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

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Items 601–700 of 1,000

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   Yi Chen, Yanhong Su, Xiaofang Cao, Ioannis Siavelis, Isabelle Rose Leo, Jianming Zeng, Panagiotis Tsagkozis, Asle Charles Hesla, Andri Papakonstantinou, Xiao Liu et al. · 2024 · Advanced Science
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6. Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics
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7. Computational proteomics tools for identification and quality control
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8. Multifunctional Activity-Based Protein Profiling of the Developing Lung
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9. Activity‐Based Protein Profiling of Chitin Catabolism
   Elias K. Zegeye, Natalie Sadler, Gerard X. Lomas, Isaac Kwame Attah, Janet K Jansson, Kirsten Hofmockel, Christopher Anderton, Aaron Wright · 2020 · ChemBioChem
10. A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations
    John C. Anders, Hannes Petruschke, Nico Jehmlich, Sven‐Bastiaan Haange, Martin von Bergen�, Peter Florian Stadler · 2021 · BMC Bioinformatics
11. Functional meta-omics provide critical insights into long- and short-read assemblies
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12. Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification
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    Kristie L. Oxford, Jason Wendler, Jason McDermott, Richard Allen White III, Joshua D. Powell, Jon Jacobs, Joshua Adkins, Katrina M. Waters · 2016 · Expert Review of Proteomics
15. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks
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16. Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night
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17. Proteogenomic Approach to UTR Peptide Identification
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18. Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping
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19. Statistical Modeling for Enhancing the Discovery Power of Citrullination from Tandem Mass Spectrometry Data
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20. Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry
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21. The utilization of the search engine, Bolt, to decrease search time and increase peptide identifications in hydroxyl radical protein footprinting‐based workflows
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22. FPIA : A database for gene fusion profiling and interactive analyses
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23. SPEQ: quality assessment of peptide tandem mass spectra with deep learning
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24. µProteInS—a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs
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25. Auxiliary ATP binding sites support DNA unwinding by RecBCD
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26. A first dataset toward a standardized community-driven global mapping of the human immunopeptidome
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27. Detection of Nα-terminally formylated native proteins by a pan-N-formyl methionine-specific antibody
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28. PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer
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29. The landscape of fusion transcripts in plants: a new insight into genome complexity
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30. An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources
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31. Approximating Isotope Distributions of Biomolecule Fragments
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32. pValid 2: A deep learning based validation method for peptide identification in shotgun proteomics with increased discriminating power
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33. N-Terminal Modifications of Ubiquitin via Methionine Excision, Deamination, and Arginylation Expand the Ubiquitin Code
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34. A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics
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35. Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome
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36. The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli
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37. A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease
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38. SpecEncoder: deep metric learning for accurate peptide identification in proteomics
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39. Proteogenomic Tools and Approaches to Explore Protein Coding Landscapes of Eukaryotic Genomes
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40. Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification
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41. proBAMconvert: A Conversion Tool for proBAM/proBed
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42. Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi
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43. Proteogenomic Refinement of the Neomegalonema perideroedes T Genome Annotation
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44. Prediction and Consequences of Cofragmentation in Metaproteomics
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45. ProtyQuant: Comparing label-free shotgun proteomics datasets using accumulated peptide probabilities
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46. Compound identification via deep classification model for electron-ionization mass spectrometry
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47. Mechanistic roles of tyrosine phosphorylation in reversible amyloids, autoinhibition, and endosomal membrane association of ALIX
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48. Proteotranscriptomics – A facilitator in omics research
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49. MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search
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50. Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics
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51. Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae)
    Carla Uranga, Majid Ghassemian, Rufina Hernández-Martínez · 2017 · Biochimie Open
52. PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search
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53. Proteoform characterization based on top-down mass spectrometry
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54. Harmonizing structural mass spectrometry analyses in the mass spec studio
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55. On the privacy risks of sharing clinical proteomics data.
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56. ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data
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57. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
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58. Functional-proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer
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59. Quorum sensing mediates morphology and motility transitions in the model archaeon Haloferax volcanii
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60. Comparative Study of the Mitochondrial Proteome From Mesophyll, Vascular, and Guard Cells in Response to Carbon Starvation
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61. Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells
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62. DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning
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63. GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry
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64. AttnPep: A Self-Attention-Based Deep Learning Method for Peptide Identification in Shotgun Proteomics
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65. Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection
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66. Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment
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68. Characterization of Cell Surface Glycoproteins Using Enzymatic Treatment and Mass Spectrometry
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69. Identification of Single Amino Acid Substitutions in Proteogenomics
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70. MS1-Level Proteome Quantification Platform Allowing Maximally Increased Multiplexity for SILAC and In Vitro Chemical Labeling
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71. Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAFV600E Mutant Glioma
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72. Defining the interactomes of proteins involved in cytoskeletal dynamics using high-throughput proximity-dependent biotinylation in cellulo
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73. Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation
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75. GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching
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76. High resolution visualization and exo‐proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger
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77. Accurate Precursor Mass Assignment Improves Peptide Identification in Data-Independent Acquisition Mass Spectrometry
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78. WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline
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79. Proteomics Mass Spectrometry Data Analysis Tools
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80. Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry
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81. UniSpec: Deep Learning for Predicting the Full Range of Peptide Fragment Ion Series to Enhance the Proteomics Data Analysis Workflow
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87. Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis
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88. Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification
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89. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies
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90. Gradients of Generative Models for Improved Discriminative Analysis of Tandem Mass Spectra
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91. Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics
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92. A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics
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95. Multi-tissue proteogenomic analysis for mechanistic toxicology studies in non-model species
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96. Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry
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97. Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases
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98. Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow
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99. Nitroreductase Activites in Giardia lamblia: ORF 17150 Encodes a Quinone Reductase with Nitroreductase Activity
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100. PASS: A Proteomics Alternative Splicing Screening Pipeline
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