All Stories

  1. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis
  2. Comprehensive and empirical evaluation of machine learning algorithms for LC retention time prediction
  3. Beyond the ribosome: proteome-wide secretability studies using SECRiFY
  4. MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go
  5. Mass spectrometrists should search for all peptides, but assess only the ones they care about
  6. A community proposal to integrate proteomics activities in ELIXIR
  7. Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products
  8. Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs
  9. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana
  10. Mass spectrometrists should search for all peptides, but assess only the ones they care about
  11. Do you speak open science? Resources and tips to learn the language
  12. Do you speak open science? Resources and tips to learn the language
  13. moFF: a robust and automated approach to extract peptide ion intensities
  14. Machine learning applications in proteomics research: How the past can boost the future
  15. DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra
  16. Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications
  17. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
  18. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways
  19. Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra
  20. Distributed computing and data storage in proteomics: Many hands make light work, and a stronger memory
  21. Asn 3 , a Reliable, Robust, and Universal Lock Mass for Improved Accuracy in LC–MS and LC–MS/MS
  22. About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium
  23. MS2PIP: a tool for MS/MS peak intensity prediction
  24. CellMissy: a tool for automated analysis of cell migration data
  25. ProteoCloud: A full-featured open source proteomics cloud computing pipeline
  26. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
  27. Bringing proteomics into the clinic: The need for the field to finally take itself seriously
  28. In praise of open research measures
  29. Resilience in the proteomics data ecosystem: How the field cares for its data
  30. Proteome-derived Peptide Libraries to Study the Substrate Specificity Profiles of Carboxypeptidases
  31. Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles
  32. Getting intimate with trypsin, the leading protease in proteomics
  33. D-score: A search engine independent MD-score
  34. Protein structure as a means to triage proposed PTM sites
  35. Crowdsourcing in proteomics: public resources lead to better experiments
  36. Searching for a needle in a stack of needles: challenges in metaproteomics data analysis
  37. The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
  38. LNCipedia: a database for annotated human lncRNA transcript sequences and structures
  39. Current methods for global proteome identification
  40. A Complex Standard for Protein Identification, Designed by Evolution
  41. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
  42. The Effect of Peptide Identification Search Algorithms on MS2-Based Label-Free Protein Quantification
  43. Integral Quantification Accuracy Estimation for Reporter Ion-based Quantitative Proteomics (iQuARI)
  44. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways
  45. Chromatographic retention time prediction for posttranslationally modified peptides
  46. Enabling Computational Proteomics by Public and Local Data Management Systems
  47. Sigpep: Calculating unique peptide signature transition sets in a complete proteome background
  48. Towards a human proteomics atlas
  49. PRIDE Inspector: a tool to visualize and validate MS proteomics data
  50. The HUPO initiative on Model Organism Proteomes, iMOP
  51. iTRAQ Data Interpretation
  52. TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
  53. Analysis of the Resolution Limitations of Peptide Identification Algorithms
  54. jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions
  55. Bioinformatics Analysis of aSaccharomyces cerevisiaeN-Terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-Translational N-Terminal Acetylation
  56. thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome DiscoverermsfFiles
  57. “4D Biology for health and disease” workshop report
  58. RIBAR and xRIBAR: Methods for Reproducible Relative MS/MS-based Label-Free Protein Quantification
  59. Combining quantitative proteomics data processing workflows for greater sensitivity
  60. A posteriori quality control for the curation and reuse of public proteomics data
  61. Peptide identification quality control
  62. Quality Control in Proteomics
  63. A global analysis of peptide fragmentation variability
  64. iTRAQ protein quantification: A quality-controlled workflow
  65. A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision
  66. A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods
  67. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
  68. A Case Study on the Comparison of Different Software Tools for Automated Quantification of Peptides
  69. Bioinformatics Challenges in Mass Spectrometry-Driven Proteomics
  70. Bioinformatics Challenges in the Proteomic Analysis of Human Plasma
  71. Data Management in Mass Spectrometry-Based Proteomics
  72. Mass Spectrometry-Driven Proteomics: An Introduction
  73. compomics-utilities: an open-source Java library for computational proteomics
  74. Submitting Proteomics Data to PRIDE Using PRIDE Converter
  75. Proteomics Databases and Repositories
  76. PRIDE and “Database on Demand” as Valuable Tools for Computational Proteomics
  77. Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research
  78. mzML—a Community Standard for Mass Spectrometry Data
  79. The Ontology Lookup Service: bigger and better
  80. PRIDE: Data Submission and Analysis
  81. XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results
