@article{Betancourt2011, abstract = {Here we describe an integrated approach for the selective separation of peptides from complex mixtures using strong cation-exchange chromatography. The procedure exploits the charge differences produced by reversible modification of primary amino groups in peptides, enabling their separation into three major fractions: 1) neutral peptides 2) peptides with one positive charge and 3) peptides with 2 or more positive charges. The procedure demonstrated an excellent selectivity which allowed restricted MS/MS ion searches with peptide-centric databases.}, author = {Betancourt, Lázaro H. and de Cossio, Jorge Fernandez and Sánchez, Aniel and Pérez, Yasset and Fernandez de Cossio, Jorge and Gil, Jeovanis and Toledo, Patricia and Iguchi, Seiji and Aimoto, Saburo and González, Luis J. and Padrón, Gabriel and Takao, Toshifumi and Besada, Vladimir}, doi = {10.1016/j.jprot.2011.04.029}, journal = {Journal of Proteomics}, month = {sep}, pages = {2210-2213}, title = {Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: Evaluation in proteomic studies using peptide-centric database searches}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/51150024_Charge_state-selective_separation_of_peptides_by_reversible_modification_of_amino_groups_and_strong_cation-exchange_chromatography_Evaluation_in_proteomic_studies_using_peptide-centric_database_search/links/0fcfd50452c330efde000000.pdf}, volume = {74}, year = {2011} } @article{Betancourt2013, abstract = {Multidimensional peptide fractionation is widely used in proteomics to reduce the complexity of peptide mixtures prior to mass spectrometric analysis. Here, we describe the sequential use of strong cation exchange and reversed phase liquid chromatography in both basic and acidic pH buffers for separating tryptic peptides from complex mixtures of proteins. Strong cation exchange exclusively separates peptide by their charge state into neutral, singly and multi-charged species. To further reduce complexity, each peptide group was separated by reversed phase liquid chromatography at basic pH and the resultant fractions were analyzed by LC-MS/MS. This workflow was applied to a soluble protein lysate from mouse embryonic fibroblast cells, and more than 5000 proteins from 29,843 peptides were identified. The high selectivity displayed during the SCX step (93% to 100%) and the overlaps between proteins identified from the SCX-separated peptide groups, are interesting assets of the procedure. Biological significance : The present work shows how complex mixture of peptides can be selectively separated by SCX based essentially on the net charge of peptides. The proposed workflow results in three well-defined subset of peptides of specific amino acid composition, which are representative of the constituent proteins. The very high selectivity obtained (93% to 99%) on the peptide side, underscores for the first time the possibility of SCX chromatography to aid in validating identified peptides.}, author = {Betancourt, Lazaro H. and De Bock, Pieter-Jan and Staes, An and Timmerman, Evy and Perez-Riverol, Yasset and Sanchez, Aniel and Besada, Vladimir and Gonzalez, Luis Javier and Vandekerckhove, Joël and Gevaert, Kris}, doi = {10.1016/j.jprot.2013.06.033}, journal = {Journal of Proteomics}, month = {jan}, pages = {164-171}, title = {SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping}, url = {https://www.researchgate.net/profile/Luis_Gonzalez23/publication/249319894_SCX_charge_state_selective_separation_of_tryptic_peptides_combined_with_2D-RP-HPLC_allows_for_detailed_proteome_mapping/links/53ed520d0cf26b9b7dc5e960.pdf}, volume = {91}, year = {2013} } @article{Borges2013, author = {Borges, Diogo and Perez-Riverol, Yasset and Nogueira, Fabio C. S. and Domont, Gilberto B. and Noda, Jesus and da Veiga Leprevost, Felipe and Besada, Vladimir and França, Felipe M. G. and Barbosa, Valmir C. and Sánchez, Aniel and Carvalho, Paulo C.}, doi = {10.1093/bioinformatics/btt106}, journal = {Bioinformatics}, month = {feb}, pages = {1343-1344}, title = {Effectively addressing complex proteomic search spaces with peptide spectrum matching}, url = {https://academic.oup.com/bioinformatics/article-pdf/29/10/1343/16911901/btt106.pdf}, volume = {29}, year = {2013} } @article{Cote2012, abstract = {The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build upon the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface (GUI) that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.