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

Cited by (999)

Items 501–600 of 999

1. Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC
   Katelyn Elizabeth Caslavka Zempel, Ajay Amar Vashisht, William D. Barshop, James Akira Wohlschlegel, Steven Gerard Clarke · 2016 · Journal of Proteome Research
2. Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer’s Disease Brain
   Stefani N. Thomas, Austin J. Yang · 2016 · Methods in molecular biology
3. Quantitative Analysis of Protein Covalent Labeling Mass Spectrometry Data in the Mass Spec Studio
   Daniel S. Ziemianowicz, Vladimir Sarpe, David C. Schriemer · 2019 · Analytical Chemistry
4. Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat
   Laurey Steinke, Gordon Slysz, Mary S. Weir Lipton, Christian G. Klatt, James Moran, Margie F. Romine, Jason M. Wood, Gordon Anderson, Donald A. Bryant, David M. Ward · 2020 · Applied and Environmental Microbiology
5. Peptidomics and proteogenomics: background, challenges and future needs
   Rui Miguel Pinheiro Vitorino, Manisha Choudhury, Sofia de Morais Guedes, Rita M. Ferreira, Visith Thongboonkerd, Lakshya Sharma, Francisco Manuel Lemos Amado, Sanjeeva Srivastava · 2021 · Expert Review of Proteomics
6. MS-PyCloud: An open-source, cloud computing-based pipeline for LC-MS/MS data analysis
   Li Chen, Bai Zhang, Michael Schnaubelt, Punit Shah, Paul Aiyetan, Daniel W. Chan, Hui Zhang, Zhen Zhang · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
7. Comparison of False Discovery Rate Control Strategies for Variant Peptide Identifications in Shotgun Proteogenomics
   Mark V. Ivanov, Anna A. Lobas, Dmitry S. Karpov, Sergei A. Moshkovskii, Mikhail V. Gorshkov · 2017 · Journal of Proteome Research
8. Bothrops atrox and Bothrops lanceolatus Venoms In Vitro Investigation: Composition, Procoagulant Effects, Co-Factor Dependency, and Correction Using Antivenoms
   Sébastien Larréché, Aurore Bousquet, Lucie Chevillard, Rabah Gahoual, Georges Jourdi, Anne-Laure Dupart, Christilla Bachelot‐Loza, Pascale Gaussem, Virginie Siguret, Jean‐Philippe Chippaux et al. · 2023 · Toxins
9. A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities
   Brian A. Risk, Nathan J Edwards, Morgan C. Giddings · 2013 · Journal of Proteome Research
10. Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project
    Jin-Young Cho, Hyoung–Joo Lee, Seul-Ki Jeong, Kwang-Youl Kim, Kyung‐Hoon Kwon, Jong Shin Yoo, Gilbert S. Omenn, Mark S. Baker, William S. Hancock, Young‐Ki Paik · 2015 · Journal of Proteome Research
11. Exploring the Environmental Physiology of the Indo-Pacific Reef Coral Seriatopora hystrix with Differential Proteomics
    Anderson B. Mayfield, Yi-Jyun Chen, Chi‐Yu Lu, Chii-Shiarng Chen · 2018 · Open Journal of Marine Science
12. Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins
    Johannes Griss, Florian Stanek, Otto Hudecz, Gerhard Dürnberger, Yasset Pérez‐Riverol, Juan Antonio Vizcaíno, Karl Mechtler · 2019 · Journal of Proteome Research
13. Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues
    Sophia Catherine Rossouw, Hocine Bendou, Rénette J. Blignaut, Liam Bell, Jonathan Rigby, Alan Gilbert Christoffels · 2021 · Pathology & Oncology Research
14. Estimating the computational limits of detection of microbial non‐model organisms
    Mathias Kuhring, Bernhard Y. Renard · 2015 · PROTEOMICS
15. High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom
    Tarcísio Liberato, Lanfranco Ranieri Paolo Troncone, Edson T. Yamashiro, Solange M.T. Serrano, André Zelanis · 2016 · Amino Acids
16. Dynamic Phosphorylation of Apoptosis Signal Regulating Kinase 1 (ASK1) in Response to Oxidative and Electrophilic Stress
    Carlos Morales Betanzos, Joel D. Federspiel, Amy M. Palubinsky, BethAnn McLaughlin, Daniel C. Liebler · 2016 · Chemical Research in Toxicology
17. Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics
