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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. Content type: Methodology article

    Principal component analysis (PCA) has been widely used to visualize high-dimensional metabolomic data in a two- or three-dimensional subspace. In metabolomics, some metabolites (e.g., the top 10 metabolites) ...

    Authors: Hiroyuki Yamamoto, Tamaki Fujimori, Hajime Sato, Gen Ishikawa, Kenjiro Kami and Yoshiaki Ohashi

    Citation: BMC Bioinformatics 2014 15:51

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  2. Content type: Methodology article

    An ion mobility (IM) spectrometer coupled with a multi-capillary column (MCC) measures volatile organic compounds (VOCs) in the air or in exhaled breath. This technique is utilized in several biotechnological ...

    Authors: Marianna D’Addario, Dominik Kopczynski, Jörg Ingo Baumbach and Sven Rahmann

    Citation: BMC Bioinformatics 2014 15:25

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  3. Content type: Methodology article

    The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, ...

    Authors: Ashlee M Benjamin, J Will Thompson, Erik J Soderblom, Scott J Geromanos, Ricardo Henao, Virginia B Kraus, M Arthur Moseley and Joseph E Lucas

    Citation: BMC Bioinformatics 2013 14:364

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  4. Content type: Research article

    Determining sample sizes for metabolomic experiments is important but due to the complexity of these experiments, there are currently no standard methods for sample size estimation in metabolomics. Since pilot...

    Authors: Gift Nyamundanda, Isobel Claire Gormley, Yue Fan, William M Gallagher and Lorraine Brennan

    Citation: BMC Bioinformatics 2013 14:338

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  5. Content type: Methodology article

    Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput...

    Authors: George Tucker, Po-Ru Loh and Bonnie Berger

    Citation: BMC Bioinformatics 2013 14:299

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  6. Content type: Software

    Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of m...

    Authors: Stephan Beisken, Thorsten Meinl, Bernd Wiswedel, Luis F de Figueiredo, Michael Berthold and Christoph Steinbeck

    Citation: BMC Bioinformatics 2013 14:257

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  7. Content type: Methodology article

    Dynamic protein phosphorylation is an essential regulatory mechanism in various organisms. In this capacity, it is involved in a multitude of signal transduction pathways. Kinase-specific phosphorylation data ...

    Authors: Liang Zou, Mang Wang, Yi Shen, Jie Liao, Ao Li and Minghui Wang

    Citation: BMC Bioinformatics 2013 14:247

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  8. Content type: Methodology article

    Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially rever...

    Authors: Varun Jaiswal, Sree Krishna Chanumolu, Ankit Gupta, Rajinder S Chauhan and Chittaranjan Rout

    Citation: BMC Bioinformatics 2013 14:211

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  9. Content type: Methodology article

    Many content-based statistical features of secondary structural elements (CBF-PSSEs) have been proposed and achieved promising results in protein structural class prediction, but until now position distributio...

    Authors: Qi Dai, Yan Li, Xiaoqing Liu, Yuhua Yao, Yunjie Cao and Pingan He

    Citation: BMC Bioinformatics 2013 14:152

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  10. Content type: Software

    Despite progress in conventional cancer therapies, cancer is still one of the leading causes of death in industrial nations. Therefore, an urgent need of progress in fighting cancer remains. A promising altern...

    Authors: Joachim von Eichborn, Anna Lena Woelke, Filippo Castiglione and Robert Preissner

    Citation: BMC Bioinformatics 2013 14:127

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  11. Content type: Research article

    Since peak alignment in metabolomics has a huge effect on the subsequent statistical analysis, it is considered a key preprocessing step and many peak alignment methods have been developed. However, existing p...

    Authors: Jaesik Jeong, Xiang Zhang, Xue Shi, Seongho Kim and Changyu Shen

    Citation: BMC Bioinformatics 2013 14:123

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  12. Content type: Methodology article

    Liquid chromatography mass spectrometry (LC-MS) maps in shotgun proteomics are often too complex to select every detected peptide signal for fragmentation by tandem mass spectrometry (MS/MS). Standard methods ...

    Authors: Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach and Knut Reinert

    Citation: BMC Bioinformatics 2013 14:56

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  13. Content type: Software

    MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and chromatographic elution features across datasets. Applicable to bo...

    Authors: Brian L LaMarche, Kevin L Crowell, Navdeep Jaitly, Vladislav A Petyuk, Anuj R Shah, Ashoka D Polpitiya, John D Sandoval, Gary R Kiebel, Matthew E Monroe, Stephen J Callister, Thomas O Metz, Gordon A Anderson and Richard D Smith

    Citation: BMC Bioinformatics 2013 14:49

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  14. Content type: Software

    Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from...