}, author = {Cote, Richard G. and Côté, Richard G. and Griss, Johannes and Dianes, José A. and Wang, Rui and Wright, James C. and van den Toorn, Henk Wp P. and van Breukelen, Bas and Heck, Albert J. R. and Hulstaert, Niels and Martens, Lennart and Reisinger, Florian and Csordas, Attila and Ovelleiro, David and Perez-Rivevol, Yasset and Barsnes, Harald and Hermjakob, Henning and Vizcaíno, Juan Antonio}, doi = {10.1074/mcp.o112.021543}, journal = {Molecular and Cellular Proteomics}, month = {sep}, pages = {1682-1689}, title = {The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium*}, url = {https://doi.org/10.1074/mcp.o112.021543}, volume = {11}, year = {2012} } @article{Masforrol2012, abstract = {A random hexapeptide library (one-bead-one-compound), containing sixteen amino acids (16(6) different sequences) was synthesized on a Tentagel resin previously modified with a dipeptide linker (Asp-Pro). This peptide bond is highly susceptible to cleavage under mild acidic conditions in a salt-free solution prepared with H(2)(16)O/H(2)(18)O (60/40% v/v). In the hydrolysis, hexapeptides are released with an additional Asp residue partially labeled with (18)O at the C-terminus. These conditions are fully compatible with ESI-MS analysis and facilitate sequencing by MS, as N- and C-terminal ions can be easily differentiated in MS/MS spectra. The peptides were sequenced manually and also with de novo sequencing programs, and identifying them in a database containing all possible heptapeptide sequences or in a filtered database. The proposed strategy is also compatible with stepwise Edman degradation using either intact beads or the released free peptides.}, author = {Masforrol, Yordanka and de-Cossío, Jorge Fernández and Gil, Jeovanis and González, Luis Javier and Pérez-Riverol, Yasset and Fernández-De-Cossío, Jorge and Sánchez, Aniel and Betancourt, Lázaro Hiram and Garay, Hilda Elisa and Cabrales, Ania and Albericio, Fernando and Yang, Hongqian and Zubarev, Roman A. and Besada, Vladimir and Acosta, Osvaldo Reyes}, doi = {10.1021/co200159r}, journal = {ACS Combinatorial Science}, month = {feb}, pages = {145-149}, title = {Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/221780380_Introducing_an_Asp-Pro_Linker_in_the_Synthesis_of_Random_One-Bead-One-Compound_Hexapeptide_Libraries_Compatible_with_ESI-MS_Analysis/links/54dd2e8e0cf282895a3b472f.pdf}, volume = {14}, year = {2012} } @article{Perez-Riverol2011, abstract = {Protein identification by mass spectrometry is mainly based on MS/MS spectra and the accuracy of molecular mass determination. However, the high complexity and dynamic ranges for any species of proteomic samples, surpass the separation capacity and detection power of the most advanced multidimensional liquid chromatographs and mass spectrometers. Only a tiny portion of signals is selected for MS/MS experiments and a still considerable number of them do not provide reliable peptide identification. In this article, an in silico analysis for a novel methodology of peptides and proteins identification is described. The approach is based on mass accuracy, isoelectric point (pI), retention time (t(R)) and N-terminal amino acid determination as protein identification criteria regardless of high quality MS/MS spectra. When the methodology was combined with the selective isolation methods, the number of unique peptides and identified proteins increases. Finally, to demonstrate the feasibility of the methodology, an OFFGEL-LC-MS/MS experiment was also implemented. We compared the more reliable peptide identified with MS/MS information, and peptide identified with three experimental features (pI, t(R), molecular mass). Also, two theoretical assumptions from MS/MS identification (selective isolation of peptides and N-terminal amino acid) were analyzed. Our results show that using the information provided by these features and selective isolation methods we could found the 93% of the high confidence protein identified by MS/MS with false-positive rate lower than 5%.