Special Issue "Advances in Proteomics Methods"


A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (31 December 2013)

Special Issue Editors

Guest Editor
Prof. Dr. Stephen R. Pennington
UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Ireland
Website: http://www.ucd.ie/research/people/medicinemedicalscience/professorstephenroypennington/
E-Mail: stephen.pennington@ucd.ie
Interests: human disease biomarker discovery and translation to clinical utility; quantitative proteomics

Guest Editor
Dr. Lisa Staunton
UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Ireland
E-Mail: lisa.staunton@ucd.ie
Interests: Biomarkers of human disease and proteomics

Guest Editor
Dr. David S. Gibson
Clinical Translational Research and Innovation Centre, School of Biomedical Science, University of Ulster, UK
Website: http://www.c-tric.com/
E-Mail: d.gibson@ulster.ac.uk
Interests: inflammatory diseases; biomarker discovery and validation; post-translational modifications

Special Issue Information

Dear Colleagues,

The ultimate goals of proteomics methods are: Whole proteome coverage at high sensitivity and with rapid throughput and whole protein coverage both structural and functional.

Currently gel- and liquid chromatography based protein and peptide separation combined with mass spectrometry form the basis of most proteomics methods and huge progress is being made in reaching the goal of ‘routine’ whole proteome coverage and the analysis of post-translational modifications. Recent developments have been such that the field of proteomics is now beginning to impact on our understanding of disease pathogenesis and has exciting opportunities in personalised medicine. Notably, improved mass spectrometry based technologies combined with developments in chemical strategies continue to play a leading role in these advances. However, many challenges remain – not least in how to improve ‘protein coverage, increase the sensitivity and sophistication of protein analysis and reach the level of throughput that many potential applications require. At the same time the quantity of data produced and its variable quality is presenting new demands – both for the handling and reliable interpretation of the data. New methods for data storage, sharing, analysis and re-analysis are in development and much needed. This special issue aims to draw together original research articles and reviews on current and projected advances in diverse proteomics methods.

Submissions covering the following topics will be welcomed:

Sample preparation methods (LCM, protein enrichment);
Label-free and isotopic labeling strategies for LC-MS/MS;
Role of miniaturisation/amplification strategies (Achieving sensitivity with smaller/limited samples);
Protein recognition (antibody, aptamer) based approaches;
Whole proteome coverage;
Software development for handling and interpreting MS data;
MRM: development and applications;
Post-translational modifications: to phosphorylation and beyond;
Advances in MS instrumentation;
Proteomics databases: data storage and sharing, data re-analysis;
Statistical approaches and novel algorithms;
Methods and instrumentation for taking proteomics to clinical utility

Please note this is not an exhaustive list

Prof.  Stephen R. Pennington
Dr. Lisa Staunton
Dr. David S. Gibson
Guest Editors


Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Published Papers (5 papers)

by ,  and
Biology 2014, 3(2), 383-402; doi:10.3390/biology3020383
Received: 17 March 2014; in revised form: 16 April 2014 / Accepted: 10 May 2014 / Published: 5 June 2014
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by , , , ,  and
Biology 2014, 3(2), 320-332; doi:10.3390/biology3020320
Received: 9 January 2014; in revised form: 13 March 2014 / Accepted: 25 March 2014 / Published: 16 April 2014
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by , , , , ,  and
Biology 2014, 3(1), 205-219; doi:10.3390/biology3010205
Received: 12 December 2013; in revised form: 31 January 2014 / Accepted: 27 February 2014 / Published: 11 March 2014
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by ,  and
Biology 2014, 3(1), 22-38; doi:10.3390/biology3010022
Received: 12 November 2013; in revised form: 15 December 2013 / Accepted: 16 December 2013 / Published: 20 December 2013
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by , ,  and
Biology 2013, 2(4), 1438-1464; doi:10.3390/biology2041438
Received: 24 September 2013; in revised form: 5 November 2013 / Accepted: 12 November 2013 / Published: 2 December 2013
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abstract graphic

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Automated Sample Preparation Platform for Mass Spectrometry-Based Plasma Proteomics and Biomarker Discovery
Authors: Vilém Guryča, Daniel Roeder, Paolo Piraino, Jens Lamerz, Axel Ducret, Hanno Langen and Paul Cutler *
Affiliation: F. Hoffmann-La Roche Ltd, Pharma Research and Early Development (pRED), Translational Technologies and Bioinformatics, Basel, Switzerland; * E-Mail: paul.cutler@roche.com
Abstract: The identification of novel biomarkers from human plasma remains a critical need in order to develop and monitor drug therapies for nearly all disease areas. The discovery of novel plasma biomarkers is however significantly hampered by the complexity and dynamic range of proteins within plasma, as well as the inherent variability in composition from patient to patient. In addition, it is widely accepted that most soluble plasma biomarkers for diseases such as cancer will be represented by tissue leakage products, circulating in plasma at low levels. It is therefore necessary to find approaches with the prerequisite level of sensitivity in such a complex biological matrix. Strategies for fractionating the plasma proteome have been suggested, but improvements in sensitivity are often negated by the resultant process variability. Here we describe an approach using multidimensional chromatography and on-line protein derivatisation, which allows for higher sensitivity, whilst minimizing the process variability. In order to evaluate the process fully we compare three levels of processing and compare sensitivity, throughput and reproducibility. We demonstrate that high sensitivity analysis of the human plasma proteome is possible down to the low ng/ml or even high pg/ml level with high levels of reproducibility.

Type of Paper: Article
Pre-Processing of Label-Free Multiple Reaction Monitoring (MRM) Experiment
Authors: Lisa Chung, Christopher Colangelo, and Hongyu Zhao
Affiliation: Department of Biostatistics, Keck Laboratory, Yale University, USA; E-Mail: hongyu.zhao@yale.edu
Abstract: Development of targeted proteomics assays enables simultaneous quantification of hundreds of peptides. This is accomplished by utilizing Multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer where we select targeted peptides, which are unique to the proteins of interest, for fragmentation and then detect predetermined fragment ions from each of the selected peptides. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics was recently selected as the Nature Method of the Year. However, many pre-processing steps still rely on manual inspection of each observation or performed only within a single run. In this paper, we discuss a pipeline to automate the MRM data pre-processing. It includes performing data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. Finally, our pipeline is applied to several real MRM data sets.

Last update: 12 August 2013

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