All Stories

  1. Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer
  2. The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF
  3. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data
  4. Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome
  5. Proteogenomics analysis of human tissues using pangenomes
  6. Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer
  7. Open‐source large language models in action: A bioinformatics chatbot for PRIDE database
  8. Open Source Large Language Models in Action: A Bioinformatics Chatbot for PRIDE database
  9. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data
  10. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  11. Abstracts from the 56th European Society of Human Genetics (ESHG) Conference: Oral Presentations
  12. Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study
  13. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023
  14. Phosphorylation in thePlasmodium falciparumproteome: A meta-analysis of publicly available data sets
  15. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome
  16. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  17. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation
  18. OpenMS 3 expands the frontiers of open-source computational mass spectrometry
  19. The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)
  20. Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments
  21. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  22. quantms: A cloud-based pipeline for proteomics reanalysis enables the quantification of 17521 proteins in 9,502 human samples.
  23. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis
  24. lesSDRF Is More: Maximizing The Value Of Proteomics Data Through Streamlined Metadata Annotation
  25. Tissue-based absolute quantification using large-scale TMT and LFQ experiments
  26. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics
  27. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
  28. Proteomic repository data submission, dissemination, and reuse: key messages
  29. The ProteomeXchange consortium at 10 years: 2023 update
  30. The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
  31. LFQ-based peptide and protein intensity downstream analysis
  32. Method for Independent Estimation of the False Localization Rate for Phosphoproteomics
  33. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics
  34. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  35. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms
  36. A comprehensive evaluation of consensus spectrum generation methods in proteomics
  37. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
  38. Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database
  39. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  40. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
  41. A method for independent estimation of false localisation rate for phosphoproteomics
  42. A proteomics sample metadata representation for multiomics integration and big data analysis
  43. Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  44. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  45. MaxDIA enables library-based and library-free data-independent acquisition proteomics
  46. Universal Spectrum Identifier for mass spectra
  47. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
  48. A proteomics sample metadata representation for multiomics integration, and big data analysis.
  49. Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison
  50. An integrated landscape of protein expression in human cancer
  51. The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and research
  52. User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
  53. BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers
  54. Deep learning embedder method and tool for mass spectra similarity search
  55. Universal Spectrum Identifier for mass spectra
  56. Proceedings of the EuBIC-MS 2020 Developers’ Meeting
  57. MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets
  58. Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
  59. Towards a sample metadata standard in public proteomics repositories
  60. BioContainers Registry: searching for bioinformatics tools, packages and containers
  61. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  62. The omics discovery REST interface
  63. User-friendly, scalable tools and workflows for single-cell analysis
  64. The Omics Discovery REST interface
  65. CHAPTER 19. Cross-platform Software Development and Distribution with Bioconda and BioContainers
  66. Phoenix Enhancer: an online service/tool for proteomics data mining using clustered spectra
  67. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
  68. Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation
  69. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
  70. Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
  71. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients
  72. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
  73. Quantifying the impact of public omics data
  74. Correction: Ten Simple Rules for Taking Advantage of Git and GitHub
  75. An integrated landscape of protein expression in human cancer
  76. Proteomics Standards Initiative Extended FASTA Format
  77. Proteomics Standards Initiative Extended FASTA Format (PEFF)
  78. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
  79. Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines
  80. Recommendations for the packaging and containerizing of bioinformatics software
  81. Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins
  82. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
  83. 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
  84. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
  85. Protein Inference Using PIA Workflows and PSI Standard File Formats
  86. The PRIDE database and related tools and resources in 2019: improving support for quantification data
  87. Expanding the Use of Spectral Libraries in Proteomics
  88. Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol
  89. Protein inference using PIA workflows and PSI standard file formats
  90. Bioconda: sustainable and comprehensive software distribution for the life sciences
  91. ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data
  92. Recommendations for the packaging and containerizing of bioinformatics software
  93. Future prospects of spectral clustering approaches in proteomics
  94. Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”
  95. A protein standard that emulates homology for the characterization of protein inference algorithms
  96. Quantifying the impact of public omics data
  97. Accurate and fast feature selection workflow for high-dimensional omics data
  98. A protein standard that emulates homology for the characterization of protein inference algorithms
  99. Bioconda: A sustainable and comprehensive software distribution for the life sciences
  100. Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
  101. OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets
  102. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
  103. Four simple recommendations to encourage best practices in research software
  104. Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data
  105. The mzIdentML data standard version 1.2, supporting advances in proteome informatics
  106. Discovering and linking public omics data sets using the Omics Discovery Index
  107. BioContainers: an open-source and community-driven framework for software standardization
  108. Synthetic human proteomes for accelerating protein research
  109. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
  110. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
  111. A multicenter study benchmarks software tools for label-free proteome quantification
  112. 2016 update of the PRIDE database and its related tools
  113. Ten Simple Rules for Taking Advantage of Git and GitHub
  114. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
  115. Omics Discovery Index - Discovering and Linking Public Omics Datasets
  116. Ten Simple Rules for Taking Advantage of git and GitHub
  117. Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins
  118. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
  119. Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences
  120. 2016 update of the PRIDE database and its related tools
  121. Computational proteomics: Integrating mass spectral data into a biological context
  122. Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells
  123. Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells
  124. PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface
  125. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics: Fig. 1.
  126. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
  127. Open source libraries and frameworks for biological data visualisation: A guide for developers
  128. Identifying novel biomarkers through data mining—A realistic scenario?
  129. On best practices in the development of bioinformatics software
  130. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
  131. Editorial (Thematic Issue: Genomics and Proteomics behind Drug Design)
  132. Bioinformatics Tools for the Functional Interpretation of Quantitative Proteomics Results
  133. A Survey of Molecular Descriptors Used in Mass Spectrometry Based Proteomics
  134. Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
  135. SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping
  136. Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics
  137. JBioWH: an open-source Java framework for bioinformatics data integration
  138. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
  139. HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions
  140. Effectively addressing complex proteomic search spaces with peptide spectrum matching
  141. Selective Isolation of Multiply Charged Peptides: A Confident Strategy for Protein Identification Using a Linear Trap Quadrupole Mass Spectrometer
  142. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
  143. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
  144. A Parallel Systematic-Monte Carlo Algorithm for Exploring Conformational Space
  145. Isoelectric point optimization using peptide descriptors and support vector machines
  146. Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis
  147. PRIDE Inspector: a tool to visualize and validate MS proteomics data
  148. 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
  149. In silico analysis of accurate proteomics, complemented by selective isolation of peptides
  150. Peptide fractionation by acid pH SDS-free electrophoresis
  151. 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
  152. 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
  153. Proteomics Based on Peptide Fractionation by SDS-Free PAGE