}, author = {Perez-Riverol, Yasset and Sánchez, Aniel and Ramos, Yassel and Schmidt, Alex and Müller, Markus and Betancourt, Lázaro and González, Luis J. and Vera, Roberto and Padron, Gabriel and Besada, Vladimir}, doi = {10.1016/j.jprot.2011.05.034}, journal = {Journal of Proteomics}, month = {may}, pages = {2071-2082}, title = {In silico analysis of accurate proteomics, complemented by selective isolation of peptides}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/51205989_In_silico_analysis_of_accurate_proteomics_complemented_by_selective_isolation_of_peptides/links/02e7e5294ffccd2395000000.pdf}, volume = {74}, year = {2011} } @article{Perez-Riverol2012, abstract = {IPG (Immobilized pH Gradient) based separations are frequently used as the first step in shotgun proteomics methods; it yields an increase in both the dynamic range and resolution of peptide separation prior to the LC-MS analysis. Experimental isoelectric point (pI) values can improve peptide identifications in conjunction with MS/MS information. Thus, accurate estimation of the pI value based on the amino acid sequence becomes critical to perform these kinds of experiments. Nowadays, pI is commonly predicted using the charge-state model [1], and/or the cofactor algorithm [2]. However, none of these methods is capable of calculating the pI value for basic peptides accurately. In this manuscript, we present an new approach that can significant improve the pI estimation, by using Support Vector Machines (SVM) [3], an experimental amino acid descriptor taken from the AAIndex database [4] and the isoelectric point predicted by the charge-state model. Our results have shown a strong correlation (R(2)=0.98) between the predicted and observed values, with a standard deviation of 0.32 pH units across the complete pH range.}, author = {Perez-Riverol, Yasset and Audain, Enrique and Millan, Aleli and Ramos, Yassel and Sanchez, Aniel and Vizcaíno, Juan Antonio and Wang, Rui and Müller, Markus and Machado, Yoan J. and Betancourt, Lazaro H. and González, Luis J. and Padrón, Gabriel and Besada, Vladimir}, doi = {10.1016/j.jprot.2012.01.029}, journal = {Journal of Proteomics}, month = {feb}, pages = {2269-2274}, title = {Isoelectric point optimization using peptide descriptors and support vector machines}, url = {https://www.researchgate.net/profile/Vladimir_Besada/publication/221825414_Isoelectric_point_optimization_using_peptide_descriptors_and_support_vector_machines/links/09e41503561f3b0787000000.pdf}, volume = {75}, year = {2012} } @article{Perez-Riverol2012_2, abstract = {Computational algorithms to explore the conformational space of small molecules are complex and computer demand field in chemoinformatics. In this paper a hybrid algorithm to explore the conformational space of organic molecules is presented. This hybrid algorithm is based in a systematic search approach combined with a Monte Carlo based method in order to obtain an ensemble of low-energy conformations simulating the flexibility of small chemical compounds. The Monte Carlo method uses the Metropolis criterion to accept or reject a conformation through an in-house implementation of the MMFF94s force field to calculate the conformational energy. The parallel design of this algorithm, based on the message passing interface (MPI) paradigm, was implemented. The results showed a performance increase in the terms of speed and efficiency.}, author = {Perez-Riverol, Yasset and Vera, Roberto and Mazola, Yuliet and Musacchio, Alexis and Mussachio, Alexis}, doi = {10.2174/156802612803989237}, journal = {Current Topics in Medicinal Chemistry}, month = {aug}, pages = {1790-1796}, title = {A Parallel Systematic-Monte Carlo Algorithm for exploring Conformational Space.}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/231816861_A_Parallel_Systematic-Monte_Carlo_Algorithm_for_exploring_Conformational_Space/links/09e4150b539907852a000000.pdf}, volume = {12}, year = {2012} } @article{Perez-Riverol2013, abstract = {The workshop "Bioinformatics for Biotechnology Applications (HavanaBioinfo 2012)", held December 8-11 2012 in Havana, aimed at exploring new bioinformatics tools and approaches for large-scale proteomics, genomics and chemoinformatics. Major conclusions of the workshop include the following: (i) Development of new applications and bioinformatics tools for proteomic repositories analysis is crucial; current proteomic repositories contain enough data (spectra/identifications) that can be used to increase the annotations in protein databases and to generate new tools for protein identification; (ii) spectral libraries, de novo sequencing and database search tools should be combined to increase the number of protein identifications; (iii) Protein probabilities and FDR are not yet sufficiently mature; (iv) computational proteomics software needs to become more intuitive; and at the same time appropriate education and training should be provided to help efficient exchange of knowledge between mass spectrometrist and experimental biologists with bioinformaticians in order to increase their bioinformatics background, especially statistics knowledge.