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

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1. A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles
   Sehyun Chae, Su‐jin Kim, Young Do Koo, Jung Hwa Lee, Hokeun Kim, Byung Yong Ahn, Yong‐Chan Ha, Yong‐Hak Kim, Mi Gyeong Jang, Kyung‐Hoi Koo et al. · 2018 · Experimental & Molecular Medicine
2. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
   Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Γεώργιος Μαρίνος et al. · 2021 · Microbiome
3. Progress and challenges in mass spectrometry-based analysis of antibody repertoires
   Igor Snapkov, Maria Chernigovskaya, Pavel G. Sinitcyn, Khang Lê Quý, Tuula A. Nyman, Victor Greiff · 2021 · Trends in biotechnology
4. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana
   Patrick J. Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme · 2017 · Molecular & Cellular Proteomics
5. The challenges of peptidomics in complementing proteomics in a clinical context
   Evelyne Maes, Eline Oeyen, Kurt Boonen, Karin Schildermans, Inge Mertens, Patrick Pauwels, Dirk Valkenborg, Geert Baggerman · 2018 · Mass Spectrometry Reviews
6. Proteomics as a new tool to study fingermark ageing in forensics
   Stijn Oonk, Tom Schuurmans, Martin Pabst, Louis C. P. M. de Smet, Marcel de Puit · 2018 · Scientific Reports
7. MS1 ion current‐based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts
   Xue Wang, Shichen Shen, Sailee Suryakant Rasam, Jun Qu · 2019 · Mass Spectrometry Reviews
8. The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum
   Jiajia Li, Tania Chroumpi, Sandra Garrigues, Roland S. Kun, Jiali Meng, Sonia Salazar-Cerezo, María Victoria Aguilar Pontes, Yu Zhang, Sravanthi Tejomurthula, Anna Lipzen et al. · 2022 · Journal of Fungi
9. Residual tissue repositories as a resource for population-based cancer proteomic studies
   Paul Piehowski, Vladislav Petyuk, Ryan L. Sontag, Marina A. Gritsenko, Karl Weitz, Thomas Fillmore, Jamie Moon, Hala R. Makhlouf, Rodrigo F. Chuaqui, Emily S. Boja et al. · 2018 · Clinical Proteomics
10. PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis
    Chang Rok Kim, Taichi Noda, Hyun-Kyung Kim, Gibeom Kim, Seongwan Park, Yongwoo Na, Seiya Oura, Keisuke Shimada, Injin Bang, Jun-Yeong Ahn et al. · 2020 · Cell Reports
11. Improved Protein and PTM Characterization with a Practical Electron-Based Fragmentation on Q-TOF Instruments
    Joseph S. Beckman, Valery G. Voinov, Michael C. Hare, Derrill Sturgeon, Yury V. Vasil’ev, Diana Oppenheimer, Jared Shaw, Shuai Wu, Rebecca S. Glaskin, Christian Klein et al. · 2021 · Journal of the American Society for Mass Spectrometry
12. Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity
    Ernesto Satoshi Nakayasu, Lisa Bramer, Charles K. Ansong, Athena Schepmoes, Thomas Fillmore, Marina Gritsenko, Therese RW Clauss, Yuqian Gao, Paul Piehowski, Bryan Stanfill et al. · 2023 · Cell Reports Medicine
13. Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry
    Aaron C. Wacholder, Anne‐Ruxandra Carvunis · 2023 · PLoS Biology
14. DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics
    James C. Wright, Jyoti Sharma Choudhary · 2016 · Journal of Proteomics & Bioinformatics
