All Stories

  1. Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer
  2. Open‐source large language models in action: A bioinformatics chatbot for PRIDE database
  3. Open Source Large Language Models in Action: A Bioinformatics Chatbot for PRIDE database
  4. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data
  5. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  6. Abstracts from the 56th European Society of Human Genetics (ESHG) Conference: Oral Presentations
  7. Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study
  8. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023
  9. Phosphorylation in thePlasmodium falciparumproteome: A meta-analysis of publicly available data sets
  10. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome
  11. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  12. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation
  13. OpenMS 3 expands the frontiers of open-source computational mass spectrometry
  14. The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)
  15. Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments
  16. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  17. quantms: A cloud-based pipeline for proteomics reanalysis enables the quantification of 17521 proteins in 9,502 human samples.
  18. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis
  19. lesSDRF Is More: Maximizing The Value Of Proteomics Data Through Streamlined Metadata Annotation
  20. Tissue-based absolute quantification using large-scale TMT and LFQ experiments
  21. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics
  22. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
  23. Proteomic repository data submission, dissemination, and reuse: key messages
  24. The ProteomeXchange consortium at 10 years: 2023 update
  25. The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
  26. LFQ-based peptide and protein intensity downstream analysis
  27. Method for Independent Estimation of the False Localization Rate for Phosphoproteomics
  28. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics
  29. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  30. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms
  31. A comprehensive evaluation of consensus spectrum generation methods in proteomics
  32. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
  33. Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database
  34. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  35. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
  36. A method for independent estimation of false localisation rate for phosphoproteomics
  37. A proteomics sample metadata representation for multiomics integration and big data analysis
  38. Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  39. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  40. MaxDIA enables library-based and library-free data-independent acquisition proteomics
  41. Universal Spectrum Identifier for mass spectra
  42. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
  43. A proteomics sample metadata representation for multiomics integration, and big data analysis.
  44. Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison
  45. An integrated landscape of protein expression in human cancer
  46. The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and research
  47. User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
  48. BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers
  49. Deep learning embedder method and tool for mass spectra similarity search
  50. Universal Spectrum Identifier for mass spectra
  51. Proceedings of the EuBIC-MS 2020 Developers’ Meeting
  52. MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets
  53. Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
  54. Towards a sample metadata standard in public proteomics repositories
  55. BioContainers Registry: searching for bioinformatics tools, packages and containers
  56. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  57. The omics discovery REST interface
  58. User-friendly, scalable tools and workflows for single-cell analysis
  59. The Omics Discovery REST interface
  60. CHAPTER 19. Cross-platform Software Development and Distribution with Bioconda and BioContainers
  61. Phoenix Enhancer: an online service/tool for proteomics data mining using clustered spectra
  62. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
  63. Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation
  64. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
  65. Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
  66. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients
  67. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
  68. Quantifying the impact of public omics data
  69. Correction: Ten Simple Rules for Taking Advantage of Git and GitHub
  70. An integrated landscape of protein expression in human cancer
  71. Proteomics Standards Initiative Extended FASTA Format
  72. Proteomics Standards Initiative Extended FASTA Format (PEFF)
  73. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
  74. Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines
  75. Recommendations for the packaging and containerizing of bioinformatics software
  76. Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins
  77. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
  78. An “on-matrix” digestion procedure for AP-MS experiments dissects the interplay between complex-conserved and serotype-specific reactivities in Dengue virus-human plasma interactome
  79. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
  80. Protein Inference Using PIA Workflows and PSI Standard File Formats
  81. The PRIDE database and related tools and resources in 2019: improving support for quantification data
  82. Expanding the Use of Spectral Libraries in Proteomics
  83. Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol
  84. Protein inference using PIA workflows and PSI standard file formats
  85. Bioconda: sustainable and comprehensive software distribution for the life sciences
  86. ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data
  87. Recommendations for the packaging and containerizing of bioinformatics software
  88. Future prospects of spectral clustering approaches in proteomics
  89. Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”
  90. A protein standard that emulates homology for the characterization of protein inference algorithms
  91. Quantifying the impact of public omics data
  92. Accurate and fast feature selection workflow for high-dimensional omics data
  93. A protein standard that emulates homology for the characterization of protein inference algorithms
  94. Bioconda: A sustainable and comprehensive software distribution for the life sciences
  95. Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
  96. OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets
  97. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
  98. Four simple recommendations to encourage best practices in research software
  99. Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data
  100. The mzIdentML data standard version 1.2, supporting advances in proteome informatics
  101. Discovering and linking public omics data sets using the Omics Discovery Index
  102. BioContainers: an open-source and community-driven framework for software standardization
  103. Synthetic human proteomes for accelerating protein research
  104. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
  105. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
  106. A multicenter study benchmarks software tools for label-free proteome quantification
  107. 2016 update of the PRIDE database and its related tools
  108. Ten Simple Rules for Taking Advantage of Git and GitHub
  109. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
  110. Omics Discovery Index - Discovering and Linking Public Omics Datasets
  111. Ten Simple Rules for Taking Advantage of git and GitHub
  112. Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins
  113. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
  114. Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences
  115. 2016 update of the PRIDE database and its related tools
  116. Computational proteomics: Integrating mass spectral data into a biological context
  117. Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells
  118. Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells
  119. PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface
  120. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics: Fig. 1.
  121. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
  122. Open source libraries and frameworks for biological data visualisation: A guide for developers
  123. Identifying novel biomarkers through data mining—A realistic scenario?
  124. On best practices in the development of bioinformatics software
  125. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
  126. Editorial (Thematic Issue: Genomics and Proteomics behind Drug Design)
  127. Bioinformatics Tools for the Functional Interpretation of Quantitative Proteomics Results
  128. A Survey of Molecular Descriptors Used in Mass Spectrometry Based Proteomics
  129. Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
  130. SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping
  131. Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics
  132. JBioWH: an open-source Java framework for bioinformatics data integration
  133. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
  134. HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions
  135. Effectively addressing complex proteomic search spaces with peptide spectrum matching
  136. Selective Isolation of Multiply Charged Peptides: A Confident Strategy for Protein Identification Using a Linear Trap Quadrupole Mass Spectrometer
  137. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
  138. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
  139. A Parallel Systematic-Monte Carlo Algorithm for Exploring Conformational Space
  140. Isoelectric point optimization using peptide descriptors and support vector machines
  141. Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis
  142. PRIDE Inspector: a tool to visualize and validate MS proteomics data
  143. 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
  144. In silico analysis of accurate proteomics, complemented by selective isolation of peptides
  145. Peptide fractionation by acid pH SDS-free electrophoresis
  146. 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
  147. Selective Isolation—Detection of Two Different Positively Charged Peptides Groups by Strong Cation Exchange Chromatography and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry: Application to Proteomics Studies
  148. Proteomics Based on Peptide Fractionation by SDS-Free PAGE