All Stories

  1. Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
  2. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
  3. Expression Atlas update: from tissues to single cells
  4. Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics
  5. A five-level classification system for proteoform identifications
  6. Quantifying the impact of public omics data
  7. An integrated landscape of protein expression in human cancer
  8. Proteomics Standards Initiative Extended FASTA Format
  9. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
  10. Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins
  11. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
  12. The functional landscape of the human phosphoproteome
  13. Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities
  14. The PRIDE database and related tools and resources in 2019: improving support for quantification data
  15. Expanding the Use of Spectral Libraries in Proteomics
  16. Future prospects of spectral clustering approaches in proteomics
  17. Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE)
  18. Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”
  19. Quantifying the impact of public omics data
  20. ProForma: a Standard Proteoform Notation.
  21. The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data
  22. Accurate and fast feature selection workflow for high-dimensional omics data
  23. Expression Atlas: gene and protein expression across multiple studies and organisms
  24. Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
  25. OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets
  26. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
  27. Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets
  28. The SysteMHC Atlas project
  29. The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
  30. A community proposal to integrate proteomics activities in ELIXIR
  31. Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data
  32. The mzIdentML data standard version 1.2, supporting advances in proteome informatics
  33. Proteomics Approaches to Uncover the Drug Resistance Mechanisms of Microbial Biofilms
  34. Discovering and linking public omics data sets using the Omics Discovery Index
  35. Synthetic human proteomes for accelerating protein research
  36. A Golden Age for Working with Public Proteomics Data
  37. Ten Simple Rules for Taking Advantage of Git and GitHub
  38. Making sense of big data in health research: Towards an EU action plan
  39. Ten Simple Rules for Taking Advantage of git and GitHub
  40. Exploring the potential of public proteomics data
  41. Delicate Metabolic Control and Coordinated Stress Response Critically Determine Antifungal Tolerance of Candida albicans Biofilm Persisters
  42. Embedding standards in metabolomics: the Metabolomics Society data standards task group
  43. Proteomics Data Visualisation
  44. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
  45. Development of data representation standards by the human proteome organization proteomics standards initiative
  46. Open source libraries and frameworks for biological data visualisation: A guide for developers
  47. Identifying novel biomarkers through data mining—A realistic scenario?
  48. Analysis of the tryptic search space in UniProt databases
  49. Meeting New Challenges: The 2014 HUPO-PSI/COSMOS Workshop
  50. How to submit MS proteomics data to ProteomeXchange via the PRIDE database
  51. Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets
  52. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
  53. jmzTab: A Java interface to the mzTab data standard
  54. qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments
  55. ProteomeXchange provides globally coordinated proteomics data submission and dissemination
  56. A Survey of Molecular Descriptors Used in Mass Spectrometry Based Proteomics
  57. Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
  58. Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
  59. Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra
  60. Preparing to Work with Big Data in Proteomics - A Report on the HUPO-PSI Spring Workshop
  61. Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML
  62. LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics
  63. From Peptidome to PRIDE : P ublic proteomics data migration at a large scale
  64. The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics
  65. Shorthand notation for lipid structures derived from mass spectrometry
  66. HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions
  67. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary
  68. PRIDE Cluster: building a consensus of proteomics data
  69. Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories
  70. Ontology Lookup Service for Controlled Vocabularies and Data Annotation
  71. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
  72. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
  73. Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop
  74. Improvements in the protein identifier cross-reference service
  75. Isoelectric point optimization using peptide descriptors and support vector machines
  76. PRIDE: Quality control in a proteomics data repository
  77. jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
  78. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data
  79. The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
  80. PRIDE Inspector: a tool to visualize and validate MS proteomics data
  81. From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland
  82. Enabling BioSharing – a report on the Annual Spring Workshop of the HUPO‐PSI April 11–13, 2011, EMBL‐Heidelberg, Germany
  83. Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations
  84. Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets
  85. Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data
  86. Quality Control in Proteomics
  87. EST Analysis Pipeline: Use of Distributed Computing Resources
  88. Proteomic Temporal Profile of Human Brain Endothelium After Oxidative Stress
  89. Submitting Proteomics Data to PRIDE Using PRIDE Converter
  90. Organelle proteomics experimental designs and analysis
  91. PRIDE and “Database on Demand” as Valuable Tools for Computational Proteomics
  92. Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research
  93. The Ontology Lookup Service: bigger and better
  94. PRIDE: Data Submission and Analysis
  95. The Proteomics Identifications database: 2010 update
  96. A guide to the Proteomics Identifications Database proteomics data repository
  97. PRIDE Converter: making proteomics data-sharing easy
  98. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
  99. Present and future of proteomics data curation at the PRIDE database
  100. Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray
  101. Charting online OMICS resources: A navigational chart for clinical researchers
  102. Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
  103. Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing
  104. High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UK
  105. The PSI formal document process and its implementation on the PSI website
  106. Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach
  107. Partial silencing of a hydroxy-methylglutaryl-CoA reductase-encoding gene in Trichoderma harzianum CECT 2413 results in a lower level of resistance to lovastatin and lower antifungal activity
  108. Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol
  109. ThPTR2, a di/tri-peptide transporter gene from Trichoderma harzianum
  110. Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene fromT. harzianum CECT 2413
  111. Cloning and characterization of the erg1 gene of Trichoderma harzianum: Effect of the erg1 silencing on ergosterol biosynthesis and resistance to terbinafine
  112. Screening of antimicrobial activities in Trichoderma isolates representing three Trichoderma sections
  113. Detection of putative peptide synthetase genes in Trichoderma species: Application of this method to the cloning of a gene from T. harzianum CECT 2413
  114. Data Standards in Systems Modeling
  115. Data Standards in Proteomics
  116. Cell wall-degrading isoenzyme profiles of Trichoderma biocontrol strains show correlation with rDNA taxonomic species
  117. Separation and Identification of Volatile Components in the Fermentation Broth of Trichoderma atroviride by Solid-Phase Extraction and Gas Chromatography--Mass Spectrometry
  118. Colour pigments of Trichoderma harzianum
  119. ProteomeXchange submissions via PRIDE
  120. PRIDE: Quick tour
  121. PRIDE and ProteomeXchange: webinar