Section edited by John Garavelli

This section incorporates all aspects of proteomic analysis including but not limited to: methods and applications for the analysis of post-translational modifications, proteomic, mass spectroscopic, and chemoinformatic data.

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  1. Research Article

    A machine learning approach for predicting methionine oxidation sites

    The oxidation of protein-bound methionine to form methionine sulfoxide, has traditionally been regarded as an oxidative damage. However, recent evidences support the view of this reversible reaction as a regul...

    Juan C. Aledo, Francisco R. Cantón and Francisco J. Veredas

    BMC Bioinformatics 2017 18:430

    Published on: 29 September 2017

  2. Software

    LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

    Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Me...

    Jeremy P. Koelmel, Nicholas M. Kroeger, Candice Z. Ulmer, John A. Bowden, Rainey E. Patterson, Jason A. Cochran, Christopher W. W. Beecher, Timothy J. Garrett and Richard A. Yost

    BMC Bioinformatics 2017 18:331

    Published on: 10 July 2017

  3. Methodology Article

    Early response index: a statistic to discover potential early stage disease biomarkers

    Identifying disease correlated features early before large number of molecules are impacted by disease progression with significant abundance change is very advantageous to biologists for developing early dise...

    Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael, Thomas G. Forsthuber and Jianqiu (Michelle) Zhang

    BMC Bioinformatics 2017 18:313

    Published on: 23 June 2017

  4. Methodology article

    EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples

    Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles...

    Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel and Carmela Giglione

    BMC Bioinformatics 2017 18:182

    Published on: 20 March 2017

  5. Research Article

    Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data

    High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between...

    Tim O. F. Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Alexander Leichtle, Jan Vybiral, Gitta Kutyniok and Christof Schütte

    BMC Bioinformatics 2017 18:160

    Published on: 9 March 2017

  6. Software

    ProteoModlR for functional proteomic analysis

    High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries...

    Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala and Alex Kentsis

    BMC Bioinformatics 2017 18:153

    Published on: 4 March 2017

  7. Research Article

    DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs

    The classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species....

    Vera Rieder, Bernhard Blank-Landeshammer, Marleen Stuhr, Tilman Schell, Karsten Biß, Laxmikanth Kollipara, Achim Meyer, Markus Pfenninger, Hildegard Westphal, Albert Sickmann and Jörg Rahnenführer

    BMC Bioinformatics 2017 18:148

    Published on: 3 March 2017

  8. Methodology article

    Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies

    High throughput metabolomics makes it possible to measure the relative abundances of numerous metabolites in biological samples, which is useful to many areas of biomedical research. However, missing values (M...

    Jasmit S. Shah, Shesh N. Rai, Andrew P. DeFilippis, Bradford G. Hill, Aruni Bhatnagar and Guy N. Brock

    BMC Bioinformatics 2017 18:114

    Published on: 20 February 2017

  9. Methodology article

    Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data

    Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based o...

    Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert D. Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe Jr. and Denise M. Scholtens

    BMC Bioinformatics 2017 18:84

    Published on: 2 February 2017

  10. Software

    ConEVA: a toolbox for comprehensive assessment of protein contacts

    In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein struct...

    Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou and Jianlin Cheng

    BMC Bioinformatics 2016 17:517

    Published on: 7 December 2016

  11. Research article

    Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease

    When combined with a clinical outcome variable, the size, complexity and nature of mass-spectrometry proteomics data impose great statistical challenges in the discovery of potential disease-associated biomark...

    Eleanor Stanley, Eleni Ioanna Delatola, Esther Nkuipou-Kenfack, William Spooner, Walter Kolch, Joost P. Schanstra, Harald Mischak and Thomas Koeck

    BMC Bioinformatics 2016 17:496

    Published on: 6 December 2016

  12. Research Article

    Large scale analysis of amino acid substitutions in bacterial proteomics

    Proteomics of bacterial pathogens is a developing field exploring microbial physiology, gene expression and the complex interactions between bacteria and their hosts. One of the complications in proteomic appr...

    Dmitry Ischenko, Dmitry Alexeev, Egor Shitikov, Alexandra Kanygina, Maja Malakhova, Elena Kostryukova, Andrey Larin, Sergey Kovalchuk, Olga Pobeguts, Ivan Butenko, Nikolay Anikanov, Ilya Altukhov, Elena Ilina and Vadim Govorun

    BMC Bioinformatics 2016 17:450

    Published on: 8 November 2016

  13. Methodology Article

    solveME: fast and reliable solution of nonlinear ME models

    Genome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challe...

    Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders and Bernhard O. Palsson

    BMC Bioinformatics 2016 17:391

    Published on: 22 September 2016

  14. Software

    CryGetter: a tool to automate retrieval and analysis of Cry protein data

    For many years, the use of chemical agents to control crop pests has been degrading the environment, bringing problems to humans and all living things. An alternative to deal with the pests is the use of biope...

    David Buzatto, Suzelei de Castro França and Sônia Marli Zingaretti

    BMC Bioinformatics 2016 17:325

    Published on: 30 August 2016

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