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1.  Mining gene functional networks to improve mass-spectrometry-based protein identification 
Bioinformatics  2009;25(22):2955-2961.
Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly.
Results: We develop a method that analyzes MS/MS experiments in the larger context of the biological processes active in a cell. Our method, MSNet, improves protein identification in shotgun proteomics experiments by considering information on functional associations from a gene functional network. MSNet substantially increases the number of proteins identified in the sample at a given error rate. We identify 8–29% more proteins than the original MS experiment when applied to yeast grown in different experimental conditions analyzed on different MS/MS instruments, and 37% more proteins in a human sample. We validate up to 94% of our identifications in yeast by presence in ground-truth reference sets.
Availability and Implementation: Software and datasets are available at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2773251  PMID: 19633097
2.  Integrating shotgun proteomics and mRNA expression data to improve protein identification 
Bioinformatics  2009;25(11):1397-1403.
Motivation: Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration.
Results: We develop a Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar experimental conditions. Our method, MSpresso, substantially increases the number of proteins identified in an MS/MS experiment at the same error rate, e.g. in yeast, MSpresso increases the number of proteins identified by ∼40%. We apply MSpresso to data from different MS/MS instruments, experimental conditions and organisms (Escherichia coli, human), and predict 19–63% more proteins across the different datasets. MSpresso demonstrates that incorporating prior knowledge of protein presence into shotgun proteomics experiments can substantially improve protein identification scores.
Availability and Implementation: Software is available upon request from the authors. Mass spectrometry datasets and supplementary information are available from
Supplementary Information: Supplementary data website:
PMCID: PMC2682515  PMID: 19318424
3.  Revisiting the negative example sampling problem for predicting protein–protein interactions 
Bioinformatics  2011;27(21):3024-3028.
Motivation: A number of computational methods have been proposed that predict protein–protein interactions (PPIs) based on protein sequence features. Since the number of potential non-interacting protein pairs (negative PPIs) is very high both in absolute terms and in comparison to that of interacting protein pairs (positive PPIs), computational prediction methods rely upon subsets of negative PPIs for training and validation. Hence, the need arises for subset sampling for negative PPIs.
Results: We clarify that there are two fundamentally different types of subset sampling for negative PPIs. One is subset sampling for cross-validated testing, where one desires unbiased subsets so that predictive performance estimated with them can be safely assumed to generalize to the population level. The other is subset sampling for training, where one desires the subsets that best train predictive algorithms, even if these subsets are biased. We show that confusion between these two fundamentally different types of subset sampling led one study recently published in Bioinformatics to the erroneous conclusion that predictive algorithms based on protein sequence features are hardly better than random in predicting PPIs. Rather, both protein sequence features and the ‘hubbiness’ of interacting proteins contribute to effective prediction of PPIs. We provide guidance for appropriate use of random versus balanced sampling.
Availability: The datasets used for this study are available at
Supplementary Information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3198576  PMID: 21908540
4.  An automated proteomic data analysis workflow for mass spectrometry 
BMC Bioinformatics  2009;10(Suppl 11):S17.
Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate huge datasets which need to be integrated and quantitatively analyzed. The Sequest™ search algorithm is a commonly used algorithm for identifying peptides and proteins from two dimensional liquid chromatography electrospray ionization tandem mass spectrometry (2-D LC ESI MS2) data. A number of proteomic pipelines that facilitate high throughput 'post data acquisition analysis' are described in the literature. However, these pipelines need to be updated to accommodate the rapidly evolving data analysis methods. Here, we describe a proteomic data analysis pipeline that specifically addresses two main issues pertinent to protein identification and differential expression analysis: 1) estimation of the probability of peptide and protein identifications and 2) non-parametric statistics for protein differential expression analysis. Our proteomic analysis workflow analyzes replicate datasets from a single experimental paradigm to generate a list of identified proteins with their probabilities and significant changes in protein expression using parametric and non-parametric statistics.
