994 ).

Article Title: Quantitative Gingival Crevicular Fluid Proteome in Health and Periodontal Disease Using Stable-Isotope Chemistries and Mass Spectrometry
Article Snippet: All MS/MS spectra from LC-ESI-MS/MS were searched against the human database, Uniprot (Universal Protein Resource, Version 9.0), which combines the data from Swiss-Prot (Version 51), TreMBL (Version 34) and PIR using Bioworks 3.3.1 software and SEQUEST search engine ( Eng et al., 1994 ).

Article Title: Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics
Article Snippet: The obtained MS/MS spectra were searched against several databases, including Uniprot, Swiss-Prot, TreMBL, and PIR, using Bioworks 3.3.1 software and the SEQUEST search engine.

Article Title: Topographical distribution of phosphorylation sites of phosvitins by mass spectrometry.
Article Snippet: Article history: Received 15 September 2012 Accepted 16 February 2013 Available online 6 March 2013

Article Title: Identification and Functional Analysis of Novel Bradykinin-Related Peptides (BRPs) from Skin Secretions of Five Asian Frogs.
Article Snippet: In recent decades, various types of bioactive substances have been identified from amphibian skin and its secretions.. Bradykinin-related peptides (BRPs) are among these compounds that make up the host defence system of amphibians.. In the present study, we identified six novel BRPs, amolopkinin-GN1, amolopkinin-RK1, amolopkinin-TR1, amolopkinin-LF1, ranakinin-MS1, and ranakinin-MS2, from five East Asian amphibians, Amolops granulosus, Amolops ricketti, Amolops torrentis, Amolops lifanensis, and Hylarana maosonensis.

Article Title: Novel bioactivity of phosvitin in connective tissue and bone organogenesis revealed by live calvarial bone organ culture models.
Article Snippet: The MS/MS data generated from the analysis of aliquots from the above samples were searched against the ratspecific database, Uniprot (Universal Protein Resources, Version 9.0), which combines the data from Swiss-Prot (version 51) TreMBL (Version 34) and PIR using the Bioworks 3.3.1 software and SEQUEST search engine (Eng et al., 1994).

Software:

Article Title: Proteomics-based network analysis characterizes biological processes and pathways activated by preconditioned mesenchymal stem cells in cardiac repair mechanisms.
Article Snippet: BACKGROUND: We have demonstrated that intramyocardial delivery of human mesenchymal stem cells preconditioned with a hyaluronan mixed ester of butyric and retinoic acid (MSCp) is more effective in preventing the decay of regional myocardial contractility in a swine model of myocardial infarction (MI).. However, the understanding of the role of MSCp in proteomic remodeling of cardiac infarcted tissue is not complete.. We therefore sought to perform a comprehensive analysis of the proteome of infarct remote (RZ) and border zone (BZ) of pigs treated with MSCp or unconditioned stem cells.

Article Title: Shotgun protein profile of human adipose tissue and its changes in relation to systemic amyloidoses.
Article Snippet: In systemic amyloidosis, accumulation of misfolded proteins as extracellular amyloid fibrils in tissues causes severe organ dysfunction, but the molecular events of tissue damage related to amyloid deposition are still largely unknown.. Through the use of the MudPIT proteomic approach, comprehensive protein profiles of human amyloid-affected adipose tissue from patients and its control (non-amyloid-affected) counterpart were acquired.. Label-free comparison between patients and controls made it possible to highlight differences related to the presence of amyloid, by describing upand down-represented proteins, connected into interacting networks.

Article Title: Quantitative Gingival Crevicular Fluid Proteome in Health and Periodontal Disease Using Stable-Isotope Chemistries and Mass Spectrometry
Article Snippet: Database search and protein/peptide identification and quantification All MS/MS spectra from LC-ESI-MS/MS were searched against the human database, Uniprot (Universal Protein Resource, Version 9.0), which combines the data from Swiss-Prot (Version 51), TreMBL (Version 34) and PIR using Bioworks 3.3.1 software and SEQUEST search engine ( Eng et al., 1994 ).