}, author = {Perez-Riverol, Yasset and Hermjakob, Henning and Kohlbacher, Oliver and Martens, Lennart and Creasy, David and Cox, Jürgen and Leprevost, Felipe and Shan, Baozhen Paul and Pérez-Nueno, Violeta I. and Blazejczyk, Michal and Punta, Marco and Vierlinger, Klemens and Valiente, Pedro A. and Valienten, Pedro A. and Leon, Kalet and Chinea, Glay and Guirola, Osmany and Bringas, Ricardo and Cabrera, Gleysin and Guillen, Gerardo and Padron, Gabriel and Gonzalez, Luis Javier and Besada, Vladimir}, doi = {10.1016/j.jprot.2013.01.019}, journal = {Journal of Proteomics}, month = {jan}, pages = {134-138}, title = {Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/235396489_Computational_Proteomics_Pitfalls_and_Challenges_HavanaBioinfo_2012_Workshop_Report/links/02e7e51780c0b9bed6000000.pdf}, volume = {87}, year = {2013} } @article{Perez-Riverol2013_2, abstract = {Peptide sequence matching algorithms used for peptide identification by tandem mass spectrometry (MS/MS) enumerate theoretical peptides from the database, predict their fragment ions, and match them to the experimental MS/MS spectra. Here, we present an approach for scoring MS/MS identifications based on the high mass accuracy matching of precursor ions, the identification of a high intensity b1 fragment ion, and partial sequence tags from phenylthiocarbamoyl-derivatized peptides. This derivatization process boosts the b1 fragment ion signal which turns it into a powerful feature for peptide identification. We demonstrate the effectiveness of our scoring system by implementing it on a computational tool called 'HI-bone' and by identifying mass spectra of an Escherichia coli sample acquired on an Orbitrap Velos instrument using HCD (Higher-energy C-trap dissociation). Following this strategy, we identified 1,614 Peptide Spectrum Matches (PSMs) with a peptide False Discovery Rate (FDR) below 1%. These results were significantly higher than those from Mascot and SEQUEST using a similar FDR.}, author = {Perez-Riverol, Yasset and Sanchez, Aniel and Noda, Jesus and Borges, Diogo and Carvalho, Paulo Costa and Wang, Rui and Vizcaíno, Juan Antonio and Betancourt, Lazaro Hiram and Ramos, Yassel and Duarte, Gabriel and Nogueira, Fabio C. S. and Gonzalez, Luis Javier and Padron, Gabriel and Tabb, David Lee and Hermjakob, Henning and Domont, Gilberto B. and Besada, Vladimir}, doi = {10.1021/ac303239g}, journal = {Analytical Chemistry}, month = {feb}, pages = {3515-3520}, title = {HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions}, url = {https://www.researchgate.net/profile/Fabio_Nogueira2/publication/235755162_HI-Bone_A_Scoring_System_for_Identifying_Phenylisothiocyanate-Derivatized_Peptides_Based_on_Precursor_Mass_and_High_Intensity_Fragment_Ions/links/0deec51d6e688e1cdc000000.pdf}, volume = {85}, year = {2013} } @article{Ramos2008, abstract = {Here we demonstrate the usefulness of peptide fractionation by SDS-free polyacrylamide gel electrophoresis and its applicability to proteomics studies. In the absence of SDS, the driving force for the electrophoretic migration toward the anode is supplied by negatively charged acidic amino acid residues and other residues as phosphate, sulfate and sialic acid, while the resulting mobility depends on both the charge and the molecular mass of the peptides. A straightforward method was achieved for SDS-PAGE of proteins, enzyme digestion, peptide transfer and fractionation by SDS-free PAGE, which was named dual-fractionation polyacrylamide gel electrophoresis (DF-PAGE). This method increases the number of identified proteins 2.5-fold with respect to the proteins identified after direct analysis, and more than 80% of assigned peptides were found in unique SDS-free gel slices. A vast majority of identified peptides (93%) have p I values below 7.0, and 7% have p I values between 7.0 and 7.35. Peptide digests that were derived from complex protein mixtures were in consequence simplified as peptides that are positively charged are not recovered in the present conditions. The analysis of a membrane protein extract from Neisseria meningitidis by this approach allowed the identification of 97 proteins, including low-abundance components.