All Stories

  1. The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF
  2. The PRIDE database at 20 years: 2025 update
  3. Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer
  4. The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF
  5. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data
  6. Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome
  7. Proteogenomics analysis of human tissues using pangenomes
  8. Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer
  9. Open‐source large language models in action: A bioinformatics chatbot for PRIDE database
  10. Open Source Large Language Models in Action: A Bioinformatics Chatbot for PRIDE database
  11. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data
  12. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  13. Abstracts from the 56th European Society of Human Genetics (ESHG) Conference: Oral Presentations
  14. Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study
  15. EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023
  16. Phosphorylation in thePlasmodium falciparumproteome: A meta-analysis of publicly available data sets
  17. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome
  18. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  19. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation
  20. OpenMS 3 expands the frontiers of open-source computational mass spectrometry
  21. The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)
  22. Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments
  23. Mass spectrometry-based proteomics data from thousands of HeLa control samples
  24. quantms: A cloud-based pipeline for proteomics reanalysis enables the quantification of 17521 proteins in 9,502 human samples.
  25. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis
  26. lesSDRF Is More: Maximizing The Value Of Proteomics Data Through Streamlined Metadata Annotation
  27. Tissue-based absolute quantification using large-scale TMT and LFQ experiments
  28. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics
  29. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
  30. Proteomic repository data submission, dissemination, and reuse: key messages
  31. The ProteomeXchange consortium at 10 years: 2023 update
  32. The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
  33. LFQ-based peptide and protein intensity downstream analysis
  34. Method for Independent Estimation of the False Localization Rate for Phosphoproteomics
  35. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics
  36. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  37. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms
  38. A comprehensive evaluation of consensus spectrum generation methods in proteomics
  39. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
  40. Mapping the Melanoma Plasma Proteome (MPP) Using Single-Shot Proteomics Interfaced with the WiMT Database
  41. A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
  42. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
  43. A method for independent estimation of false localisation rate for phosphoproteomics
  44. A proteomics sample metadata representation for multiomics integration and big data analysis
  45. Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  46. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  47. MaxDIA enables library-based and library-free data-independent acquisition proteomics
  48. Universal Spectrum Identifier for mass spectra
  49. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
  50. A proteomics sample metadata representation for multiomics integration, and big data analysis.
  51. Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison
  52. An integrated landscape of protein expression in human cancer
  53. The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS): an open community for bioinformatics training and research
  54. User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
  55. BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers
  56. Deep learning embedder method and tool for mass spectra similarity search
  57. Universal Spectrum Identifier for mass spectra
  58. Proceedings of the EuBIC-MS 2020 Developers’ Meeting
  59. MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets
  60. Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
  61. Towards a sample metadata standard in public proteomics repositories
  62. BioContainers Registry: searching for bioinformatics tools, packages and containers
  63. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
  64. The omics discovery REST interface
  65. User-friendly, scalable tools and workflows for single-cell analysis
  66. The Omics Discovery REST interface
  67. CHAPTER 19. Cross-platform Software Development and Distribution with Bioconda and BioContainers
  68. Phoenix Enhancer: an online service/tool for proteomics data mining using clustered spectra
  69. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
  70. Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation
  71. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
  72. Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
  73. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients
  74. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
  75. Quantifying the impact of public omics data
  76. Correction: Ten Simple Rules for Taking Advantage of Git and GitHub
  77. An integrated landscape of protein expression in human cancer
  78. Proteomics Standards Initiative Extended FASTA Format
  79. Proteomics Standards Initiative Extended FASTA Format (PEFF)
  80. ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
  81. Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines
  82. Recommendations for the packaging and containerizing of bioinformatics software
  83. Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins
  84. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics
  85. 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
  86. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
  87. Protein Inference Using PIA Workflows and PSI Standard File Formats
  88. The PRIDE database and related tools and resources in 2019: improving support for quantification data
  89. Expanding the Use of Spectral Libraries in Proteomics
  90. Mass spectrometry evaluation of a neuroblastoma SH-SY5Y cell culture protocol
  91. Protein inference using PIA workflows and PSI standard file formats
  92. Bioconda: sustainable and comprehensive software distribution for the life sciences
  93. ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data
  94. Recommendations for the packaging and containerizing of bioinformatics software
  95. Future prospects of spectral clustering approaches in proteomics
  96. Response to “Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra”
  97. A protein standard that emulates homology for the characterization of protein inference algorithms
  98. Quantifying the impact of public omics data
  99. Accurate and fast feature selection workflow for high-dimensional omics data
  100. A protein standard that emulates homology for the characterization of protein inference algorithms
  101. Bioconda: A sustainable and comprehensive software distribution for the life sciences
  102. Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach
  103. OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets
  104. Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
  105. Four simple recommendations to encourage best practices in research software
  106. Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data
  107. The mzIdentML data standard version 1.2, supporting advances in proteome informatics
  108. Discovering and linking public omics data sets using the Omics Discovery Index
  109. BioContainers: an open-source and community-driven framework for software standardization
  110. Synthetic human proteomes for accelerating protein research
  111. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
  112. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
  113. A multicenter study benchmarks software tools for label-free proteome quantification
  114. 2016 update of the PRIDE database and its related tools
  115. Ten Simple Rules for Taking Advantage of Git and GitHub
  116. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets
  117. Omics Discovery Index - Discovering and Linking Public Omics Datasets
  118. Ten Simple Rules for Taking Advantage of git and GitHub
  119. Novel interactions of domain III from the envelope glycoprotein of dengue 2 virus with human plasma proteins
  120. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets
  121. Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences
  122. 2016 update of the PRIDE database and its related tools
  123. Computational proteomics: Integrating mass spectral data into a biological context
  124. Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells
  125. Comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells
  126. PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface
  127. ms-data-core-api: an open-source, metadata-oriented library for computational proteomics: Fig. 1.
  128. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
  129. Open source libraries and frameworks for biological data visualisation: A guide for developers
  130. Identifying novel biomarkers through data mining—A realistic scenario?
  131. On best practices in the development of bioinformatics software
  132. The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
  133. Editorial (Thematic Issue: Genomics and Proteomics behind Drug Design)
  134. Bioinformatics Tools for the Functional Interpretation of Quantitative Proteomics Results
  135. A Survey of Molecular Descriptors Used in Mass Spectrometry Based Proteomics
  136. Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
  137. SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping
  138. Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics
  139. JBioWH: an open-source Java framework for bioinformatics data integration
  140. Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
  141. HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions
  142. Effectively addressing complex proteomic search spaces with peptide spectrum matching
  143. Selective Isolation of Multiply Charged Peptides: A Confident Strategy for Protein Identification Using a Linear Trap Quadrupole Mass Spectrometer
  144. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
  145. The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
  146. A Parallel Systematic-Monte Carlo Algorithm for Exploring Conformational Space
  147. Isoelectric point optimization using peptide descriptors and support vector machines
  148. Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis
  149. PRIDE Inspector: a tool to visualize and validate MS proteomics data
  150. 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
  151. In silico analysis of accurate proteomics, complemented by selective isolation of peptides
  152. Peptide fractionation by acid pH SDS-free electrophoresis
  153. 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
  154. 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
  155. Proteomics Based on Peptide Fractionation by SDS-Free PAGE