The input for our workflow is Bioworks™ 3.2 Sequest (or a later version, including cluster) output in XML format. We use a decoy database approach to assign probability to peptide identifications. The user has the option to select "quality thresholds" on peptide identifications based on the P value. We also estimate probability for protein identification. Proteins identified with peptides at a user-specified threshold value from biological experiments are grouped as either control or treatment for further analysis in ProtQuant. ProtQuant utilizes a parametric (ANOVA) method, for calculating differences in protein expression based on the quantitative measure ΣXcorr. Alternatively ProtQuant output can be further processed using non-parametric Monte-Carlo resampling statistics to calculate P values for differential expression. Correction for multiple testing of ANOVA and resampling P values is done using Benjamini and Hochberg's method. The results of these statistical analyses are then combined into a single output file containing a comprehensive protein list with probabilities and differential expression analysis, associated P values, and resampling statistics.
For biologists carrying out proteomics by mass spectrometry, our workflow facilitates automated, easy to use analyses of Bioworks (3.2 or later versions) data. All the methods used in the workflow are peer-reviewed and as such the results of our workflow are compliant with proteomic data submission guidelines to public proteomic data repositories including PRIDE. Our workflow is a necessary intermediate step that is required to link proteomics data to biological knowledge for generating testable hypotheses.
PMCID: PMC3226188  PMID: 19811682
5.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs 
BMC Bioinformatics  2002;3:2.
Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields.
We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems.
This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.
PMCID: PMC65690  PMID: 11869452
6.  Aptamer Database 
Nucleic Acids Research  2004;32(Database issue):D95-D100.
The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at
PMCID: PMC308828  PMID: 14681367
7.  IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering 
Journal of proteome research  2009;8(8):3872-3881.
Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. A number of database searching algorithms have been developed to assign peptide sequences to tandem mass spectra. Assembling the peptide identifications to proteins, however, is a challenging issue because many peptides are shared among multiple proteins. IDPicker is an open-source protein assembly tool that derives a minimum protein list from peptide identifications filtered to a specified False Discovery Rate. Here, we update IDPicker to increase confident peptide identifications by combining multiple scores produced by database search tools. By segregating peptide identifications for thresholding using both the precursor charge state and the number of tryptic termini, IDPicker retrieves more peptides for protein assembly. The new version is more robust against false positive proteins, especially in searches using multispecies databases, by requiring additional novel peptides in the parsimony process. IDPicker has been designed for incorporation in many identification workflows by the addition of a graphical user interface and the ability to read identifications from the pepXML format. These advances position IDPicker for high peptide discrimination and reliable protein assembly in large-scale proteomics studies. The source code and binaries for the latest version of IDPicker are available from
PMCID: PMC2810655  PMID: 19522537
bioinformatics; parsimony; protein assembly; protein inference; false discovery rate
8.  An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results 
BMC Bioinformatics  2004;5:9.
Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data.
In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG) as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML) schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here.
The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at . Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.
PMCID: PMC341449  PMID: 15005801
9.  The Galaxy Framework as a Unifying Bioinformatics Solution for ‘omics’ Core Facilities 
Integration of different omics data (genomic, transcriptomic, proteomic) reveals novel discoveries into biological systems. Integration of these datasets is challenging however, involving use of multiple disparate software in a sequential manner. However, the use of multiple, disparate software in a sequential manner makes the integration of multi-omic data a serious challenge. We describe the extension of Galaxy for mass spectrometric-based proteomics software, enabling advanced multi-omic applications in proteogenomics and metaproteomics. We will demonstrate the benefits of Galaxy for these analyses, as well as its value for software developers seeking to publish new software. We will also share insights on the benefits of the Galaxy framework as a bioinformatics solution for proteomic/metabolomic core facilities. Multiple datasets for proteogenomics research (3D-fractionated salivary dataset and oral pre-malignant lesion (OPML) dataset) and metaproteomics research (OPML dataset and Severe Early Childhood Caries (SECC) dataset). Software required for analytical steps such as peaklist generation, database generation (RNA-Seq derived and others), database search (ProteinPilot and X! tandem) and for quantitative proteomics were deployed, tested and optimized for use in workflows. The software are shared in Galaxy toolshed ( Usage of analytical workflows resulted in reliable identification of novel proteoforms (proteogenomics) or microorganisms (metaproteomics). Proteogenomics analysis identified novel proteoforms in the salivary dataset (51) and OPML dataset (38). Metaproteomics analysis led to microbial identification in OPML and SECC datasets using MEGAN software. As examples, workflows for proteogenomics analysis ( and metaproteomic analysis ( are available at the website. Tutorials for workflow usage within Galaxy-P framework are also available ( We demonstrate the use of Galaxy for integrated analysis of multi-omic data, in an accessible, transparent and reproducible manner. Our results and experiences using this framework demonstrate the potential for Galaxy to be a unifying bioinformatics solution for ‘omics core facilities.