Article Title: Quantitative Gingival Crevicular Fluid Proteome in Health and Periodontal Disease Using Stable-Isotope Chemistries and Mass Spectrometry
Article Snippet: All MS/MS spectra from LC-ESI-MS/MS were searched against the human database, Uniprot (Universal Protein Resource, Version 9.0), which combines the data from Swiss-Prot (Version 51), TreMBL (Version 34) and PIR using Bioworks 3.3.1 software and SEQUEST search engine ( Eng et al., 1994 ).

Article Title: Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics
Article Snippet: The obtained MS/MS spectra were searched against several databases, including Uniprot, Swiss-Prot, TreMBL, and PIR, using Bioworks 3.3.1 software and the SEQUEST search engine.

Article Title: Topographical distribution of phosphorylation sites of phosvitins by mass spectrometry.
Article Snippet: Article history: Received 15 September 2012 Accepted 16 February 2013 Available online 6 March 2013

Article Title: Identification and Functional Analysis of Novel Bradykinin-Related Peptides (BRPs) from Skin Secretions of Five Asian Frogs.
Article Snippet: In recent decades, various types of bioactive substances have been identified from amphibian skin and its secretions.. Bradykinin-related peptides (BRPs) are among these compounds that make up the host defence system of amphibians.. In the present study, we identified six novel BRPs, amolopkinin-GN1, amolopkinin-RK1, amolopkinin-TR1, amolopkinin-LF1, ranakinin-MS1, and ranakinin-MS2, from five East Asian amphibians, Amolops granulosus, Amolops ricketti, Amolops torrentis, Amolops lifanensis, and Hylarana maosonensis.

Article Title: Novel bioactivity of phosvitin in connective tissue and bone organogenesis revealed by live calvarial bone organ culture models.
Article Snippet: The MS/MS data generated from the analysis of aliquots from the above samples were searched against the ratspecific database, Uniprot (Universal Protein Resources, Version 9.0), which combines the data from Swiss-Prot (version 51) TreMBL (Version 34) and PIR using the Bioworks 3.3.1 software and SEQUEST search engine (Eng et al., 1994).

Generated:

Article Title: Proteomics-based network analysis characterizes biological processes and pathways activated by preconditioned mesenchymal stem cells in cardiac repair mechanisms.
Article Snippet: BACKGROUND: We have demonstrated that intramyocardial delivery of human mesenchymal stem cells preconditioned with a hyaluronan mixed ester of butyric and retinoic acid (MSCp) is more effective in preventing the decay of regional myocardial contractility in a swine model of myocardial infarction (MI).. However, the understanding of the role of MSCp in proteomic remodeling of cardiac infarcted tissue is not complete.. We therefore sought to perform a comprehensive analysis of the proteome of infarct remote (RZ) and border zone (BZ) of pigs treated with MSCp or unconditioned stem cells.

Article Title: Shotgun protein profile of human adipose tissue and its changes in relation to systemic amyloidoses.
Article Snippet: In systemic amyloidosis, accumulation of misfolded proteins as extracellular amyloid fibrils in tissues causes severe organ dysfunction, but the molecular events of tissue damage related to amyloid deposition are still largely unknown.. Through the use of the MudPIT proteomic approach, comprehensive protein profiles of human amyloid-affected adipose tissue from patients and its control (non-amyloid-affected) counterpart were acquired.. Label-free comparison between patients and controls made it possible to highlight differences related to the presence of amyloid, by describing upand down-represented proteins, connected into interacting networks.

Article Title: Quantitative Gingival Crevicular Fluid Proteome in Health and Periodontal Disease Using Stable-Isotope Chemistries and Mass Spectrometry
Article Snippet: Database search and protein/peptide identification and quantification All MS/MS spectra from LC-ESI-MS/MS were searched against the human database, Uniprot (Universal Protein Resource, Version 9.0), which combines the data from Swiss-Prot (Version 51), TreMBL (Version 34) and PIR using Bioworks 3.3.1 software and SEQUEST search engine ( Eng et al., 1994 ).