    Anna A. Lobas, Mikhail A. Pyatnitskiy, Alexey L. Chernobrovkin, Irina Y. Ilina, Dmitry S. Karpov, Elizaveta M. Solovyeva, Ksenia G. Kuznetsova, Mark V. Ivanov, E. Yu. Lyssuk, Anna A. Kliuchnikova et al. · 2018 · Journal of Proteome Research
18. Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling
    Tong Zhang, Matthew J. Gaffrey, Matthew E Monroe, Dennis Thomas, Karl Weitz, Paul Piehowski, Vladislav Petyuk, Ronald Jay Moore, Brian D. Thrall, Weijun Qian · 2020 · Journal of Proteome Research
19. gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes
    Muzaffer Arıkan, Thilo Muth · 2024 · GigaScience
20. Defining candidate mRNA and protein EV biomarkers to discriminate ccRCC and pRCC from non-malignant renal cells in vitro
    Richard C. Zieren, Liang Dong, David J. Clark, Morgan D. Kuczler, Kengo Horie, Leandro F. Moreno, T. Mamie Lih, Michael Schnaubelt, Louis Vermeulen, Hui Zhang et al. · 2021 · Medical Oncology
21. Protein–lipid Association in Lizard Chemical Signals
    Marco Mangiacotti, Simon Baeckens, Marco Fumagalli, José M. Martín, Stefano Scali, Roberto Sacchi · 2023 · Integrative Organismal Biology
22. Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome
    Seok Heo, Taewook Kang, Alexei M. Bygrave, Martin R. Larsen, Richard L. Huganir · 2023 · Molecular & Cellular Proteomics
23. Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification
    Xinpei Yi, Bo Wen, Shuyi Ji, Alexander B. Saltzman, Eric J. Jaehnig, Jonathan Thomas Lei, Qiang Gao, Bing Zhang · 2023 · Molecular & Cellular Proteomics
24. metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis
    Yingying Sun, Ziyuan Xing, Shuang Liang, Zelei Miao, Lai‐Bao Zhuo, Wenhao Jiang, Hui Zhao, Huanhuan Gao, Yuting Xie, Yan Zhou et al. · 2024 · Molecular & Cellular Proteomics
25. Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource
    Julia M. Kelliher, Yan Xu, Mark C. Flynn, Michal Babinski, Richard Shane Canon, Eric Cavanna, Alicia Clum, Yuri Corilo, Grant M. Fujimoto, Cameron M. Giberson et al. · 2024 · Computational and Structural Biotechnology Journal
26. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes
    Jia Zhang, Mingkun Yang, Honghui Zeng, Feng Ge · 2016 · Molecular & Cellular Proteomics
27. SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
    Stefan Schulze, Anne Oltmanns, Christian Fufezan, Julia Kraegenbring, Michael Mormann, Mechthild Pohlschröder, Michael Hippler · 2020 · Bioinformatics
28. An in vivo Interaction Network of DNA-Repair Proteins: A Snapshot at Double Strand Break Repair in Deinococcus radiodurans
    Aman Kumar Ujaoney, Mahesh Kumar Padwal, Bhakti Basu · 2021 · Journal of Proteome Research
29. The in vivo fate of tobacco mosaic virus nanoparticle theranostic agents modified by the addition of a polydopamine coat
    Christian Isalomboto Nkanga, Young Hun Chung, Sourabh Shukla, Jingcheng Zhou, Jesse V. Jokerst, Nicole F. Steinmetz · 2021 · Biomaterials Science
30. Deep-Sea Anemones Are Prospective Source of New Antimicrobial and Cytotoxic Compounds
    Кветкина Александра Николаевна, Elena Kostina, Irina N. Gladkikh, Viktoria E. Chausova, Ekaterina A. Yurchenko, Irina Yu. Bakunina, Пивкин Михаил Викторович, Stanislav D. Anastyuk, Roman Sergeevich Popov, Margarita Monastyrnaya et al. · 2021 · Marine Drugs
31. Assessment and Comparison of Database Search Engines for Peptidomic Applications
    Eduardo A. De La Toba, Krishna D. B. Anapindi, Jonathan V. Sweedler · 2023 · Journal of Proteome Research
32. Computational Methods in Mass Spectrometry-Based Proteomics
    Sujun Li, Haixu Tang · 2016 · Advances in experimental medicine and biology
33. Flagging False Positives Following Untargeted LC–MS Characterization of Histone Post-Translational Modification Combinations