PMCID: PMC4162280
10.  Verification of a Parkinson's Disease Protein Signature by Multiple Reaction Monitoring 
OBJECTIVE: Integration of different ‘omics data (genomic, transcriptomic, proteomic) reveals novel discoveries into biological systems. Integration of these datasets is challenging however, involving use of multiple disparate software in a sequential manner. However, the use of multiple, disparate software in a sequential manner makes the integration of multi-omic data a serious challenge. We describe the extension of Galaxy for mass spectrometric-based proteomics software, enabling advanced multi-omic applications in proteogenomics and metaproteomics. We will demonstrate the benefits of Galaxy for these analyses, as well as its value for software developers seeking to publish new software. We will also share insights on the benefits of the Galaxy framework as a bioinformatics solution for proteomic/metabolomic core facilities. METHODS: Multiple datasets for proteogenomics research (3D-fractionated salivary dataset and oral pre-malignant lesion (OPML) dataset) and metaproteomics research (OPML dataset and Severe Early Childhood Caries (SECC) dataset). Software required for analytical steps such as peaklist generation, database generation (RNA-Seq derived and others), database search (ProteinPilot and X! tandem) and for quantitative proteomics were deployed, tested and optimized for use in workflows. The software are shared in Galaxy toolshed ( Results: Usage of analytical workflows resulted in reliable identification of novel proteoforms (proteogenomics) or microorganisms (metaproteomics). Proteogenomics analysis identified novel proteoforms in the salivary dataset (51) and OPML dataset (38). Metaproteomics analysis led to microbial identification in OPML and SECC datasets using MEGAN software. As examples, workflows for proteogenomics analysis ( and metaproteomic analysis ( are available at the website. Tutorials for workflow usage within Galaxy-P framework are also available ( CONCLUSIONS: We demonstrate the use of Galaxy for integrated analysis of multi-omic data, in an accessible, transparent and reproducible manner. Our results and experiences using this framework demonstrate the potential for Galaxy to be a unifying bioinformatics solution for ‘omics core facilities.
PMCID: PMC4162281
11.  The Ruby UCSC API: accessing the UCSC genome database using Ruby 
BMC Bioinformatics  2012;13:240.
The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby.
The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.
The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby).
Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at under the Ruby license. Feedback and help is provided via the website at
PMCID: PMC3542311  PMID: 22994508
12.  BioRuby: bioinformatics software for the Ruby programming language 
Bioinformatics  2010;26(20):2617-2619.
Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.
Availability: BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from
PMCID: PMC2951089  PMID: 20739307
13.  jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data 
Proteomics  2012;12(6):790-794.
We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at
PMCID: PMC3933944  PMID: 22539429
Bioinformatics; Java API; mzIdentML; Proteomics standards initiative (PSI); XML
14.  AANT: the Amino Acid–Nucleotide Interaction Database 
Nucleic Acids Research  2004;32(Database issue):D174-D181.
We have created an Amino Acid–Nucleotide Interaction Database (AANT; that categorizes all amino acid–nucleotide interactions from experimentally determined protein–nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid–nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids × 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid–nucleotide interactions facilitates understanding the specificity of protein–nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.
PMCID: PMC308862  PMID: 14681388
15.  PEPPI: a peptidomic database of human protein isoforms for proteomics experiments 
BMC Bioinformatics  2010;11(Suppl 6):S7.
Protein isoform generation, which may derive from alternative splicing, genetic polymorphism, and posttranslational modification, is an essential source of achieving molecular diversity by eukaryotic cells. Previous studies have shown that protein isoforms play critical roles in disease diagnosis, risk assessment, sub-typing, prognosis, and treatment outcome predictions. Understanding the types, presence, and abundance of different protein isoforms in different cellular and physiological conditions is a major task in functional proteomics, and may pave ways to molecular biomarker discovery of human diseases. In tandem mass spectrometry (MS/MS) based proteomics analysis, peptide peaks with exact matches to protein sequence records in the proteomics database may be identified with mass spectrometry (MS) search software. However, due to limited annotation and poor coverage of protein isoforms in proteomics databases, high throughput protein isoform identifications, particularly those arising from alternative splicing and genetic polymorphism, have not been possible.