}, author = {Ramos, Yassel and de-Cossio, Jorge Fernández and ́Betancourt, Laźa and Gutierrez, Elain and Machado, Yoan and Sánchez, Aniel and Castellanos-Serra, Lila and González, Luis J. and Gonza\éz, Luis J. and Fernández-De-Cossio, Jorge and Pérez-Riverol, Yasset and Betancourt, Lázaro and Gil, Jeovanis and Padrón, Gabriel and Besada, Vladimir and Besada, Gabriel Padroń a ́Vladimir}, doi = {10.1021/pr700840y}, journal = {Journal of Proteome Research}, month = {apr}, pages = {2427-2434}, title = {Proteomics based on peptide fractionation by SDS-free PAGE}, url = {https://www.researchgate.net/profile/Vladimir_Besada/publication/5431019_Proteomics_based_on_peptide_fractionation_by_SDS-free_PAGE/links/0912f50355c4ac1a82000000.pdf}, volume = {7}, year = {2008} } @article{Ramos2011, abstract = {SDS-free polyacrylamide gel electrophoresis is an effective alternative approach to peptide fractionation. Here we describe a discontinuous buffer system at acid pH that improves the separation of acidic peptides from tryptic digestion. MOPS and chloride act as trailing and leading ions, respectively, in this system, while histidine operates as counterion and buffers all solutions. In these electrophoretic conditions, peptides with pI below 5.5 migrate with low overall electrophoretic mobilities but high differences from one another, which allows for their efficient resolution. In silico analysis of several proteomes shows that the acid pH system allows a peptide simplification of 2.5-fold with respect to the total peptide mixture, and still a proteome coverage of about 95% is achievable. A straightforward method with a protocol including proteomic studies was achieved for SDS-PAGE of proteins, enzyme treatment and further peptide fractionation by SDS-free acid PAGE.}, author = {Ramos, Yassel and Garcia, Yairet and Pérez-Riverol, Yasset and Leyva, Alejandro and Padrón, Gabriel and Sánchez, Aniel and Castellanos-Serra, Lila and González, Luis J. and Besada, Vladimir}, doi = {10.1002/elps.201000677}, journal = {ELECTROPHORESIS}, month = {may}, pages = {1323-1326}, title = {Peptide fractionation by acid pH SDS-free electrophoresis}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/51094357_Peptide_fractionation_by_acid_pH_SDS-free_electrophoresis/links/53dd6e730cf2a76fb667c9f4.pdf}, volume = {32}, year = {2011} } @article{Sanchez2010, abstract = {Edman degradation in the gas phase has been observed by collision activated dissociation of N-terminal phenylthiocarbamoyl (PTC) protonated peptide to yield abundant complementary b₁ and y(n-1) ion pairs. Here, we demonstrated the relation between the observed losses of aniline and/or the entire PTC derivatizing group with the availability of mobile protons using electrospray ionization mass spectrometry. In order to select the peptides with more efficient fragmentation, while simplifying the mixture of peptides, we extend the phenylisotiocyanate (PITC) derivatization of amino groups to the selective isolation of multiply charged peptides (those having the number of arginines and histidines residues higher than one) using a procedure previously developed in our group. Thus, it was possible to identify in the filtered protein database the sequence of the isolated multiply charged peptides derived from a single protein and a complex mixture of proteins extracted from Escherichia coli using only the molecular mass and the N-terminal amino acid information. For this purpose, we developed a novel bioinformatic tool for automatic identification of peptides from liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments, which potentially can be used in high-throughput proteomics.