    Sander Willems, Maarten Dhaenens, Elisabeth Govaert, Laura De Clerck, Paulien Meert, Christophe Van Neste, Filip Van Nieuwerburgh, Dieter L. D. Deforce · 2016 · Journal of Proteome Research
34. A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M
    Xiaodong Zai, Qiaoling Yang, Kun Liu, Ruihua Li, Mengying Qian, Taoran Zhao, Yaohui Li, Ying Yin, Dayong Dong, Ling Fu et al. · 2017 · BMC Genomics
35. Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine
    Daniela Strenkert, Stefan Schmollinger, Yuntao Hu, Christian Hofmann, Kristen Holbrook, Helen W. Liu, Samuel Owen Purvine, Carrie Nicora, Si Chen, Mary S. Weir Lipton et al. · 2023 · Metallomics
36. Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines
    Kevin A. Kovalchik, David J. Hamelin, Peter Kubiniok, Benoîte Bourdin, Fatima Mostefai, Raphaël Poujol, Bastien Paré, Shawn M. Simpson, John Sidney, Éric Bonneil et al. · 2024 · Nature Communications
37. Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments
    Honglan Li, Jonghun Park, Hyunwoo Kim, Kyu‐Baek Hwang, Eunok Paek · 2017 · Journal of Proteome Research
38. Glomerular filtrate proteins in acute cardiorenal syndrome
    Rumie Wakasaki, Katsuyuki Matsushita, Kirsti Golgotiu, Sharon Anderson, Mahaba B. Eiwaz, Danny Orton, Sang Jun Han, H. Thomas Lee, Richard D. Smith, Karin Rodland et al. · 2019 · JCI Insight
39. The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom
    Maxine H. Tan, Sarah R. Smith, Kim K. Hixson, Justin Tan, James K. McCarthy, Adam B. Kustka, Andrew Ellis Allen · 2020 · Biology
40. Thermal proteome profiling identifies PIP4K2A and ZADH2 as off‐targets of Polo‐like kinase 1 inhibitor volasertib
    Oksana Goroshchuk, Iryna Kolosenko, Elena Kunold, Linda Vidarsdóttir, Mohammad Pirmoradian, Alireza Azimi, Rozbeh Jafari, Caroline Palm‐Apergi · 2021 · The FASEB Journal
41. Mass Spectrometry-Based Biomarkers in Drug Development
    Michelle Robinson, Ronald A. Miller, Daniel S. Spellman · 2019 · Advances in experimental medicine and biology
42. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra
    John T. Halloran, Jeff Bilmes, William Stafford Noble · 2016 · Journal of Proteome Research
43. A proteogenomic approach for protein-level evidence of genomic variants in cancer cells
    Jeonghun Yeom, Mohammad Humayun Kabir, Byungho Lim, Hee‐Sung Ahn, Seon‐Young Kim, Cheolju Lee · 2016 · Scientific Reports
44. A Matter of Time: Faster Percolator Analysis via Efficient SVM Learning for Large-Scale Proteomics
    John T. Halloran, David M. Rocke · 2018 · Journal of Proteome Research
45. Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production
    Mingkun Yang, Zhuo Zhu, Zhenhong Zhuang, Youhuang Bai, Shihua Wang, Feng Ge · 2020 · Molecular & Cellular Proteomics
46. Deep Convolutional Neural Networks Help Scoring Tandem Mass Spectrometry Data in Database-Searching Approaches
    Polina Kudriavtseva, Matvey Kashkinov, Attila Kertész‐Farkas · 2021 · Journal of Proteome Research
47. Protein turnover models for LC–MS data of heavy water metabolic labeling
    Rovshan G. Sadygov · 2021 · Briefings in Bioinformatics
48. Targeted curation of the gut microbial gene content modulating human cardiovascular disease
    Mikayla Borton, Michael Shaffer, David W Hoyt, Ruisheng Jiang, Jared Ellenbogen, Samuel Owen Purvine, Carrie Nicora, Elizabeth Eder, Allison R. Wong, Alan George Smulian et al. · 2023 · mBio
49. Computational approaches to identify sites of phosphorylation
    Alex W. Joyce, Brian C. Searle · 2023 · PROTEOMICS
50. Delineating functional and molecular impact of ex vivo sample handling in precision medicine
    Nona Struyf, Albin Österroos, Mattias Vesterlund, Cornelia Arnroth, Tojo James, Stephanie Sunandar, Georgios Mermelekas, Anna Bohlin, Kerstin Hamberg Levedahl, Sofia Bengtzén et al. · 2024 · npj Precision Oncology
51. RNA splicing junction landscape reveals abundant tumor-specific transcripts in human cancer