Therefore, we present the PEPtidomics Protein Isoform Database (PEPPI,, a comprehensive database of computationally-synthesized human peptides that can identify protein isoforms derived from either alternatively spliced mRNA transcripts or SNP variations. We collected genome, pre-mRNA alternative splicing and SNP information from Ensembl. We synthesized in silico isoform transcripts that cover all exons and theoretically possible junctions of exons and introns, as well as all their variations derived from known SNPs. With three case studies, we further demonstrated that the database can help researchers discover and characterize new protein isoform biomarkers from experimental proteomics data.
We developed a new tool for the proteomics community to characterize protein isoforms from MS-based proteomics experiments. By cataloguing each peptide configurations in the PEPPI database, users can study genetic variations and alternative splicing events at the proteome level. They can also batch-download peptide sequences in FASTA format to search for MS/MS spectra derived from human samples. The database can help generate novel hypotheses on molecular risk factors and molecular mechanisms of complex diseases, leading to identification of potentially highly specific protein isoform biomarkers.
PMCID: PMC3026381  PMID: 20946618
16.  pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool 
The pep2pro database was built to support effective high-throughput proteome data analysis. Its database schema allows the coherent integration of search results from different database-dependent search algorithms and filtering of the data including control for unambiguous assignment of peptides to proteins. The capacity of the pep2pro database has been exploited in data analysis of various Arabidopsis proteome datasets. The diversity of the datasets and the associated scientific questions required thorough querying of the data. This was supported by the relational format structure of the data that links all information on the sample, spectrum, search database, and algorithm to peptide and protein identifications and their post-translational modifications. After publication of datasets they are made available on the pep2pro website at Further, the pep2pro data analysis pipeline also handles data export do the PRIDE database ( and data retrieval by the MASCP Gator ( The utility of pep2pro will continue to be used for analysis of additional datasets and as a data warehouse. The capacity of the pep2pro database for proteome data analysis has now also been made publicly available through the release of pep2pro4all, which consists of a database schema and a script that will populate the database with mass spectrometry data provided in mzIdentML format.
PMCID: PMC3371593  PMID: 22701464
database; mzIdentML; pep2pro; plant proteomics; standard format
17.  The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button 
BMC Bioinformatics  2010;11(Suppl 12):S12.
There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.
The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.
In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure.
The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at
PMCID: PMC3040526  PMID: 21210979
18.  ISPIDER Central: an integrated database web-server for proteomics 
Nucleic Acids Research  2008;36(Web Server issue):W485-W490.
Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (, an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.
PMCID: PMC2447780  PMID: 18440977
19.  BioC implementations in Go, Perl, Python and Ruby 
As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site:
Database URL:
PMCID: PMC4067548  PMID: 24961236
20.  Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity 
In this paper we present a method for the multi-resolution comparison of biomolecular electrostatic potentials without the need for global structural alignment of the biomolecules. The underlying computational geometry algorithm uses multi-resolution attributed contour trees (MACTs) to compare the topological features of volumetric scalar fields. We apply the MACTs to compute electrostatic similarity metrics for a large set of protein chains with varying degrees of sequence, structure, and function similarity. For calibration, we also compute similarity metrics for these chains by a more traditional approach based upon 3D structural alignment and analysis of Carbo similarity indices. Moreover, because the MACT approach does not rely upon pairwise structural alignment, its accuracy and efficiency promises to perform well on future large-scale classification efforts across groups of structurally-diverse proteins. The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method; i.e., it is able to accurately cluster proteins into functionally-relevant groups which demonstrate strong dependence on ligand binding sites. The results of the analyses are available from the linked web databases and The MACT analysis tools are available as part of the public domain library of the Topological Analysis and Quantitative Tools (TAQT) from the Center of Computational Visualization, at the University of Texas at Austin ( The Carbo software is available for download with the open-source APBS software package at
PMCID: PMC2561295  PMID: 18841247
electrostatic; contour tree; similarity; clustering; Poisson-Boltzmann
21.  Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs 
BMC Bioinformatics  2014;15:121.