}, author = {Sanchez, Aniel and Perez-Riverol, Yasset and González, Luis Javier and Noda, Jesus and Betancourt, Lazaro and Ramos, Yassel and Gil, Jeovanis and Vera, Roberto and Padrón, Gabriel and Besada, Gabriel Padro\ ́and Vladimir}, doi = {10.1021/ac1012738}, journal = {Analytical Chemistry}, month = {sep}, pages = {8492-8501}, title = {Evaluation of Phenylthiocarbamoyl-Derivatized Peptides by Electrospray Ionization Mass Spectrometry: Selective Isolation and Analysis of Modified Multiply Charged Peptides for Liquid Chromatography-Tandem Mass Spectrometry Experiments}, url = {https://www.researchgate.net/profile/Yasset_Perez-Riverol/publication/46379371_Evaluation_of_Phenylthiocarbamoyl-Derivatized_Peptides_by_Electrospray_Ionization_Mass_Spectrometry_Selective_Isolation_and_Analysis_of_Modified_Multiply_Charged_Peptides_for_Liquid_Chromatography-Tan/links/0fcfd50452c5ba2bfe000000.pdf}, volume = {82}, year = {2010} } @article{Sanchez2012, abstract = { In this work, a method devised for the selective isolation of multiply-charged peptide applied to a complex protein mixture was evaluated for the first time using a mass spectrometer with low resolution (LTQ). In this procedure, all primary amino groups of tryptic peptides derived from human liver tissue interstitial fluid (TIF) are blocked, restricting their positive charge, at acidic pH, to the presence of histidine and arginine residues. After strong cation exchange chromatography, multiply-charged peptides (#R + #H > 1) are retained in the column and separated with high selectivity from singly (#R + #H = 1) and neutral peptides (#R + #H = 0) which are collected together in the flow-through. Using liquid chromatography electrospray ionization tandem mass spectrometry analysis the retained fraction displayed a 95% enrichment of multiply charged peptides while in the flow-through; only 4% of multiply-charged peptides were identified. }, author = {Sanchez, Aniel and Sun, Wei and Ma, Jie and Jie, and Betancourt, Lazaro and de-Cossio, Jorge Fernandez and Padron, Gabriel and Perez-Riverol, Yasset and Jiang, Ying and He, Fuchu and Gonzalez, Luis Javier and Besada, Vladimir}, doi = {10.1255/ejms.1204}, journal = {European Journal of Mass Spectrometry}, month = {jan}, pages = {505-508}, title = {Selective isolation of multiply charged peptides: a confident strategy for protein identification using a linear trap quadrupole mass spectrometer}, url = {https://www.researchgate.net/profile/Vladimir_Besada/publication/236662413_Selective_isolation_of_multiply_charged_peptides_a_confident_strategy_for_protein_identification_using_a_linear_trap_quadrupole_mass_spectrometer/links/562a1e7508aef25a243fc856.pdf}, volume = {18}, year = {2012} } @article{Vera2013, abstract = {The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307.}, author = {Vera, Roberto and Perez-Riverol, Yasset and Perez, Sonia and Ligeti, Balázs and Kertész-Farkas, Attila and Pongor, Sándor}, doi = {10.1093/database/bat051}, journal = {Database}, month = {jul}, pages = {bat051-bat051}, title = {JBioWH: an open-source Java framework for bioinformatics data integration}, url = {http://dx.doi.org/10.1093/database/bat051}, volume = {2013}, year = {2013} } @article{Vizcaíno2012, abstract = {The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.}, author = {Vizcaíno, Juan Antonio and Côté, Richard G. and Cote, R. G. and Csordas, Attila and Dianes, José A. and Fabregat, Antonio and Foster, Joseph M. and Griss, Johannes and Alpi, Emanuele and Birim, Melih and Contell, Javier and O'Kelly, Gavin and O’Kelly, Gavin and Schoenegger, Andreas and Ovelleiro, David and Pérez-Riverol, Yasset and Reisinger, Florian and Ríos, Daniel and Wang, Rui and Hermjakob, Henning}, doi = {10.1093/nar/gks1262}, journal = {Nucleic Acids Research}, month = {nov}, pages = {D1063-D1069}, title = {The Proteomics Identifications (PRIDE) database and associated tools: status in 2013}, url = {https://doi.org/10.1093/nar/gks1262}, volume = {41}, year = {2012} } @article{Wang2012, abstract = {PRIDE Inspector thus provides a user-friendly, comprehensive tool for the browsing, inspection, and evaluation of data in the PRIDE database, or in a compatible standard file format. As such, we believe that PRIDE Inspector will substantially increase the ability of researchers, editors and peer-reviewers to explore, review, evaluate, and reuse proteomics data.}, author = {Wang, Rui and Fabregat, Antonio and Ríos, Daniel and Ovelleir, David and Ovelleiro, David and Foster, Joseph M. and Cote, Richard G. and Côté, Richard G. and Griss, Johannes and Csordas, Attila and Perez-Riverol, Yasset and Reisinger, Florian and Hermjakob, Henning and Martens, Lennart and Vizcaíno, Juan Antonio}, doi = {10.1038/nbt.2112}, journal = {Nature Biotechnology}, month = {feb}, pages = {135-137}, title = {PRIDE Inspector: a tool to visualize and validate MS proteomics data}, url = {http://www.nature.com/nbt/journal/v30/n2/pdf/nbt.2112.pdf}, volume = {30}, year = {2012} }