15. A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics
    Bramer, Lisa M., Irvahn, Jan, Piehowski, Paul D., Rodland, Karin D., Webb-Robertson, Bobbie-Jo M. · 2021 · Journal of Proteome Research
16. Cellular costs underpin micronutrient limitation in phytoplankton
    J. Scott P. McCain, Alessandro Tagliabue, Edward Susko, Eric P. Achterberg, Andrew Ellis Allen, Erin M. Bertrand · 2021 · Science Advances
17. Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR
    Ilya R. Akberdin, David A. Collins, Richard Hamilton, Dmitry Y. Oshchepkov, Anil K. Shukla, Carrie Nicora, Ernesto Satoshi Nakayasu, Joshua Adkins, Marina Kalyuzhnaya · 2018 · Frontiers in Microbiology
18. Circulating proteomic panels for diagnosis and risk stratification of acute-on-chronic liver failure in patients with viral hepatitis B
    Zeyu Sun, Xiaoli Liu, Daxian Wu, Hainv Gao, Jing Jiang, Ying Yang, Jie Wu, Qikang Gao, Jie Wang, Zhengyi Jiang et al. · 2019 · Theranostics
19. Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells
    Isaac A. Babarinde, Gang Ma, Yuhao Li, Boping Deng, Zhiwei Luo, Hao Liu, Mazid Md. Abdul, Carl Ward, Minchun Chen, Xiuling Fu et al. · 2021 · Nucleic Acids Research
20. Deep thermal profiling for detection of functional proteoform groups
    Nils Kurzawa, Isabelle Rose Leo, Matthias M. S. Stahl, Elena Kunold, Isabelle Becher, Anastasia Audrey, Georgios Mermelekas, Wolfgang K. Huber, André Mateus, Mikhail M. Savitski et al. · 2023 · Nature Chemical Biology
21. The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues
    Ulrich Eckhard, Giada Marino, Simon R. Abbey, Grace Tharmarajah, Ian Matthew, Christopher M. Overall · 2015 · Journal of Proteome Research
22. Transfection by cationic gemini lipids and surfactants
    Mark Damen, A. Groenen, Stijn F. M. van Dongen, Roeland J. M. Nolte, Bob J. Scholte, Martinus C. Feiters · 2018 · MedChemComm
23. Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment
    Matheus Dyczynski, Mattias Vesterlund, Ann-Charlotte Björklund, Vasilios Zachariadis, Jerry Janssen, Héctor Gallart‐Ayala, Evangelia Daskalaki, Craig Edward Wheelock, Janne Lehtiö, Dan Grandér et al. · 2018 · Cell Death and Disease
24. Comprehensive proteomics and meta-analysis of COVID-19 host response
    Haris Babačić, Wanda Christ, José Eduardo Araújo, Georgios Mermelekas, Nidhi Sharma, Janne Tynell, Marina García, Renata Varnaitė, Hilmir Ásgeirsson, Hedvig Glans et al. · 2023 · Nature Communications
25. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis
    Yana Safonova, Stefano R. Bonissone, Eugene Kurpilyansky, Ekaterina V. Starostina, Alla L Lapidus, Jeremy Stinson, Laura DePalatis, Wendy N. Sandoval, Jennie Rebecca Lill, Pavel A. Pevzner · 2015 · Bioinformatics
26. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments
    Meena Choi, Zeynep Filiz EREN DOĞU, Christopher M. Colangelo, John S. Cottrell, Michael R. Hoopmann, Eugene A. Kapp, Sangtae Kim, Henry Lam, Thomas A. Neubert, Magnus Palmblad et al. · 2016 · Journal of Proteome Research
27. Comprehensive Glycoproteomic Analysis of Chinese Hamster Ovary Cells
    Ganglong Yang, Yingwei Hu, Shisheng Sun, Chuanzi OuYang, Weiming Yang, Qiong Wang, Michael J. Betenbaugh, Hui Zhang · 2018 · Analytical Chemistry
