1
|
Rodríguez JM, Jorge I, Martinez-Val A, Barrero-Rodríguez R, Magni R, Núñez E, Laguillo A, Devesa CA, López JA, Camafeita E, Vázquez J. iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data. Comput Struct Biotechnol J 2024; 23:452-459. [PMID: 38235360 PMCID: PMC10792623 DOI: 10.1016/j.csbj.2023.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
Many bioinformatics tools are available for the quantitative analysis of proteomics experiments. Most of these tools use a dedicated statistical model to derive absolute quantitative protein values from mass spectrometry (MS) data. Here, we present iSanXoT, a standalone application that processes relative abundances between MS signals and then integrates them sequentially to upper levels using the previously published Generic Integration Algorithm (GIA). iSanXoT offers unique capabilities that complement conventional quantitative software applications, including statistical weighting and independent modeling of error distributions in each integration, aggregation of technical or biological replicates, quantification of posttranslational modifications, and analysis of coordinated protein behavior. iSanXoT is a standalone, user-friendly application that accepts output from popular proteomics pipelines and enables unrestricted creation of quantification workflows and fully customizable reports that can be reused across projects or shared among users. Numerous publications attest the successful application of diverse integrative workflows constructed using the GIA for the analysis of high-throughput quantitative proteomics experiments. iSanXoT has been tested with the main operating systems. Download links for the corresponding distributions are available at https://github.com/CNIC-Proteomics/iSanXoT/releases.
Collapse
Affiliation(s)
- Jose Manuel Rodríguez
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Inmaculada Jorge
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ana Martinez-Val
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Rafael Barrero-Rodríguez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Ricardo Magni
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Estefanía Núñez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Andrea Laguillo
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Cristina A. Devesa
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Juan A. López
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Emilio Camafeita
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| |
Collapse
|