iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data

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 re...

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Published in:	Computational and structural biotechnology journal Vol. 23; pp. 452 - 459
Main Authors:	Rodríguez, Jose Manuel, Jorge, Inmaculada, Martinez-Val, Ana, Barrero-Rodríguez, Rafael, Magni, Ricardo, Núñez, Estefanía, Laguillo, Andrea, Devesa, Cristina A., López, Juan A., Camafeita, Emilio, Vázquez, Jesús
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01.12.2024 Research Network of Computational and Structural Biotechnology Elsevier
Subjects:	algorithms bioinformatics biotechnology computer software Generic integration algorithm Mass spectrometry Protein coordination proteomics Proteomics pipeline quantitative analysis Quantitative proteomics Software/Web Server statistical models WSPP model WSPP model Protein coordination Quantitative proteomics Proteomics pipeline Generic integration algorithm Mass spectrometry
ISSN:	2001-0370, 2001-0370
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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. [Display omitted]
AbstractList	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. 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. ga1 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. [Display omitted] 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.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.
Author	Vázquez, Jesús Barrero-Rodríguez, Rafael Martinez-Val, Ana Camafeita, Emilio Núñez, Estefanía López, Juan A. Devesa, Cristina A. Laguillo, Andrea Magni, Ricardo Rodríguez, Jose Manuel Jorge, Inmaculada
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Cites_doi	10.1016/j.ebiom.2022.103874 10.1016/j.jprot.2019.103624 10.1074/mcp.M800260-MCP200 10.1016/j.jacc.2020.02.058 10.1038/s41467-022-28693-y 10.1161/CIRCULATIONAHA.121.055313 10.1126/sciadv.abb7242 10.1038/nbt.3685 10.1074/mcp.M110.003335 10.1093/bioinformatics/bty815 10.1038/s41467-021-22933-3 10.1016/j.celrep.2018.05.080 10.1016/j.cell.2020.08.031 10.1016/j.cmet.2020.09.001 10.1074/mcp.M111.016469 10.1038/nprot.2016.136 10.1016/j.jacc.2020.11.059 10.1021/acs.jproteome.2c00624 10.1021/pr4006958 10.1038/s41586-020-2993-2 10.1038/nmeth.4256 10.1074/mcp.M115.055905
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References	Nicolas-Avila, Lechuga-Vieco, Esteban-Martinez, Sanchez-Diaz, Diaz-Garcia (bib16) 2020; 183 Al-Mashhadi, Al-Mashhadi, Nasr, Mortensen, Lewis (bib15) 2021; 77 Lorenzo, Delgado, Busse, Sanz-Bravo, Martos-Folgado (bib13) 2021; 589 Martinez-Acedo, Nunez, Gomez, Moreno, Ramos (bib8) 2012; 11 Nunez, Fuster, Gomez-Serrano, Valdivielso, Fernandez-Alvira (bib10) 2022; 76 Deutsch, Mendoza, Shteynberg, Hoopmann, Sun (bib3) 2023; 22 Trevisan-Herraz, Bagwan, Garcia-Marques, Rodriguez, Jorge (bib4) 2019; 35 de la Fuente-Alonso, Toral, Alfayate, Ruiz-Rodriguez, Bonzon-Kulichenko (bib14) 2021; 12 Bonzon-Kulichenko, Perez-Hernandez, Nunez, Martinez-Acedo, Navarro (bib23) 2011; 10 Garcia-Garcia, Sanchez-Perales, Jarabo, Calvo, Huyton (bib11) 2022; 13 Sanchez-Lopez, Espinos-Estevez, Gonzalez-Gomez, Gonzalo, Andres-Manzano (bib12) 2021; 144 Jorge, Navarro, Martinez-Acedo, Nunez, Serrano (bib6) 2009; 8 Martin-Cofreces, Chichon, Calvo, Torralba, Bustos-Moran (bib18) 2020; 6 Navarro, Kuharev, Gillet, Bernhardt, MacLean (bib22) 2016; 34 Kong, Leprevost, Avtonomov, Mellacheruvu, Nesvizhskii (bib2) 2017; 14 Navarro, Trevisan-Herraz, Bonzon-Kulichenko, Nunez, Martinez-Acedo (bib7) 2014; 13 Gonzalez-Amor, Garcia-Redondo, Jorge, Zalba, Becares (bib21) 2021 Bonzon-Kulichenko, Camafeita, Lopez, Gomez-Serrano, Jorge (bib20) 2020; 214 Martinez-Lopez, Roldan-Montero, Garcia-Marques, Nunez, Jorge (bib17) 2020; 75 Forte, Garcia-Fernandez, Sanchez-Aguilera, Stavropoulou, Fielding (bib19) 2020; 32 Bagwan, Bonzon-Kulichenko, Calvo, Lechuga-Vieco, Michalakopoulos (bib9) 2018; 23 Tyanova, Temu, Cox (bib1) 2016; 11 