MS-GF+ makes progress towards a universal database search tool for proteomics

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13. Accurate de novo peptide sequencing using fully convolutional neural networks
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14. Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung
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16. In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta
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17. Fatiguing contractions increase protein S-glutathionylation occupancy in mouse skeletal muscle
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18. Beyond Target–Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics
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19. Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains
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20. IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts
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21. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery
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23. Systematic and Quantitative Assessment of Hydrogen Peroxide Reactivity With Cysteines Across Human Proteomes
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24. Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides
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26. A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes
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28. Untargeted, spectral library‐free analysis of data‐independent acquisition proteomics data generated using Orbitrap mass spectrometers
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29. Surface Glycoproteins of Exosomes Shed by Myeloid-Derived Suppressor Cells Contribute to Function
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30. The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics
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31. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes
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32. Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification
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33. Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples
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34. Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
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35. Degradation of cocoa proteins into oligopeptides during spontaneous fermentation of cocoa beans
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36. DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics
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37. Data Independent Acquisition analysis in ProHits 4.0
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38. The SEQUEST Family Tree
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39. Moisture modulates soil reservoirs of active DNA and RNA viruses
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40. Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution
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41. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome
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42. Data Dependent–Independent Acquisition (DDIA) Proteomics
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45. Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
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46. Dinosaur: A Refined Open-Source Peptide MS Feature Detector
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47. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics
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48. Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
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49. Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment
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50. Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning
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51. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
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52. Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi
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53. DeMix-Q: Quantification-Centered Data Processing Workflow
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54. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
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55. Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans
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56. caAtlas: An immunopeptidome atlas of human cancer
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57. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation
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59. Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition
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65. Combinatorial Approach to Nanoarchitectonics for Nonviral Delivery of Nucleic Acids
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66. Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma
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67. A tissue-based draft map of the murine MHC class I immunopeptidome
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68. Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach
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74. IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics
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76. Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics
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84. Computational quality control tools for mass spectrometry proteomics
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86. Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle
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87. MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms
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88. Changes of Protein Turnover in Aging Caenorhabditis elegans
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91. Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines
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95. Tankyrase inhibition preserves osteoarthritic cartilage by coordinating cartilage matrix anabolism via effects on SOX9 PARylation
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96. Stochiometric quantification of the thiol redox proteome of macrophages reveals subcellular compartmentalization and susceptibility to oxidative perturbations
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97. An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1
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98. IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing
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99. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts
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100. Genome Annotation of a Model Diatom Phaeodactylum tricornutum Using an Integrated Proteogenomic Pipeline
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