    Qin Li, Ziteng Li, Bing Chen, Jingjing Zhao, Hongwu Yu, Jia Ni Hu, Hongyan Lai, Hena Zhang, Yan Li, Zhiqiang Meng et al. · 2024 · Cell Reports
52. Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes
    Geicho Nakatsu, Duhyun Ko, Monia Michaud, Eric A. Franzosa, Xochitl C. Morgan, Curtis Huttenhower, Wendy S. Garrett · 2025 · mBio
53. Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides
    Austin Gluth, Jeffrey J. Czajka, Xiaolu Li, Kent Bloodsworth, Josie Eder, Jennifer E Kyle, Rosalie Chu, Bin Yang, Weijun Qian, Pavlo Bohutskyi et al. · 2025 · Biotechnology for Biofuels and Bioproducts
54. Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
    Marie A. Brunet, Xavier Roucou · 2019 · Journal of Visualized Experiments
55. The Antibody Repertoire of Colorectal Cancer
    Seong Won Cha, Stefano R. Bonissone, Seungjin Na, Pavel A. Pevzner, Vineet Bafna · 2017 · Molecular & Cellular Proteomics
56. An SDS-PAGE based proteomic approach for N-terminome profiling
    Prashant Kaushal, Yu Mi Kwon, Shinyeong Ju, Cheolju Lee · 2019 · The Analyst
57. Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120
    Shengchao Yu, Mingkun Yang, Jie Xiong, Qi Zhang, Xinxin Gao, Wei Miao, Feng Ge · 2021 · Microbiology Spectrum
58. MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides
    Jiawei Mao, He Zhu, Luyao Liu, Zheng Fang, Mingming Dong, Hongqiang Qin, Mingliang Ye · 2022 · Bioinformatics
59. DeepSCP: utilizing deep learning to boost single-cell proteome coverage
    Bing Wang, Yue Wang, Yu Chen, Mengmeng Gao, Jie Ren, Yueshuai Guo, Chenghao Situ, Yaling Qi, Hui Zhu, Yan Li et al. · 2022 · Briefings in Bioinformatics
60. Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
    Gueto-Tettay, Carlos, Tang, Di, Happonen, Lotta, Heusel, Moritz, Khakzad, Hamed, Malmström, Johan, Malmström, Lars · 2023 · PLOS Computational Biology
61. Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities
    Samuel E. Miller, Albert S. Colman, Jacob Waldbauer · 2023 · mSystems
62. Elucidating regulatory processes of intense physical activity by multi-omics analysis
    Ernesto Satoshi Nakayasu, Marina Gritsenko, Young‐Mo Kim, Jennifer E Kyle, Kelly G. Stratton, Carrie Nicora, Nathalie Munoz Munoz, Kathleen M. Navarro, Daniel M. Claborne, Yuqian Gao et al. · 2023 · Military Medical Research
63. Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics
    Hui Wang, Christopher E. Barbieri, Jintang He, Yuqian Gao, Tujin Shi, Chaochao Wu, Athena Schepmoes, Thomas Fillmore, Sung‐Suk Chae, Dennis Huang et al. · 2017 · Journal of Translational Medicine
64. Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection
    Susan L. Stevens, Tao Liu, Frances Rena Bahjat, Vladislav Petyuk, Athena Schepmoes, Ryan L. Sontag, Marina A. Gritsenko, Chaochao Wu, Sheng Wang, Anil K. Shukla et al. · 2018 · Translational Stroke Research
65. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis
    Tim Van Den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Dirk Benndorf, Bernhard Y. Renard, Bart Mesuere, Lennart Martens, Thilo Muth · 2020 · Journal of Proteome Research
66. New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics
    Yisu Peng, Shantanu Jain, Yong Fuga Li, Michal Greguš, Alexander R. Ivanov, Olga Vitek A, Predrag Radivojac A · 2020 · Bioinformatics
67. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation
    Damien B. Wilburn, Alicia Richards, Danielle L. Swaney, Brian C. Searle · 2021 · Journal of Proteome Research
68. Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus
    Shuang Hui Deng, Joonhoon Kim, Kyle Pomraning, Yuqian Gao, James E. Evans, Beth A. Hofstad, Ziyu Dai, Bobbie‐Jo Webb‐Robertson, Samantha M. Powell, Irina Vasilievna Novikova et al. · 2023 · Metabolic Engineering
69. Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation
    J. Robert O’Neill, Marcos Yébenes Mayordomo, Goran Mitulović, Sofian Al Shboul, Georges Bedran, Jakub Faktor, Lenka Hernychová, Lukáš Uhrík, Maria Gómez-Herranz, Mikołaj Kocikowski et al. · 2024 · Molecular & Cellular Proteomics
70. Functional surface expression of immunoglobulin cleavage systems in a candidate Mycoplasma vaccine chassis
    Sergi Torres-Puig, Silvia Crespo-Pomar, Hatice Akarsu, Thatcha Yimthin, Valentina Cippà, Thomas Démoulins, Horst Posthaus, Nicolas Ruggli, Peter Kuhnert, Fabien Labroussaa et al. · 2024 · Communications Biology
71. Exercise alters molecular profiles of inflammation and substrate metabolism in human white adipose tissue
    Maria F. Pino, Pieter Ubele Dijkstra, Katie L. Whytock, Cheehoon Ahn, Gongxin Yu, James A. Sanford, Joshua Hansen, Chelsea M. Hutchinson, Marina Gritsenko, Paul Piehowski et al. · 2025 · American Journal of Physiology-Endocrinology and Metabolism
72. Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model
    Dolena R. Ledee, Min A. Kang, Masaki Kajimoto, Samuel Owen Purvine, Heather M. Brewer, Ljiljana Paša‐Tolić, Michael A. Portman · 2017 · American Journal of Physiology-Heart and Circulatory Physiology
73. De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods
    Kira Vyatkina, Lennard J. M. Dekker, Si Wu, Martijn M. VanDuijn, Xiaowen Liu, Nikola Tolić, Theo M. Luider, Ljiljana Paša‐Tolić · 2017 · PROTEOMICS
74. Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes
    David L. Tabb, Brandon D. Murugan, Javan Okendo, Omesan Nair, Jonathan Michael Blackburn, Sindisiwe G. Buthelezi, Stoyan Stoychev · 2019 · International Journal of Mass Spectrometry
75. Mass spectrometry-based proteomics of single cells and organoids: The new generation of cancer research
    P.V. Migisha Ntwali, Chae Eun Heo, Jong Yoon Han, Soo Yeon Chae, Minji Kim, Hung M. Vu, Min‐Sik Kim, Hugh I. Kim · 2020 · TrAC Trends in Analytical Chemistry
76. An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics
    Chaochao Wu, Matthew E Monroe, Zhe Xu, Gordon Slysz, Samuel Payne, Karin Rodland, Tao Liu, Richard D. Smith · 2015 · Journal of the American Society for Mass Spectrometry
77. Hydrogen-Deuterium Exchange Mass Spectrometry Reveals a Novel Binding Region of a Neutralizing Fully Human Monoclonal Antibody to Anthrax Protective Antigen
    Mulin Fang, Zhe Wang, Kathleen Norris, Judith A. James, Si Wu, Kenneth Smith · 2022 · Toxins
78. Proteomic analysis of the umbilical cord in fetal growth restriction and preeclampsia
    Matthew S. Conrad, Miranda L. Gardner, Christine Miguel, Michael A. Freitas, Kara M. Rood, Marwan Ma’ayeh · 2022 · PLoS ONE
79. Analyzing the mechanisms that facilitate the subtype-specific assembly of γ-aminobutyric acid type A receptors
    Catherine Choi, Joshua L. Smalley, Abigail H. S. Lemons, Qiu Ren, Christopher E. Bope, Jake S. Dengler, Paul A Davies, Stephen J. Moss · 2022 · Frontiers in Molecular Neuroscience
80. In silico model of atherosclerosis with individual patient calibration to enable precision medicine for cardiovascular disease
    Andrew J. Buckler, David Marlevi, Nikolaos Taxiarchis Skenteris, Mariette Lengquist, Malin Kronqvist, Ljubica Perisic Matic, Ulf Hedin · 2022 · Computers in Biology and Medicine
81. Quality Control for the Target Decoy Approach for Peptide Identification
    Elke Debrie, Milan Malfait, Ralf Gabriels, Arthur Declerq, Adriaan Sticker, Lennart Martens, Lieven Clement · 2023 · Journal of Proteome Research
82. Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients
    Surbhi Bihani, Aryan Gupta, Subina Mehta, Andrew T. Rajczewski, James E. Johnson, Dhanush Borishetty, Timothy J. Griffin, Sanjeeva Srivastava, Pratik Dilip Jagtap · 2023 · Journal of Proteome Research
83. Target‐decoy false discovery rate estimation using Crema
    Andy Lin, Donavan See, William E. Fondrie, Uri Keich, William Stafford Noble · 2024 · PROTEOMICS