Garcia-Marques, Trevisan-Herraz, Martinez-Martinez, Camafeita, Jorge (bib5) 2016; 15 Gonzalez-Amor (10.1016/j.csbj.2023.12.034_bib21) 2021 Jorge (10.1016/j.csbj.2023.12.034_bib6) 2009; 8 Martin-Cofreces (10.1016/j.csbj.2023.12.034_bib18) 2020; 6 Bonzon-Kulichenko (10.1016/j.csbj.2023.12.034_bib23) 2011; 10 Forte (10.1016/j.csbj.2023.12.034_bib19) 2020; 32 Trevisan-Herraz (10.1016/j.csbj.2023.12.034_bib4) 2019; 35 Navarro (10.1016/j.csbj.2023.12.034_bib7) 2014; 13 Garcia-Garcia (10.1016/j.csbj.2023.12.034_bib11) 2022; 13 Sanchez-Lopez (10.1016/j.csbj.2023.12.034_bib12) 2021; 144 Martinez-Lopez (10.1016/j.csbj.2023.12.034_bib17) 2020; 75 Kong (10.1016/j.csbj.2023.12.034_bib2) 2017; 14 Al-Mashhadi (10.1016/j.csbj.2023.12.034_bib15) 2021; 77 Bagwan (10.1016/j.csbj.2023.12.034_bib9) 2018; 23 Bonzon-Kulichenko (10.1016/j.csbj.2023.12.034_bib20) 2020; 214 Martinez-Acedo (10.1016/j.csbj.2023.12.034_bib8) 2012; 11 Nunez (10.1016/j.csbj.2023.12.034_bib10) 2022; 76 Nicolas-Avila (10.1016/j.csbj.2023.12.034_bib16) 2020; 183 Tyanova (10.1016/j.csbj.2023.12.034_bib1) 2016; 11 Deutsch (10.1016/j.csbj.2023.12.034_bib3) 2023; 22 Garcia-Marques (10.1016/j.csbj.2023.12.034_bib5) 2016; 15 de la Fuente-Alonso (10.1016/j.csbj.2023.12.034_bib14) 2021; 12 Navarro (10.1016/j.csbj.2023.12.034_bib22) 2016; 34 Lorenzo (10.1016/j.csbj.2023.12.034_bib13) 2021; 589
References_xml	– volume: 144 start-page: 1777 year: 2021 end-page: 1794 ident: bib12 article-title: Cardiovascular Progerin Suppression and Lamin A Restoration Rescue Hutchinson-Gilford Progeria Syndrome publication-title: Circulation – volume: 12 year: 2021 ident: bib14 article-title: Aortic disease in Marfan syndrome is caused by overactivation of sGC-PRKG signaling by NO publication-title: Nat Commun – volume: 13 year: 2022 ident: bib11 article-title: Mechanical control of nuclear import by Importin-7 is regulated by its dominant cargo YAP publication-title: Nat Commun – volume: 22 start-page: 615 year: 2023 end-page: 624 ident: bib3 article-title: Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite publication-title: J Proteome Res – volume: 13 start-page: 1234 year: 2014 end-page: 1247 ident: bib7 article-title: General statistical framework for quantitative proteomics by stable isotope labeling publication-title: J Proteome Res – volume: 183 start-page: 94 year: 2020 end-page: 109 ident: bib16 article-title: A Network of Macrophages Supports Mitochondrial Homeostasis in the Heart publication-title: Cell – volume: 77 start-page: 575 year: 2021 end-page: 589 ident: bib15 article-title: Local Pressure Drives Low-Density Lipoprotein Accumulation and Coronary Atherosclerosis in Hypertensive Minipigs publication-title: J Am Coll Cardiol – volume: 34 start-page: 1130 year: 2016 end-page: 1136 ident: bib22 article-title: A multicenter study benchmarks software tools for label-free proteome quantification publication-title: Nat Biotechnol – volume: 589 start-page: 287 year: 2021 end-page: 292 ident: bib13 article-title: ALDH4A1 is an atherosclerosis auto-antigen targeted by protective antibodies publication-title: Nature – volume: 11 start-page: 2301 year: 2016 end-page: 2319 ident: bib1 article-title: The MaxQuant computational platform for mass spectrometry-based shotgun proteomics publication-title: Nat Protoc – volume: 8 start-page: 1130 year: 2009 end-page: 1149 ident: bib6 article-title: Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: application to the study of vascular endothelial growth factor-induced angiogenesis in endothelial cells publication-title: Mol Cell Prote: MCP – volume: 10 year: 2011 ident: bib23 article-title: A robust method for quantitative high-throughput analysis of proteomes by 18O labeling publication-title: Mol Cell Proteom – volume: 32 start-page: 829 year: 2020 end-page: 843 ident: bib19 article-title: Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy publication-title: Cell Metab – volume: 76 year: 2022 ident: bib10 article-title: Unbiased