28. Mass spectrometrists should search for all peptides, but assess only the ones they care about
    Adriaan Sticker, Lennart Martens, Lieven Clement · 2017 · Nature Methods
29. Disruption of nucleocytoplasmic trafficking as a cellular senescence driver.
    Park, Ji-Hwan, Ryu, Sung Jin, Kim, Byung Ju, Cho, Hyun-Ji, Park, Chi Hyun, Choi, Hyo Jei Claudia, Jang, Eun-Jin, Yang, Eun Jae, Hwang, Jeong-A, Woo, Seung-Hwa et al. · 2021 · Experimental & Molecular Medicine
30. Proteogenomic analysis reveals non-small cell lung cancer subtypes predicting chromosome instability, and tumor microenvironment
    Kyu Jin Song, Seunghyuk Choi, Kwoneel Kim, Hee Sang Hwang, Eunhyong Chang, Ji Soo Park, Seok Bo Shim, Seunghwan Choi, Yong Jin Heo, Dae Yul Yang et al. · 2024 · Nature Communications
31. Proteomic analysis of Toxocara canis excretory and secretory (TES) proteins
    Rita Leal Sperotto, Frederico Schmitt Kremer, Maria Elisabeth Aires Berne, Luciana Farias da Costa de Ávila, Luciano da Silva Pinto, Karina Mariante Monteiro, Karin Silva Caumo, Henrique Bunselmeyer Ferreira, Natália Pinheiro Berne, Sibele Borsuk · 2016 · Molecular and Biochemical Parasitology
32. Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data
    Bryan Stanfill, Ernesto Satoshi Nakayasu, Lisa Bramer, Allison M. Thompson, Charles K. Ansong, Therese RW Clauss, Marina A. Gritsenko, Matthew E Monroe, Ronald Moore, Danny Orton et al. · 2018 · Molecular & Cellular Proteomics
33. De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments
    Bahar Behsaz, Hosein Mohimani, Alexey A. Gurevich, Andrey D. Prjibelski, Mark F. Fisher, Fernando Vargas, Larry L. Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner · 2019 · Cell Systems
34. RUNX3 methylation drives hypoxia-induced cell proliferation and antiapoptosis in early tumorigenesis
    Sun Hee Lee, Do Young Hyeon, Soo-Hyun Yoon, Ji-Hak Jeong, Saeng-Myung Han, Ju-Won Jang, Minh Phuong Nguyen, Xin‐Zi Chi, Sojin An, Kyung-gi Hyun et al. · 2020 · Cell Death and Differentiation
35. Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma
    Xiaofang Cao, AnnSofi Sandberg, José Eduardo Araújo, Filip Cvetkovski, Erik Berglund, Lars E. Eriksson, Maria Pernemalm · 2021 · Journal of Proteome Research
36. Investigating Therapeutic Protein Structure with Diethylpyrocarbonate Labeling and Mass Spectrometry
    Nicholas B. Borotto, Yuping Zhou, Stephen R. Hollingsworth, John E. Hale, Eric M. Graban, Robert C. Vaughan, Richard W. Vachet · 2015 · Analytical Chemistry
37. Dual‐compartmental transcriptomic + proteomic analysis of a marine endosymbiosis exposed to environmental change
    Anderson B. Mayfield, Yu‐Bin Wang, Chii‐Shiarng Chen, Shu‐Hwa Chen, Chung‐Yen Lin · 2016 · Molecular Ecology
38. Translating Immunopeptidomics to Immunotherapy‐Decision‐Making for Patient and Personalized Target Selection
    Jens Fritsche, Barbara Rakitsch, Franziska Hoffgaard, Michael Römer, Heiko Schuster, Daniel Johannes Kowalewski, Martin Priemer, Vlatka Stos‐Zweifel, Helen Hörzer, Arun Satelli et al. · 2018 · PROTEOMICS
39. Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics
    Steven Verbruggen, Siegfried Gessulat, Ralf Gabriels, Anna Matsaroki, Hendrik Van de Voorde, Bernhard Küster, Sven Degroeve, Lennart Martens, Wim Van Criekinge, Mathias Wilhelm et al. · 2021 · Molecular & Cellular Proteomics
40. Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress
