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Proteome Software Inc scaffold perspectives
$Serum proteomics workflow for the isolation and analysis of the molecular-form proteomes of IgA1. IgA1-containing immune complexes (IgA1-IC) from sera of 20 patients with IgA nephropathy (IgAN) and 20 healthy controls (HCs) were isolated by lectin-affinity chromatography followed by size-exclusion chromatography (SEC) to separate IgA1-IC from monomeric and polymeric IgA1 (I–III). IgA-specific protease and liquid chromatography mass spectrometry (LC-MS) sequence-grade trypsin digestion were followed by LC-MS (IV–V). After standard proteomic database searches, LC-MS results were curated by Scaffold <t>perSPECtives</t> to identify proteins of high abundance in IgA1-IC fractions of serum from patients with IgAN versus IgA1-IC from HCs with label-free quantification (LFQ). Additional comparisons were made to polymeric IgA1 (VI). Created with BioRender.com .$
Scaffold Perspectives, 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/workflow+software+interactive+data+language/scaffold/pmc12545556-79-19-23
Average 86 stars, based on 1 article reviews

scaffold perspectives - by Bioz Stars, 2026-11

86/100 stars

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1) Product Images from "Proteomic Analysis of Circulating IgA1-Containing Immune Complexes in Patients with IgA Nephropathy"

Article Title: Proteomic Analysis of Circulating IgA1-Containing Immune Complexes in Patients with IgA Nephropathy

Journal: Kidney International Reports

doi: 10.1016/j.ekir.2025.07.005

$Serum proteomics workflow for the isolation and analysis of the molecular-form proteomes of IgA1. IgA1-containing immune complexes (IgA1-IC) from sera of 20 patients with IgA nephropathy (IgAN) and 20 healthy controls (HCs) were isolated by lectin-affinity chromatography followed by size-exclusion chromatography (SEC) to separate IgA1-IC from monomeric and polymeric IgA1 (I–III). IgA-specific protease and liquid chromatography mass spectrometry (LC-MS) sequence-grade trypsin digestion were followed by LC-MS (IV–V). After standard proteomic database searches, LC-MS results were curated by Scaffold perSPECtives to identify proteins of high abundance in IgA1-IC fractions of serum from patients with IgAN versus IgA1-IC from HCs with label-free quantification (LFQ). Additional comparisons were made to polymeric IgA1 (VI). Created with BioRender.com .$
Figure Legend Snippet: Serum proteomics workflow for the isolation and analysis of the molecular-form proteomes of IgA1. IgA1-containing immune complexes (IgA1-IC) from sera of 20 patients with IgA nephropathy (IgAN) and 20 healthy controls (HCs) were isolated by lectin-affinity chromatography followed by size-exclusion chromatography (SEC) to separate IgA1-IC from monomeric and polymeric IgA1 (I–III). IgA-specific protease and liquid chromatography mass spectrometry (LC-MS) sequence-grade trypsin digestion were followed by LC-MS (IV–V). After standard proteomic database searches, LC-MS results were curated by Scaffold perSPECtives to identify proteins of high abundance in IgA1-IC fractions of serum from patients with IgAN versus IgA1-IC from HCs with label-free quantification (LFQ). Additional comparisons were made to polymeric IgA1 (VI). Created with BioRender.com .

Techniques Used: Isolation, Affinity Chromatography, Size-exclusion Chromatography, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy, Sequencing, Quantitative Proteomics

other:

Article Title: Deciphering resistance mechanisms to auxin-inducible protein degradation in mammalian cells.
Article Snippet: The search results were validated with a 1 % false-discovery rate 805 (FDR) protein threshold and a 90 % peptide threshold using Scaffold (v5.3.0, Proteome Software).

Article Title: Post-AI uterine lavage and PRP infusion reduce some uterine inflammation parameters but do not improve fertility in jennies inseminated with frozen semen.
Article Snippet: Mascot identifications were statistically validated using Scaffold version 3.6.4 (Proteome Software Inc., Portland, OR).

Article Title: Evolutionary remodeling of ubiquinone biosynthesis in Toxoplasma gondii reveals an essential bi-functional monooxygenase.
Article Snippet: Scaffold (version Scaffold_4.8.9; Proteome Software Inc., Portland, OR) was used to validate MS/MSbased peptide and protein identifications.

Article Title: Novel COX-2–Targeted Nanobodies for Molecular Endoscopic Imaging of Colorectal Adenomas
Article Snippet: Search results were assembled using Scaffold 4.3.2. (Proteome Software).

Article Title: Disordered protein COSA-2 maintains crossover-specific repair compartments to ensure meiotic crossover maturation
Article Snippet: Tandem mass spectra were extracted by Proteome Discoverer (v2.4, ThermoFisher Scientific) and analyzed using Mascot (Matrix Science, London, UK; version 2.8.3).

Oligomer Restriction:

Article Title: Licosin, a multifunctional defensin peptide originated from the clinical fungus Lichtheimia corymbifera with antibacterial and potassium ion channel blocking effects
Article Snippet: .. Scaffold version 4.4.3 (Proteome Software Inc., Portland, OR) was utilized to calculate spectral counts and validate peptide/protein identifications, with a confidence level of 95%. .. The linear mature defensin (reduced form, licosin-Re) was obtained via solid phase synthesis by GL Biochem (Shanghai, China) Ltd. or DGpeptides Co., Ltd. (Wuhan, Hubei, China) with a purity of more than 95%.

Tandem Mass Spectroscopy:

Article Title: CD1a-Mediated Presentation of Canonical Microbial Peptides to T Cells
Article Snippet: .. Scaffold (version Scaffold_4.3.2, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. ..

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