Article Title: Quantitative Gingival Crevicular Fluid Proteome in Health and Periodontal Disease Using Stable-Isotope Chemistries and Mass Spectrometry
Article Snippet: All MS/MS spectra from LC-ESI-MS/MS were searched against the human database, Uniprot (Universal Protein Resource, Version 9.0), which combines the data from Swiss-Prot (Version 51), TreMBL (Version 34) and PIR using Bioworks 3.3.1 software and SEQUEST search engine ( Eng et al., 1994 ).

Article Title: Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics
Article Snippet: The obtained MS/MS spectra were searched against several databases, including Uniprot, Swiss-Prot, TreMBL, and PIR, using Bioworks 3.3.1 software and the SEQUEST search engine.

Article Title: Topographical distribution of phosphorylation sites of phosvitins by mass spectrometry.
Article Snippet: Article history: Received 15 September 2012 Accepted 16 February 2013 Available online 6 March 2013

Article Title: Identification and Functional Analysis of Novel Bradykinin-Related Peptides (BRPs) from Skin Secretions of Five Asian Frogs.
Article Snippet: In recent decades, various types of bioactive substances have been identified from amphibian skin and its secretions.. Bradykinin-related peptides (BRPs) are among these compounds that make up the host defence system of amphibians.. In the present study, we identified six novel BRPs, amolopkinin-GN1, amolopkinin-RK1, amolopkinin-TR1, amolopkinin-LF1, ranakinin-MS1, and ranakinin-MS2, from five East Asian amphibians, Amolops granulosus, Amolops ricketti, Amolops torrentis, Amolops lifanensis, and Hylarana maosonensis.

Article Title: Novel bioactivity of phosvitin in connective tissue and bone organogenesis revealed by live calvarial bone organ culture models.
Article Snippet: The MS/MS data generated from the analysis of aliquots from the above samples were searched against the ratspecific database, Uniprot (Universal Protein Resources, Version 9.0), which combines the data from Swiss-Prot (version 51) TreMBL (Version 34) and PIR using the Bioworks 3.3.1 software and SEQUEST search engine (Eng et al., 1994).



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Identification of Torpedo proteins listed in public access databases . To validate tandem mass spectrometry (MS/MS) data against species-specific sequences, spectra acquired via MS/MS analysis of electric organ fractions were analyzed by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing known and characterized Torpedo proteins listed in GenBank. Peptide acceptance criteria was set at ΔCn >0.1, a variable threshold of Xcorr versus charge state: Xcorr = 1.9 for z = 1, Xcorr = 2.2 for z = 2, and Xcorr = 2.5 for z = 3, protein Xcorr >40, and a peptide probability based score with a P value <0.01. Protein identifications were compared with a search against UniProtKB (Swiss-Prot and TrEMBL) release 14.0, all species, to maintain consistency with databases used and protein accession numbers reported. Proteins identified are categorized by the likelihood and appropriateness of detection based on protein subcellular location or on the quality of data on public access databases.

Journal: Skeletal Muscle

Article Title: Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

doi: 10.1186/2044-5040-1-20

Figure Lengend Snippet: Identification of Torpedo proteins listed in public access databases . To validate tandem mass spectrometry (MS/MS) data against species-specific sequences, spectra acquired via MS/MS analysis of electric organ fractions were analyzed by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing known and characterized Torpedo proteins listed in GenBank. Peptide acceptance criteria was set at ΔCn >0.1, a variable threshold of Xcorr versus charge state: Xcorr = 1.9 for z = 1, Xcorr = 2.2 for z = 2, and Xcorr = 2.5 for z = 3, protein Xcorr >40, and a peptide probability based score with a P value <0.01. Protein identifications were compared with a search against UniProtKB (Swiss-Prot and TrEMBL) release 14.0, all species, to maintain consistency with databases used and protein accession numbers reported. Proteins identified are categorized by the likelihood and appropriateness of detection based on protein subcellular location or on the quality of data on public access databases.