    Xiaolu Li, Nicholas J. Day, Song Feng, Matthew J. Gaffrey, Tai‐Du Lin, Vanessa Paurus, Matthew E Monroe, Ronald Jay Moore, Bin Yang, Ming Xian et al. · 2021 · Redox Biology
41. False discovery rate: the Achilles’ heel of proteogenomics
    Suruchi Aggarwal, Anurag Raj, Dhirendra Kumar, Debasis Dash, Amit Kumar Yadav · 2022 · Briefings in Bioinformatics
42. Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy
    Navratan Bagwan, Elena Bonzón‐Kulichenko, Enrique Calvo, Ana Victoria Lechuga‐Vieco, Spiros Michalakopoulos, Marco Trevisán-Herraz, Iakes Ezkurdia, José Manuel Rodrı́guez, Ricardo Magni, Ana Latorre-Pellicer et al. · 2018 · Cell Reports
43. Automated workflow composition in mass spectrometry-based proteomics
    Magnus Palmblad, Anna-Lena Lamprecht, Jon Ison, Veit Schwämmle · 2018 · Bioinformatics
44. IDENTIFICATION OF MHC PEPTIDES USING MASS SPECTROMETRY FOR NEOANTIGEN DISCOVERY AND CANCER VACCINE DEVELOPMENT
    Rui Chen, Kelly M. Fulton, Susan M. Twine, Jianjun Li · 2019 · Mass Spectrometry Reviews
45. Repeat-Preserving Decoy Database for False Discovery Rate Estimation in Peptide Identification
    Johra Muhammad Moosa, Shenheng Guan, Michael F. Moran, Bin Ma · 2020 · Journal of Proteome Research
46. Schistosoma haematobium Extracellular Vesicle Proteins Confer Protection in a Heterologous Model of Schistosomiasis
    Gebeyaw Getnet Mekonnen, Bemnet Tedla, Darren Pickering, Luke Becker, Lei Wang, Bin Zhan, María Elena Bottazzi, Alex C. Loukas, Javier Sotillo, Mark S. Pearson · 2020 · Vaccines
47. The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer
    Eleazer P. Resurreccion, Ka-wing Fong · 2022 · Metabolites
48. PepQuery2 democratizes public MS proteomics data for rapid peptide searching
    Bo Wen, Bing Zhang · 2023 · Nature Communications
49. Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection
    D. Tabb, Kyowon Jeong, K. Druart, Megan S. Gant, Kyle A. Brown, C. Nicora, Mo-Wei Zhou, Sneha P. Couvillion, E. Nakayasu, Janet E. Williams et al. · 2023 · Journal of Proteome Research
50. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
    Elizabeth McDaniel, Matthew Scarborough, Daniel Mulat, Xuan Lin, Pranav Sampara, Heather M. Olson, Robert Young, Elizabeth Eder, Isaac Kwame Attah, Lye Meng Markillie et al. · 2023 · The ISME Journal
51. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery
    Zhang, Bing, Bassani-Sternberg, Michal · 2023 · Journal for ImmunoTherapy of Cancer
52. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
    Xiaoxiang Huang, Ziao Gan, Haowei Cui, Tian Lan, Yansheng Liu, Étienne Caron, Wenguang Shao · 2023 · Nucleic Acids Research
53. E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer
    Gabriella C. Russo, Ashleigh J. Crawford, David Clark, Julie Cui, Ryan Carney, Michelle N. Karl, Boyang Su, Bartholomew Starich, T. Mamie Lih, Pratik Kamat et al. · 2024 · Oncogene
54. From data to knowledge: The future of multi-omics data analysis for the rhizosphere
    Richard Allen White III, Mark Borkum, Albert Rivas‐Ubach, Aivett Bilbao Pena, Jason Wendler, Sean Colby, Martina Köberl, Christer Jansson · 2017 · Rhizosphere
55. Dichomitus squalens partially tailors its molecular responses to the composition of solid wood
    Paul Daly, Sara Casado López, Mao Peng, Christopher S. Lancefield, Samuel Owen Purvine, Young‐Mo Kim, Erika Zink, Alice C. Dohnalkova, Vasanth R. Singan, Anna Lipzen et al. · 2018 · Environmental Microbiology
56. Features of Peptide Fragmentation Spectra in Single-Cell Proteomics