84. Cardiovascular proteomics in the era of big data: experimental and computational advances
    Maggie P. Y. Lam, Edward Lau, Dominic C. M. Ng, Ding Wang, Peipei Ping · 2016 · Clinical Proteomics
85. Improvement of peptide identification with considering the abundance of mRNA and peptide
    Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu · 2017 · BMC Bioinformatics
86. Hypoxia-ischemia modifies postsynaptic GluN2B-containing NMDA receptor complexes in the neonatal mouse brain
    Fuxin Lu, Guo Shao, Yongqiang Wang, Shenheng Guan, Alma L. Burlingame, Xuemei Liu, Xiao Liang, Renatta N. Knox, Donna Marie Ferriero, Xiangning Jiang · 2017 · Experimental Neurology
87. Computational identification of micro-structural variations and their proteogenomic consequences in cancer
    Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagić, Iman Sarrafi, Swati Mishra, Andrew McPherson, Colin C. Collins, Milan Radovich et al. · 2017 · Bioinformatics
88. Quantitative Proteomic Analysis of Changes Related to Age and Calorie Restriction in Rat Liver Tissue
    Younah Kim, Oh Kwang Kwon, Sehyun Chae, Heejung Jung, Sang Hyun Ahn, Ju Mi Jeon, Eunji Sung, Sun‐Joo Kim, Sung Hwan Ki, Ki Wung Chung et al. · 2017 · PROTEOMICS
89. High throughput discovery of protein variants using proteomics informed by transcriptomics
    Shyamasree Saha, David A. Matthews, Conrad Bessant · 2018 · Nucleic Acids Research
90. Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing
    Samuel E. Miller, Adriana I. Rizzo, Jacob Waldbauer · 2018 · Journal of Proteome Research
91. Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors
    Larry Sai Weng Loo, Heidrun Vethe, Andreas Alvin Purnomo Soetedjo, João A. Paulo, Joanita Binte Jasmen, Nicholas M. Jackson, Yngvild Bjørlykke, Ivan Valdez, Marc Vaudel, Harald Barsnes et al. · 2019 · Stem Cells
92. Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry
    Daniel S. Ziemianowicz, Justin L. MacCallum, David C. Schriemer · 2020 · Journal of the American Society for Mass Spectrometry
93. A Fast and Memory‐Efficient Spectral Library Search Algorithm Using Locality‐Sensitive Hashing
    Lei Wang, Kaiyuan Liu, Sujun Li, Haixu Tang · 2020 · PROTEOMICS
94. Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells
    Tamara Scheidt, Oliver Alka, Humberto Gonczarowska-Jorge, Wolfgang Gruber, Florian Rathje, Margherita Dell’Aica, Marc Rurik, Oliver Kohlbacher, René Peiman Zahedi, Fritz Aberger et al. · 2020 · Cell Communication and Signaling
95. Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy
    Elham Sherafat, Jordan Force, Ion Măndoiu · 2020 · BMC Bioinformatics
96. Pipelines and Systems for Threshold-Avoiding Quantification of LC–MS/MS Data
    Alejandro Sánchez Brotons, Jonatan O. Eriksson, Marcel Kwiatkowski, Justina Clarinda Wolters, Ido P. Kema, Andrei Barcaru, Folkert Kuipers, Stephan J. L. Bakker, Rainer Bischoff, Frank Suits et al. · 2021 · Analytical Chemistry
97. MSTracer: A Machine Learning Software Tool for Peptide Feature Detection from Liquid Chromatography–Mass Spectrometry Data
    Xiangyuan Zeng, Bin Ma · 2021 · Journal of Proteome Research
98. MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides
    Xiaoyu Yang, Pedatsur Neta, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Concepcion A. Remoroza, Meghan C. Burke, Yuxue Liang, Sanford P. Markey, Stephen E. Stein · 2021 · Journal of Proteome Research
99. Chemical Derivatization of Affinity Matrices Provides Protection from Tryptic Proteolysis
    William D. Barshop, Hee Jong Kim, Xiaorui Fan, Jihui Sha, Shima Rayatpisheh, James Akira Wohlschlegel · 2019 · Journal of Proteome Research
100. TAILS N-terminomic and proteomic datasets of healthy human dental pulp
     Ulrich Eckhard, Giada Marino, Simon R. Abbey, Ian Matthew, Christopher M. Overall · 2015 · Data in Brief