Article Snippet: Raw spectra were analyzed by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing our T. californica cDNA library translated into six reading frames and The Universal Protein Resource (UniProtKB/Swiss-Prot) release 14.0 [ ].

Techniques: Mass Spectrometry, Tandem Mass Spectroscopy, Software

Sequence alignments between uncharacterized human open reading frames (ORF) and Torpedo cDNA . Two human ORFs were identified by tandem mass spectrometry (MS/MS) analysis of electric organ fractions by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing our in-house Torpedo californica cDNA library translated into six reading frames. Comprehensive alignments of nucleotide and protein sequences between uncharacterized human ORFs (blue text) and Torpedo cDNA (black text) were compiled from individual ClustalW alignments (default parameters with gonnet matrix) for C1orf123 (a) and C6orf130 (b) . ClustalW protein alignment is shown separately to highlight protein sequence similarity with the translated cDNA sequence (Expasy translate tool) and peptides identified by mass spectral mapping (highlighted in red). Start and stop amino acids are highlighted in yellow.

Journal: Skeletal Muscle

Article Title: Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

doi: 10.1186/2044-5040-1-20

Figure Lengend Snippet: Sequence alignments between uncharacterized human open reading frames (ORF) and Torpedo cDNA . Two human ORFs were identified by tandem mass spectrometry (MS/MS) analysis of electric organ fractions by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing our in-house Torpedo californica cDNA library translated into six reading frames. Comprehensive alignments of nucleotide and protein sequences between uncharacterized human ORFs (blue text) and Torpedo cDNA (black text) were compiled from individual ClustalW alignments (default parameters with gonnet matrix) for C1orf123 (a) and C6orf130 (b) . ClustalW protein alignment is shown separately to highlight protein sequence similarity with the translated cDNA sequence (Expasy translate tool) and peptides identified by mass spectral mapping (highlighted in red). Start and stop amino acids are highlighted in yellow.

Article Snippet: Raw spectra were analyzed by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing our T. californica cDNA library translated into six reading frames and The Universal Protein Resource (UniProtKB/Swiss-Prot) release 14.0 [ ].

Techniques: Sequencing, Mass Spectrometry, Tandem Mass Spectroscopy, Software, cDNA Library Assay

Electric organ proteome overlaps with mouse skeletal muscle proteome but shows tissue-specific protein expression . Mouse skeletal muscle (tibialis anterior muscle or gastrocnemius muscle) and the Torpedo electric organ were fractionated and processed under similar conditions as stated under Figure 1. Mouse skeletal muscle proteins were identified by BioWorks 3.3.1 referencing only UniProtKB/Swiss-Prot. Electric organ (EO) and skeletal muscle proteins were compared and graphed in Microsoft Excel 2007 based on the number of peptides per protein identified in each tissue. EO proteins are mapped (#peptides/protein) on the × axis and mouse skeletal muscle on the y axis. The lower two graphs represent zoomed sections for visual clarity.

Journal: Skeletal Muscle

Article Title: Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction

doi: 10.1186/2044-5040-1-20

Figure Lengend Snippet: Electric organ proteome overlaps with mouse skeletal muscle proteome but shows tissue-specific protein expression . Mouse skeletal muscle (tibialis anterior muscle or gastrocnemius muscle) and the Torpedo electric organ were fractionated and processed under similar conditions as stated under Figure 1. Mouse skeletal muscle proteins were identified by BioWorks 3.3.1 referencing only UniProtKB/Swiss-Prot. Electric organ (EO) and skeletal muscle proteins were compared and graphed in Microsoft Excel 2007 based on the number of peptides per protein identified in each tissue. EO proteins are mapped (#peptides/protein) on the × axis and mouse skeletal muscle on the y axis. The lower two graphs represent zoomed sections for visual clarity.

Article Snippet: Raw spectra were analyzed by the SEQUEST algorithm in BioWorks 3.3.1 software, crossreferencing our T. californica cDNA library translated into six reading frames and The Universal Protein Resource (UniProtKB/Swiss-Prot) release 14.0 [ ].

Techniques: Expressing