  82. jmzML, an open-source Java API for mzML, the PSI standard for MS data
  83. Peptide and protein quantification: A map of the minefield
  84. jTraqX: A free, platform independent tool for isobaric tag quantitation at the protein level
  85. ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
  86. A report on the ESF workshop on quality control in proteomics
  87. FragmentationAnalyzer: An open-source tool to analyze MS/MS fragmentation data
  88. OLS Dialog: An open-source front end to the Ontology Lookup Service
  89. Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis
  90. The Proteomics Identifications database: 2010 update
  91. Improved visualization of protein consensus sequences by iceLogo
  92. The PSI semantic validator: A framework to check MIAPE compliance of proteomics data
  93. Database on Demand - An online tool for the custom generation of FASTA-formatted sequence databases
  94. Toward a Successful Clinical Neuroproteomics The 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece
  95. A guide to the Proteomics Identifications Database proteomics data repository
  96. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)
  97. PRIDE Converter: making proteomics data-sharing easy
  98. OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results
  99. Proteomics Data Collection - 5th ProDaC Workshop 4 March 2009, Kolympari, Crete, Greece
  100. Erratum: Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
  101. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics
  102. Proteomics Data Collection - 4thProDaC Workshop 15 August 2008, Amsterdam, The Netherlands
  103. Algorithms and Databases
  104. Charting online OMICS resources: A navigational chart for clinical researchers
  105. Proteomics Data Collection - 3rdProDaC Workshop April 22nd2008, Toledo, Spain
  106. Peptizer, a Tool for Assessing False Positive Peptide Identifications and Manually Validating Selected Results
  107. OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine
  108. The HUPO Brain Proteome Project Wish List – Summary of the 9th HUPO BPP Workshop 9–10 January 2008, Barbados
  109. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
  110. 6th HUPO Annual World Congress – Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, Korea
  111. Proteomics Data Collection – 2nd ProDaC Workshop 5 October 2007, Seoul, Korea
  112. Using the Proteomics Identifications Database (PRIDE)
  113. Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
  114. Human Proteinpedia enables sharing of human protein data
  115. Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing
  116. Data Standards and Controlled Vocabularies for Proteomics
  117. PRIDE: new developments and new datasets
  118. Computational Methods for Mass Spectrometry Proteomics
  119. Implementation and application of a versatile clustering tool for tandem mass spectrometry data
  120. Proteomics Data Collection – The 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France
  121. High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7–9, 2007 Wellcome Trust Conference Centre, Hinxton, UK
  122. A la carte proteomics with an emphasis on gel-free techniques
  123. The minimum information about a proteomics experiment (MIAPE)
  124. The PSI formal document process and its implementation on the PSI website
  125. Large-Scale Identification of N-Terminal Peptides in the Halophilic ArchaeaHalobacteriumsalinarumandNatronomonaspharaonis
  126. Proteomics for everyday use: Activities of the HUPO Brain Proteome Project during the 5th HUPO World Congress
  127. Annotating the human proteome: Beyond establishing a parts list
  128. MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results
  129. Proteomics data validation: why all must provide data
  130. The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases
  131. A New Functional, Chemical Proteomics Technology To Identify Purine Nucleotide Binding Sites in Complex Proteomes
  132. A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies
  133. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase
  134. Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study
  135. HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
  136. Proteome-wide Characterization of N-Glycosylation Events by Diagonal Chromatography
  137. The power of cooperative investigation: Summary and comparison of the HUPO Brain Proteome Project pilot study results
  138. Four Stage Liquid Chromatographic Selection of Methionyl Peptides for Peptide-Centric Proteome Analysis:  The Proteome of Human Multipotent Adult Progenitor Cells
  139. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
  140. The HUPO Brain Proteome Project Jamboree: Centralised summary of the pilot studies
  141. PRIDE: a public repository of protein and peptide identifications for the proteomics community
  142. Diagonal reverse-phase chromatography applications in peptide-centric proteomics: Ahead of catalogue-omics?
  143. Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis
  144. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK - Setting the Analysis Frame
  145. Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC
  146. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project
  147. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
  148. PRIDE: The proteomics identifications database
  149. The human platelet proteome mapped by peptide-centric proteomics: A functional protein profile
  150. DBToolkit: processing protein databases for peptide-centric proteomics
  151. Global Differential Non-Gel Proteomics by Quantitative and Stable Labeling of Tryptic Peptides with Oxygen-18
  152. Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies
  153. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
  154. Chromatographic Isolation of Methionine-containing Peptides for Gel-free Proteome Analysis