Proteome Software, Inc. software

Scaffold DDA is a quantitative analysis platform developed by Proteome Software to facilitate experiment-driven labeled and label-free analysis. Designed primarily for the processing of iTRAQ, TMT, and SILAC data, Scaffold DDA integrates with multiple search engines, including Sage and MSFragger, to offer versatile analytical capabilities. It supports quantification of differential expression and statistical significance testing, and provides normalization, roll-up, and interpretation of biological differences while identifying technical variation sources. The platform uses Percolator to derive peptide and protein probabilities, which are crucial for false discovery rate (FDR) thresholding. Scaffold DDA is particularly beneficial for managing core facilities or shared resource departments, as it assists in streamlining software pipelines and enhances the ease of sharing results, thus optimizing proteomics research processes.

Scaffold DIA is a versatile software designed for data-independent acquisition (DIA) proteomics analysis. It stands out by enabling the analysis of raw DIA data against various data-dependent acquisition (DDA) library formats, including Prosit predictions and custom DIA-only libraries. This flexibility allows users to process data from major instrument vendors like Thermo, Sciex, and Agilent efficiently. The software supports advanced statistical analysis, featuring built-in heatmaps and principal component analysis (PCA) to track quantitative trends. Furthermore, it facilitates data sharing through the Scaffold DIA Viewer, Excel exports, and high-quality publication images. Scaffold DIA is ideal for core facilities and researchers looking for a comprehensive solution for their proteomics research, offering tools to manage software pipelines and explore new proteomics methods effectively. The software caters to users by providing an intuitive interface and comprehensive tutorials available on their YouTube channel.

Scaffold 5, developed by Proteome Software, is a prominent data-dependent acquisition (DDA) MS/MS proteomics tool that facilitates researchers in processing complex proteomic data. It integrates seamlessly with MS Fragger for direct raw data searches and supports loading precursor intensity data from FragPipe. Users can also import data from other platforms such as Mascot, Proteome Discoverer, and MaxQuant. Scaffold 5 provides tools to visualize differential expression and assess statistical significance using either spectrum counting or precursor intensity. This platform offers collaborative options via the cross-platform, free Scaffold Viewer, alongside facilities for generating Excel reports and mzIdentML exports. Although Scaffold 5/Q+S will be phased out, users are encouraged to transition to Scaffold DDA for enhanced quantitative analysis capabilities. The current version, 5.3.4, continues to support core facilities and shared resource departments in refining their software pipeline.

The Scaffold Q+S software suite by Proteome Software provides a comprehensive set of tools for quantitative analysis in proteomics. It supports quantification using various labeling techniques such as iTRAQ, TMT, and SILAC, along with precursor intensity values. The platform enables the visualization of protein-level changes across samples through fold changes, intensity values, or quantitative ratios. It facilitates the comparison of independent groups, repeated measures, or time-course experiments. Proteome Software is moving towards newer platforms like Scaffold DDA, a cutting-edge quantitative platform with improved features. The company also offers solutions for core facilities and shared resource departments, addressing gaps in software pipelines and introducing new methods like DIA proteomics. Proteome Software provides technical support including tutorials via its YouTube channel, aiming to offer user-friendly solutions across various levels of expertise in proteomic research.

Proteome Software's suite of Scaffold products offers a comprehensive solution for the identification and quantification of small molecules through LC-MS analysis, catering to researchers who demand both elegance and simplicity in their data processing workflows. Compatible with raw data from leading vendor instrumentation like Thermo, Sciex, and Agilent, Scaffold supports both MS1 and MS/MS data. Users can leverage multiple spectral libraries such as NIST, HMDB, and LIPID MAPS or construct personalized spectral libraries from their own instrument-generated spectra, enhancing customization in analysis. The software is particularly suited for managing core facilities or shared resource departments, addressing gaps in software pipelines, and exploring advanced methods such as DIA proteomics. Proteome Software also emphasizes education and support through detailed tutorials, videos, and an active YouTube channel, helping users from beginners to advanced practitioners efficiently utilize their Scaffold products.