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Structured Review

Proteome Software Inc scaffold q s software
Scaffold Q S Software, supplied by Proteome Software Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/scaffold+q+software/scaffold/bio_rxiv__64898__2026__03__31__715582-286-5-9
Average 86 stars, based on 1 article reviews
scaffold q s software - by Bioz Stars, 2026-09
86/100 stars

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Related Articles

Software:

Article Title: Hypoxia Triggers the Intravasation of Clustered Circulating Tumor Cells.
Article Snippet: .. Next, the database search results were imported to the Scaffold Q+ software (version 4.3.2, Proteome Software Inc., Portland, OR) and the protein FDR rate was set to 1%. ..

Article Title: Supporting Information Lesson from the stoichiometry determination of the cohesin complex; a short protease mediated elution increases the recovery from crosslinked antibody- conjugated beads
Article Snippet: .. Spectra acquired on LTQ Orbitrap were searched against the human IPI database and compared using Scaffold Q+ software (v 3.0, Proteome Software). ..

Article Title: Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis.
Article Snippet: .. Next, the database search results were imported to the Scaffold Q+ software (version 4.3.2, Proteome Software Inc., Portland, OR) and the protein false identification rate was set to 1% based on the number of decoy hits. ..

Article Title: Quantitative proteomic and phosphoproteomic comparison of human colon cancer DLD-1 cells differing in ploidy and chromosome stability
Article Snippet: .. Next, the database search results were imported to the Scaffold Q+ software (version 4.3.2, Proteome Software Inc., Portland, OR) and the protein false identification rate was set to 1% based on the number of decoy hits. ..

Article Title: Deciphering the oviductal extracellular vesicles content across the estrous cycle: implications for the gametes-oviduct interactions and the environment of the potential embryo.
Article Snippet: .. For comparative analysis, we employed Scaffold Q+ software (version 4.4, Proteome Software, Portland, USA) for spectral counting label-free quantitative method with “Weighed Spectra” option on protein clusters. ..

Modification:

Article Title: Extracellular vesicles released from Marek’s disease virus-transformed T-cells impact immune cell proliferation
Article Snippet: .. The abundance of identified proteins was estimated by calculating the exponentially modified protein abundance index (emPAI) using Scaffold Q+software (version 4.3, Proteome Software, Portland, USA). .. Gene Ontology (GO) term annotations for the biological processes and cellular components categories provided by the GO consortium ( http://www.geneontology.org/ ) were investigated using a protein database with UniprotKB ( http://www.uniprot.org ) and genomic databases with Ensembl ( http://www.ensembl.org ) and NCBI ( https://www.ncbi.nlm.nih.gov ).

Article Title: Extracellular vesicles released from Marek's disease virus-transformed T-cells impact immune cell proliferation.
Article Snippet: .. The abundance of identified proteins was estimated by calculating the exponentially modified protein abundance index (emPAI) using Scaffold Q+software (version 4.3, Proteome Software, Portland, USA). .. Functional annotation using gene ontology Gene Ontology (GO) term annotations for the biological processes and cellular components categories provided by the GO consortium (http://www.geneontology.org/) were investigated using a protein database with UniprotKB (http://www. uniprot.org) and genomic databases with Ensembl (http://www.ensembl.org) and NCBI (https://www.ncbi.nlm.nih.gov).

Quantitative Proteomics:

Article Title: Extracellular vesicles released from Marek’s disease virus-transformed T-cells impact immune cell proliferation
Article Snippet: .. The abundance of identified proteins was estimated by calculating the exponentially modified protein abundance index (emPAI) using Scaffold Q+software (version 4.3, Proteome Software, Portland, USA). .. Gene Ontology (GO) term annotations for the biological processes and cellular components categories provided by the GO consortium ( http://www.geneontology.org/ ) were investigated using a protein database with UniprotKB ( http://www.uniprot.org ) and genomic databases with Ensembl ( http://www.ensembl.org ) and NCBI ( https://www.ncbi.nlm.nih.gov ).

Article Title: Extracellular vesicles released from Marek's disease virus-transformed T-cells impact immune cell proliferation.
Article Snippet: .. The abundance of identified proteins was estimated by calculating the exponentially modified protein abundance index (emPAI) using Scaffold Q+software (version 4.3, Proteome Software, Portland, USA). .. Functional annotation using gene ontology Gene Ontology (GO) term annotations for the biological processes and cellular components categories provided by the GO consortium (http://www.geneontology.org/) were investigated using a protein database with UniprotKB (http://www. uniprot.org) and genomic databases with Ensembl (http://www.ensembl.org) and NCBI (https://www.ncbi.nlm.nih.gov).



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