    Hannah Boekweg, Daisha Van Der Watt, Thy Truong, S. Madisyn Johnston, Amanda J. Guise, Edward D. Plowey, Ryan Kelly, Samuel Payne · 2021 · Journal of Proteome Research
57. Transcriptional drifts associated with environmental changes in endothelial cells
    Yalda Afshar, Feyiang Ma, Austin Quach, Anhyo Jeong, Hannah Sunshine, Vanessa M. Freitas, Yasaman Jami‐Alahmadi, Raphaël Helaers, Xinmin Li, Matteo A. Pellegrini et al. · 2023 · eLife
58. Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments
    Josué A. Rodríguez-Ramos, Mikayla Borton, Bridget B. McGivern, Garrett J. Smith, Lindsey Solden, Michael Shaffer, Rebecca A. Daly, Samuel Owen Purvine, Carrie Nicora, Elizabeth Eder et al. · 2022 · mSystems
59. Optimized Proteomics Workflow for the Detection of Small Proteins
    Jürgen Bartel, Adithi R. Varadarajan, Thomas Sura, Christian H. Ahrens, Sandra Maaß, Dörte Becher · 2020 · Journal of Proteome Research
60. Wnt-inducible Lrp6-APEX2 interacting proteins identify ESCRT machinery and Trk-fused gene as components of the Wnt signaling pathway
    Gabriele Colozza, Yasaman Jami‐Alahmadi, Alyssa Dsouza, Nydia Tejeda‐Muñoz, Lauren Veronica Albrecht, Eric Sosa, James Akira Wohlschlegel, Edward M. De Robertis · 2020 · Scientific Reports
61. Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens
    Rong Xiang, Leyao Ma, Ming‐Yu Yang, Zetian Zheng, Xiaofang Chen, Fujian Jia, Fanfan Xie, Yiming Zhou, Fuqiang Li, Kui Wu et al. · 2021 · Communications Biology
62. Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics
    Christopher Campbell, Claire Fingleton, Merve Suzan Zeden, Emilio Bueno, Laura A. Gallagher, Dhananjay D. Shinde, Jongsam Ahn, Heather M. Olson, Thomas Fillmore, Joshua Adkins et al. · 2021 · mBio
63. Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary With Species and Time as a Function of Secretome Composition
    Carolyn A. Zeiner, Samuel Owen Purvine, Erika Zink, Si Wu, Ljiljana Paša‐Tolić, Dominique L. Chaput, Cara M. Santelli, Colleen M. Hansel · 2021 · Frontiers in Microbiology
64. Identification of structural and regulatory cell-shape determinants in Haloferax volcanii
    Heather Schiller, Yirui Hong, Joshua Kouassi, Theopi Rados, Jasmin Kwak, Anthony DiLucido, Daniel Safer, Anita Marchfelder, Friedhelm Pfeiffer, Alexandre W. Bisson Filho et al. · 2024 · Nature Communications
65. Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus
    Brooke L. Whitelaw, Jan M. Strugnell, Pierre Faou, Rute R. da Fonseca, Nathan E. Hall, Mark D. Norman, Julian Finn, Ira Cooke · 2016 · Journal of Proteome Research
66. Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
    Yasset Pérez‐Riverol, Pablo A Moreno · 2019 · PROTEOMICS
67. Comparative Proteomics Analysis between Maize and Sorghum Uncovers Important Proteins and Metabolic Pathways Mediating Drought Tolerance
    Ali Elnaeim Elbasheir Ali, Lizex Hüsselmann, David L. Tabb, Ndiko Ludidi · 2023 · Life
68. ProteoStorm: An Ultrafast Metaproteomics Database Search Framework
    Doruk Beyter, Miin S. Lin, Yanbao Yu, Rembert Pieper, Vineet Bafna · 2018 · Cell Systems
69. In-depth proteomic characterization of Schistosoma haematobium: Towards the development of new tools for elimination
    Javier Sotillo, Mark S. Pearson, Luke Becker, Gebeyaw Getnet Mekonnen, Abena Serwaa Amoah, Govert J. van Dam, Paul L. A. M. Corstjens, Janice Murray, Takafira Mduluza, Francisca Mutapi et al. · 2019 · PLoS neglected tropical diseases