plasma proteomics discovery of biomarkers for improved detection of subclinical atherosclerosis publication-title: EBioMedicine – volume: 214 year: 2020 ident: bib20 article-title: Improved integrative analysis of the thiol redox proteome using filter-aided sample preparation publication-title: J Proteom – volume: 14 start-page: 513 year: 2017 end-page: 520 ident: bib2 article-title: MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics publication-title: Nat Methods – volume: 15 start-page: 1740 year: 2016 end-page: 1760 ident: bib5 article-title: A Novel Systems-Biology Algorithm for the Analysis of Coordinated Protein Responses Using Quantitative Proteomics publication-title: Mol Cell Prote: MCP – volume: 35 start-page: 1594 year: 2019 end-page: 1596 ident: bib4 article-title: SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments publication-title: Bioinformatics – volume: 6 year: 2020 ident: bib18 article-title: The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles publication-title: Sci Adv – year: 2021 ident: bib21 article-title: Interferon stimulated gene 15 pathway is a novel mediator of endothelial dysfunction and aneurysms development in angiotensin II infused mice through increased oxidative stress publication-title: Cardiovasc Res – volume: 11 start-page: 800 year: 2012 end-page: 813 ident: bib8 article-title: A novel strategy for global analysis of the dynamic thiol redox proteome publication-title: Mol Cell Prote: MCP – volume: 75 start-page: 1926 year: 2020 end-page: 1941 ident: bib17 article-title: Complement C5 Protein as a Marker of Subclinical Atherosclerosis publication-title: J Am Coll Cardiol – volume: 23 start-page: 3685 year: 2018 end-page: 3697 ident: bib9 article-title: Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy publication-title: Cell Rep – volume: 76 year: 2022 ident: 10.1016/j.csbj.2023.12.034_bib10 article-title: Unbiased plasma proteomics discovery of biomarkers for improved detection of subclinical atherosclerosis publication-title: EBioMedicine doi: 10.1016/j.ebiom.2022.103874 – volume: 214 year: 2020 ident: 10.1016/j.csbj.2023.12.034_bib20 article-title: Improved integrative analysis of the thiol redox proteome using filter-aided sample preparation publication-title: J Proteom doi: 10.1016/j.jprot.2019.103624 – volume: 8 start-page: 1130 issue: 5 year: 2009 ident: 10.1016/j.csbj.2023.12.034_bib6 article-title: Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: application to the study of vascular endothelial growth factor-induced angiogenesis in endothelial cells publication-title: Mol Cell Prote: MCP doi: 10.1074/mcp.M800260-MCP200 – year: 2021 ident: 10.1016/j.csbj.2023.12.034_bib21 article-title: Interferon stimulated gene 15 pathway is a novel mediator of endothelial dysfunction and aneurysms development in angiotensin II infused mice through increased oxidative stress publication-title: Cardiovasc Res – volume: 75 start-page: 1926 issue: 16 year: 2020 ident: 10.1016/j.csbj.2023.12.034_bib17 article-title: Complement C5 Protein as a Marker of Subclinical Atherosclerosis publication-title: J Am Coll Cardiol doi: 10.1016/j.jacc.2020.02.058 – volume: 13 issue: 1 year: 2022 ident: 10.1016/j.csbj.2023.12.034_bib11 article-title: Mechanical control of nuclear import by Importin-7 is regulated by its dominant cargo YAP publication-title: Nat Commun doi: 10.1038/s41467-022-28693-y – volume: 144 start-page: 1777 issue: 22 year: 2021 ident: 10.1016/j.csbj.2023.12.034_bib12 article-title: Cardiovascular Progerin Suppression and Lamin A Restoration Rescue Hutchinson-Gilford Progeria Syndrome publication-title: Circulation doi: 10.1161/CIRCULATIONAHA.121.055313 – volume: 6 issue: 49 year: 2020 ident: 10.1016/j.csbj.2023.12.034_bib18 article-title: The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles publication-title: Sci Adv doi: 10.1126/sciadv.abb7242 – volume: 34 start-page: 1130 issue: 11 year: 2016 ident: 10.1016/j.csbj.2023.12.034_bib22 article-title: