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bioworks 3.1 software  (BioWorks Inc)

 
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    BioWorks Inc bioworks 3.1 software
    Bioworks 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
    https://www.bioz.com/result/bioworks 3.1 software/product/BioWorks Inc
    Average 90 stars, based on 1 article reviews
    bioworks 3.1 software - by Bioz Stars, 2026-04
    90/100 stars

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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