    Authors: Karan Uppal, Quinlyn A Soltow, Frederick H Strobel, W Stephen Pittard, Kim M Gernert, Tianwei Yu and Dean P Jones

    Citation: BMC Bioinformatics 2013 14:15

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  15. Content type: Software

    For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications ...

    Authors: Steven Lewis, Attila Csordas, Sarah Killcoyne, Henning Hermjakob, Michael R Hoopmann, Robert L Moritz, Eric W Deutsch and John Boyle

    Citation: BMC Bioinformatics 2012 13:324

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  16. Content type: Methodology article

    It is desirable in genomic studies to select biomarkers that differentiate between normal and diseased populations based on related data sets from different platforms, including microarray expression and prote...

    Authors: Shicheng Wu, Yawen Xu, Zeny Feng, Xiaojian Yang, Xiaogang Wang and Xin Gao

    Citation: BMC Bioinformatics 2012 13:320

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  17. Content type: Software

    Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of t...

    Authors: Sean McIlwain, Michael Mathews, Michael S Bereman, Edwin W Rubel, Michael J MacCoss and William Stafford Noble

    Citation: BMC Bioinformatics 2012 13:308

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  18. Content type: Software

    Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in c...

    Authors: C Hart Poskar, Jan Huege, Christian Krach, Mathias Franke, Yair Shachar-Hill and Björn H Junker

    Citation: BMC Bioinformatics 2012 13:295

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  19. Content type: Methodology article

    The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlapping patt...

    Authors: Martin Slawski, Rene Hussong, Andreas Tholey, Thomas Jakoby, Barbara Gregorius, Andreas Hildebrandt and Matthias Hein

    Citation: BMC Bioinformatics 2012 13:291

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  20. Content type: Software

    Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryote...

    Authors: Gorka Prieto, Kerman Aloria, Nerea Osinalde, Asier Fullaondo, Jesus M Arizmendi and Rune Matthiesen

    Citation: BMC Bioinformatics 2012 13:288

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  21. Content type: Methodology article

    Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC...

    Authors: Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus and Jens Stoye

    Citation: BMC Bioinformatics 2012 13:214

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  22. Content type: Software

    Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics...

    Authors: Aaron TL Lun, Jason WH Wong and Kevin M Downard

    Citation: BMC Bioinformatics 2012 13:208

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  23. Content type: Research article

    An approach to molecular classification based on the comparative expression of protein pairs is presented. The method overcomes some of the present limitations in using peptide intensity data for class predict...

    Authors: Parminder Kaur, Daniela Schlatzer, Kenneth Cooke and Mark R Chance

    Citation: BMC Bioinformatics 2012 13:191

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  24. Content type: Database

    Prokaryotic ubiquitin-like protein (Pup), the firstly identified post-translational protein modifier in prokaryotes, is an important signal for the selective degradation of proteins. Recently, large-scale prot...

    Authors: Chun-Wei Tung

    Citation: BMC Bioinformatics 2012 13:40

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  25. Content type: Methodology article

    Recent development of novel technologies paved the way for quantitative proteomics. One of the most important among them is iTRAQ, employing isobaric tags for relative or absolute quantitation. Despite large p...

    Authors: Chris Bauer, Frank Kleinjung, Dorothea Rutishauser, Christian Panse, Alexandra Chadt, Tanja Dreja, Hadi Al-Hasani, Knut Reinert, Ralph Schlapbach and Johannes Schuchhardt

    Citation: BMC Bioinformatics 2012 13:34

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  26. Content type: Research article

    Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS) has been used for metabolite profiling in metabolomics. However, there is still much experimental variation to b...

    Authors: Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim and Changyu Shen

    Citation: BMC Bioinformatics 2012 13:27

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  27. Content type: Software

    Caspases are a family of cysteinyl proteases that regulate apoptosis and other biological processes. Caspase-3 is considered the central executioner member of this family with a wide range of substrates. Ident...

    Authors: Muneef Ayyash, Hashem Tamimi and Yaqoub Ashhab

    Citation: BMC Bioinformatics 2012 13:14

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  28. Content type: Research article

    One of the main goals in cancer studies including high-throughput microRNA (miRNA) and mRNA data is to find and assess prognostic signatures capable of predicting clinical outcome. Both mRNA and miRNA expressi...