A multicenter study benchmarks software tools for label-free proteome quantification publication-title: Nat Biotechnol doi: 10.1038/nbt.3685 – volume: 10 issue: 1 year: 2011 ident: 10.1016/j.csbj.2023.12.034_bib23 article-title: A robust method for quantitative high-throughput analysis of proteomes by 18O labeling publication-title: Mol Cell Proteom doi: 10.1074/mcp.M110.003335 – volume: 35 start-page: 1594 issue: 9 year: 2019 ident: 10.1016/j.csbj.2023.12.034_bib4 article-title: SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty815 – volume: 12 issue: 1 year: 2021 ident: 10.1016/j.csbj.2023.12.034_bib14 article-title: Aortic disease in Marfan syndrome is caused by overactivation of sGC-PRKG signaling by NO publication-title: Nat Commun doi: 10.1038/s41467-021-22933-3 – volume: 23 start-page: 3685 issue: 12 year: 2018 ident: 10.1016/j.csbj.2023.12.034_bib9 article-title: Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy publication-title: Cell Rep doi: 10.1016/j.celrep.2018.05.080 – volume: 183 start-page: 94 issue: 1 year: 2020 ident: 10.1016/j.csbj.2023.12.034_bib16 article-title: A Network of Macrophages Supports Mitochondrial Homeostasis in the Heart publication-title: Cell doi: 10.1016/j.cell.2020.08.031 – volume: 32 start-page: 829 issue: 5 year: 2020 ident: 10.1016/j.csbj.2023.12.034_bib19 article-title: Bone Marrow Mesenchymal Stem Cells Support Acute Myeloid Leukemia Bioenergetics and Enhance Antioxidant Defense and Escape from Chemotherapy publication-title: Cell Metab doi: 10.1016/j.cmet.2020.09.001 – volume: 11 start-page: 800 issue: 9 year: 2012 ident: 10.1016/j.csbj.2023.12.034_bib8 article-title: A novel strategy for global analysis of the dynamic thiol redox proteome publication-title: Mol Cell Prote: MCP doi: 10.1074/mcp.M111.016469 – volume: 11 start-page: 2301 issue: 12 year: 2016 ident: 10.1016/j.csbj.2023.12.034_bib1 article-title: The MaxQuant computational platform for mass spectrometry-based shotgun proteomics publication-title: Nat Protoc doi: 10.1038/nprot.2016.136 – volume: 77 start-page: 575 issue: 5 year: 2021 ident: 10.1016/j.csbj.2023.12.034_bib15 article-title: Local Pressure Drives Low-Density Lipoprotein Accumulation and Coronary Atherosclerosis in Hypertensive Minipigs publication-title: J Am Coll Cardiol doi: 10.1016/j.jacc.2020.11.059 – volume: 22 start-page: 615 issue: 2 year: 2023 ident: 10.1016/j.csbj.2023.12.034_bib3 article-title: Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite publication-title: J Proteome Res doi: 10.1021/acs.jproteome.2c00624 – volume: 13 start-page: 1234 issue: 3 year: 2014 ident: 10.1016/j.csbj.2023.12.034_bib7 article-title: General statistical framework for quantitative proteomics by stable isotope labeling publication-title: J Proteome Res doi: 10.1021/pr4006958 – volume: 589 start-page: 287 issue: 7841 year: 2021 ident: 10.1016/j.csbj.2023.12.034_bib13 article-title: ALDH4A1 is an atherosclerosis auto-antigen targeted by protective antibodies publication-title: Nature doi: 10.1038/s41586-020-2993-2 – volume: 14 start-page: 513 issue: 5 year: 2017 ident: 10.1016/j.csbj.2023.12.034_bib2 article-title: MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics publication-title: Nat Methods doi: 10.1038/nmeth.4256 – volume: 15 start-page: 1740 issue: 5 year: 2016 ident: 10.1016/j.csbj.2023.12.034_bib5 article-title: A Novel Systems-Biology Algorithm for the Analysis of Coordinated Protein Responses Using Quantitative Proteomics publication-title: Mol Cell Prote: MCP doi: 10.1074/mcp.M115.055905
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SubjectTerms	algorithms bioinformatics biotechnology computer software Generic integration algorithm Mass spectrometry Protein coordination proteomics Proteomics pipeline quantitative analysis Quantitative proteomics Software/Web Server statistical models WSPP model
Title	iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data
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