70. MODplus: Robust and Unrestrictive Identification of Post-Translational Modifications Using Mass Spectrometry
    Seungjin Na, Jihyung Kim, Eunok Paek · 2019 · Analytical Chemistry
71. Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa
    Maria Augusta Crivelente Horta, Nils Thieme, Yuqian Gao, Kristin Burnum-Johnson, Carrie Nicora, Marina Gritsenko, Mary S. Weir Lipton, Karthikeyan Mohanraj, Leandro José de Assis, Liangcai Lin et al. · 2019 · Frontiers in Microbiology
72. Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry
    Kyung-Cho Cho, David J. Clark, Michael Schnaubelt, Guo Ci Teo, Felipe da Veiga Leprevost, William Bocik, Emily S. Boja, Tara Hiltke, Alexey I. Nesvizhskii, Hui Zhang · 2020 · Analytical Chemistry
73. High-throughput hydrogen deuterium exchange mass spectrometry (HDX-MS) coupled with subzero-temperature ultrahigh pressure liquid chromatography (UPLC) separation for complex sample analysis
    Mulin Fang, Zhe Wang, Kellye A. Cupp‐Sutton, Thomas Welborn, Kenneth Smith, Si Wu · 2020 · Analytica Chimica Acta
74. Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay
    Lara Contu, Giuseppe Balistreri, Michal Domanski, Anne‐Christine Uldry, Oliver Mühlemann · 2021 · PLoS Pathogens
75. Neuronal Preconditioning Requires the Mitophagic Activity of C-terminus of HSC70-Interacting Protein
    Britney N. Lizama, Amy M. Palubinsky, Vineeth Andisseryparambil Raveendran, Annah M. Moore, Joel D. Federspiel, Simona G. Codreanu, Daniel C. Liebler, BethAnn McLaughlin · 2018 · Journal of Neuroscience
76. IPeak: An open source tool to combine results from multiple MS/MS search engines
    Bo Wen, Chaoqin Du, Gui-lin Li, Fawaz Ghali, Andrew R. Jones, Lukas Käll, Shaohang Xu, Ruo Zhou, Zhe Ren, Qiang Feng et al. · 2015 · PROTEOMICS
77. Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data
    Chengjian Tu, Quanhu Sheng, Jun Li, Danjun Ma, Xiaomeng Shen, Xue Wang, Yu Shyr, Zhengping Yi, Jun Qu · 2015 · Journal of Proteome Research
78. A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics
    Haixu Tang, Sujun Li, Yuzhen Ye · 2016 · PLoS Computational Biology
79. Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov.
    Miguel Ángel Martínez, Ben J. Woodcroft, J. Cesar Ignacio‐Espinoza, Ahmed A. Zayed, Caitlin M. Singleton, Joel A. Boyd, Yueh‐Fen Li, Samuel Owen Purvine, Heather Maughan, Suzanne B. Hodgkins et al. · 2018 · Systematic and Applied Microbiology
80. B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma
    Johannes Griss, Wolfgang Michael Bauer, Christine Wagner, Margarita Maurer‐Granofszky, Martin Simon, Minyi Chen, Peter Steinberger, Katharina Grabmeier‐Pfistershammer, Florian Roka, Thomas Penz et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
81. Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications
    Hao Yang, Hao Chi, Wenjing Zhou, Wenfeng Zeng, Kun He, Chao Liu, Rui-Xiang Sun, Si‐Min He · 2016 · Journal of Proteome Research
82. The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization
    Qian Dong, Yuxue Liang, Xinjian Yan, Sanford P. Markey, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Tallat H. Bukhari, Stephen E. Stein · 2018 · mAbs
83. π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing
    Xiang Zhang, Tianze Ling, Zhi Xiang Jin, Sheng Yong Xu, Zhiqiang Gao, Boyan Sun, Zijie Qiu, Jiaqi Wei, Nanqing Dong, Guangshuai Wang et al. · 2025 · Nature Communications
84. Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction
    Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P. Diamandis, George S. Charames · 2017 · Critical Reviews in Clinical Laboratory Sciences
85. Characterization of the Molecular Mechanisms Underlying Glucose Stimulated Insulin Secretion from Isolated Pancreatic β-cells Using Post-translational Modification Specific Proteomics (PTMomics)
    Taewook Kang, Pia Jensen, Honggang Huang, Gitte Lund Christensen, Nils Billestrup, Martin R. Larsen · 2017 · Molecular & Cellular Proteomics
86. Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation
    Dhirendra Kumar, Amit Kumar Yadav, Xinying Jia, Jason P. Mulvenna, Debasis Dash · 2015 · Molecular & Cellular Proteomics
87. Data‐independent acquisition proteomics methods for analyzing post‐translational modifications
    Yi Yang, Liang Qiao · 2022 · PROTEOMICS
88. Integrated analysis of global proteome, phosphoproteome and glycoproteome enables complementary interpretation of disease-related protein networks
    Jong‐Moon Park, Ji-Hwan Park, Dong‐Gi Mun, Jingi Bae, Jae Hun Jung, Seunghoon Back, Hangyeore Lee, Hokeun Kim, Hee-Jung Jung, Hark Kyun Kim et al. · 2015 · Scientific Reports
89. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer
    Sunghee Woo, Seong Won Cha, Stefano R. Bonissone, Seungjin Na, David L. Tabb, Pavel A. Pevzner, Vineet Bafna · 2015 · Journal of Proteome Research
90. Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process
    Xiaodong Feng, Liwei Li, Jianhong Zhang, Yunping Zhu, Cheng Chang, Kunxian Shu, Jie Ma · 2017 · BMC Genomics
91. Identification of Matrix Metalloproteinase-1-Suppressive Peptides in Feather Keratin Hydrolysate
    Hyeon‐Su Jin, Kyeongseop Song, Je‐Hyun Baek, Jae-Eun Lee, Da Jeong Kim, Gaewon Nam, Nam Joo Kang, Dong‐Woo Lee · 2018 · Journal of Agricultural and Food Chemistry
92. Isolation and Characterization of Multi-Protein Complexes Enriched in the K-Cl Co-transporter 2 From Brain Plasma Membranes
    Joshua L. Smalley, Georgina Kontou, Catherine Choi, Qiu Ren, David Albrecht, Krithika Abiraman, Miguel A. Rodriguez Santos, Christopher E. Bope, Tarek Z. Deeb, Paul A Davies et al. · 2020 · Frontiers in Molecular Neuroscience
93. Biosaur: An open‐source Python software for liquid chromatography–mass spectrometry peptide feature detection with ion mobility support
    Daniil A. Abdrakhimov, Julia A. Bubis, Vladimir Gorshkov, Frank Kjeldsen, Mikhail V. Gorshkov, Mark V. Ivanov · 2021 · Rapid Communications in Mass Spectrometry
94. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
    Manuel Kleiner, Angela Kouris, Marlene J. Violette, Grace D’Angelo, Yihua Liu, Abigail Korenek, Nikola Tolić, Timo T. Sachsenberg, Janine McCalder, Mary S. Weir Lipton et al. · 2023 · Microbiome
95. PIPI: PTM-Invariant Peptide Identification Using Coding Method
    Fengchao Yu, Ning Li, Weichuan Yu · 2016 · Journal of Proteome Research
96. Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*
    Jun Fan, Shyamasree Saha, Gary Barker, Kate J. Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews, Conrad Bessant · 2015 · Molecular & Cellular Proteomics
97. Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
    Jelle van Wesemael, Yann Hueber, Ewaut Kissel, Nádia Alves Campos, Rony L. Swennen, Sébastien Carpentier · 2018 · Scientific Reports
98. Identification of novel ejaculate proteins in a seed beetle and division of labour across male accessory reproductive glands
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