    Authors: Stephan Gade, Christine Porzelius, Maria Fälth, Jan C Brase, Daniela Wuttig, Ruprecht Kuner, Harald Binder, Holger Sültmann and Tim Beißbarth

    Citation: BMC Bioinformatics 2011 12:488

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  29. Content type: Methodology article

    Multimodal data, especially imaging and non-imaging data, is being routinely acquired in the context of disease diagnostics; however, computational challenges have limited the ability to quantitatively integra...

    Authors: Abhishek Golugula, George Lee, Stephen R Master, Michael D Feldman, John E Tomaszewski, David W Speicher and Anant Madabhushi

    Citation: BMC Bioinformatics 2011 12:483

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  30. Content type: Research article

    Current approaches of predicting protein functions from a protein-protein interaction (PPI) dataset are based on an assumption that the available functions of the proteins (a.k.a. annotated proteins) will dete...

    Authors: Xiaoxiao Chi and Jingyu Hou

    Citation: BMC Bioinformatics 2011 12:437

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  31. Content type: Methodology article

    Quantification of protein expression by means of mass spectrometry (MS) has been introduced in various proteomics studies. In particular, two label-free quantification methods, such as spectral counting and sp...

    Authors: Seungmook Lee, Min-Seok Kwon, Hyoung-Joo Lee, Young-Ki Paik, Haixu Tang, Jae K Lee and Taesung Park

    Citation: BMC Bioinformatics 2011 12:423

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  32. Content type: Methodology article

    Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the anal...

    Authors: Trung N Vu, Dirk Valkenborg, Koen Smets, Kim A Verwaest, Roger Dommisse, Filip Lemière, Alain Verschoren, Bart Goethals and Kris Laukens

    Citation: BMC Bioinformatics 2011 12:405

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  33. Content type: Research article

    Mass spectrometry (MS) based metabolite profiling has been increasingly popular for scientific and biomedical studies, primarily due to recent technological development such as comprehensive two-dimensional ga...

    Authors: Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim and Changyu Shen

    Citation: BMC Bioinformatics 2011 12:392

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  34. Content type: Research article

    Genomics and proteomics experiments produce a large amount of data that are awaiting functional elucidation. An important step in analyzing such data is to identify functional units, which consist of proteins ...

    Authors: Meghana Chitale, Shriphani Palakodety and Daisuke Kihara

    Citation: BMC Bioinformatics 2011 12:373

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  35. Content type: Research article

    Clustering is a widely applicable pattern recognition method for discovering groups of similar observations in data. While there are a large variety of clustering algorithms, very few of these can enforce cons...

    Authors: Rudolf Frühwirth, D R Mani and Saumyadipta Pyne

    Citation: BMC Bioinformatics 2011 12:358

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  36. Content type: Research article

    The analysis of mass spectra suggests that the existence of derivative peaks is strongly dependent on the intensity of the primary peaks. Peak selection from tandem mass spectrum is used to filter out noise an...

    Authors: Shenghui Zhang, Yaojun Wang, Dongbo Bu, Hong Zhang and Shiwei Sun

    Citation: BMC Bioinformatics 2011 12:346

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  37. Content type: Software

    One of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectrosc...

    Authors: Xu Song, Bo-Li Zhang, Hong-Min Liu, Bo-Yang Yu, Xiu-Mei Gao and Li-Yuan Kang

    Citation: BMC Bioinformatics 2011 12:337

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  38. Content type: Database

    Volatile compounds comprise diverse chemical groups with wide-ranging sources and functions. These compounds originate from major pathways of secondary metabolism in many organisms and play essential roles in ...

    Authors: Kirsten Skogerson, Gert Wohlgemuth, Dinesh K Barupal and Oliver Fiehn

    Citation: BMC Bioinformatics 2011 12:321

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  39. Content type: Research article

    The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is infer...

    Authors: Eugenia G Giannopoulou, George Lepouras and Elias S Manolakos

    Citation: BMC Bioinformatics 2011 12:308

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  40. Content type: Methodology article

    Analysis of Cerebrospinal Fluid (CSF) samples holds great promise to diagnose neurological pathologies and gain insight into the molecular background of these pathologies. Proteomics and metabolomics methods p...

    Authors: Lionel Blanchet, Agnieszka Smolinska, Amos Attali, Marcel P Stoop, Kirsten AM Ampt, Hans van Aken, Ernst Suidgeest, Tinka Tuinstra, Sybren S Wijmenga, Theo Luider and Lutgarde MC Buydens

    Citation: BMC Bioinformatics 2011 12:254

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


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