Tandem mass spectrometry-based database searching is currently the main method for protein identification in shotgun proteomics. The explosive growth of protein and peptide databases, which is a result of genome translations, enzymatic digestions, and post-translational modifications (PTMs), is making computational efficiency in database searching a serious challenge. Profile analysis shows that most search engines spend 50%-90% of their total time on the scoring module, and that the spectrum dot product (SDP) based scoring module is the most widely used. As a general purpose and high performance parallel hardware, graphics processing units (GPUs) are promising platforms for speeding up database searches in the protein identification process.
We designed and implemented a parallel SDP-based scoring module on GPUs that exploits the efficient use of GPU registers, constant memory and shared memory. Compared with the CPU-based version, we achieved a 30 to 60 times speedup using a single GPU. We also implemented our algorithm on a GPU cluster and achieved an approximately favorable speedup.
Our GPU-based SDP algorithm can significantly improve the speed of the scoring module in mass spectrometry-based protein identification. The algorithm can be easily implemented in many database search engines such as X!Tandem, SEQUEST, and pFind. A software tool implementing this algorithm is available at
PMCID: PMC4049470  PMID: 24773593
22.  The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience* 
Molecular & Cellular Proteomics : MCP  2014;13(10):2765-2775.
The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R.
We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.
PMCID: PMC4189001  PMID: 24980485
23.  An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQTM 
Proteome Science  2007;5:4.
Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed.
We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQTM reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQTM reported intensities from Mascot output, into a valid PRIDE XML entry.
We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQTM data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from .
PMCID: PMC1796855  PMID: 17270041
24.  Protein-Protein Docking with F2Dock 2.0 and GB-Rerank 
PLoS ONE  2013;8(3):e51307.
Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F2 Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA) based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error.
The improved affinity functions show superior performance compared to their traditional counterparts in finding correct docking poses at higher ranks. We found that the new filters and the GBSA based reranking individually and in combination significantly improve the accuracy of docking predictions with only minor increase in computation time. We compared F2 Dock 2.0 with ZDock 3.0.2 and found improvements over it, specifically among 176 complexes in ZLab Benchmark 4.0, F2 Dock 2.0 finds a near-native solution as the top prediction for 22 complexes; where ZDock 3.0.2 does so for 13 complexes. F2 Dock 2.0 finds a near-native solution within the top 1000 predictions for 106 complexes as opposed to 104 complexes for ZDock 3.0.2. However, there are 17 and 15 complexes where F2 Dock 2.0 finds a solution but ZDock 3.0.2 does not and vice versa; which indicates that the two docking protocols can also complement each other.
The docking protocol has been implemented as a server with a graphical client (TexMol) which allows the user to manage multiple docking jobs, and visualize the docked poses and interfaces. Both the server and client are available for download. Server: Client:
PMCID: PMC3590208  PMID: 23483883
25.  Inductive matrix completion for predicting gene–disease associations 
Bioinformatics  2014;30(12):i60-i68.
Motivation: Most existing methods for predicting causal disease genes rely on specific type of evidence, and are therefore limited in terms of applicability. More often than not, the type of evidence available for diseases varies—for example, we may know linked genes, keywords associated with the disease obtained by mining text, or co-occurrence of disease symptoms in patients. Similarly, the type of evidence available for genes varies—for example, specific microarray probes convey information only for certain sets of genes. In this article, we apply a novel matrix-completion method called Inductive Matrix Completion to the problem of predicting gene-disease associations; it combines multiple types of evidence (features) for diseases and genes to learn latent factors that explain the observed gene–disease associations. We construct features from different biological sources such as microarray expression data and disease-related textual data. A crucial advantage of the method is that it is inductive; it can be applied to diseases not seen at training time, unlike traditional matrix-completion approaches and network-based inference methods that are transductive.
Results: Comparison with state-of-the-art methods on diseases from the Online Mendelian Inheritance in Man (OMIM) database shows that the proposed approach is substantially better—it has close to one-in-four chance of recovering a true association in the top 100 predictions, compared to the recently proposed Catapult method (second best) that has <15% chance. We demonstrate that the inductive method is particularly effective for a query disease with no previously known gene associations, and for predicting novel genes, i.e. genes that are previously not linked to diseases. Thus the method is capable of predicting novel genes even for well-characterized diseases. We also validate the novelty of predictions by evaluating the method on recently reported OMIM associations and on associations recently reported in the literature.
Availability: Source code and datasets can be downloaded from
PMCID: PMC4058925  PMID: 24932006

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