A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

HUPO Test Sample Working Group, Bell, Alexander W, Deutsch, Eric W, Au, Catherine E, Kearney, Robert E, Beavis, Ron, Sechi, Salvatore, Nilsson, Tommy +1 more·2009·Nature Methods
DOI 10.1038/nmeth.1333

Cited by (358)

Items 201–300 of 358

  1. Variance Component Analysis of a Multi-Site Study for the Reproducibility of Multiple Reaction Monitoring Measurements of Peptides in Human Plasma
    Jessie Q. Xia, Nell Sedransk, Xingdong Feng · 2011 · PLoS ONE
  2. A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors
    Jerome A. Staal, Yanxin Pei, Brian R. Rood · 2016 · International Journal of Molecular Sciences
  3. Quality meets quantity – quality control, data standards and repositories
    Martin Eisenacher, Anke Schnabel, Christian Stephan · 2011 · PROTEOMICS
  4. Challenges for proteomics core facilities
    Kathryn Susan Lilley, Michael J. Deery, Laurent Gatto · 2011 · PROTEOMICS
  5. Immunoreactivity of anti-gelsolin antibodies: implications for biomarker validation
    Nicole A. Haverland, Gwënaël Pottiez, Jayme L. Wiederin, Pawel S. Ciborowski · 2010 · Journal of Translational Medicine
  6. Prioritization of Biomarker Targets in Human Umbilical Cord Blood: Identification of Proteins in Infant Blood Serving as Validated Biomarkers in Adults
    Nicole Hansmeier, Tzu‐Chiao Chao, Lynn R. Goldman, Frank R. Witter, Rolf U. Halden · 2012 · Environmental Health Perspectives
  7. To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry
    Abdul-Khalek, Naim, Picciani, Mario, Shouman, Omar, Wimmer, Reinhard, Overgaard, Michael Toft, Wilhelm, Mathias, Gregersen Echers, Simon · 2025 · Journal of Proteome Research
  8. ncBAF enhances PXR-mediated transcriptional activation in the human and mouse liver
    Kiamu Kurosawa, Masataka Nakano, Itsuki Yokoseki, Mai Nagaoka, Seiya Takemoto, Yoshiyuki Sakai, Kaoru Kobayashi, Yasuhiro Kazuki, Tatsuki Fukami, Miki Nakajima · 2023 · Biochemical Pharmacology
  9. Proteomics quality and standard: From a regulatory perspective
    Qiang Gu, Li‐Rong Yu · 2013 · Journal of Proteomics
  10. Design and Application of a Data-Independent Precursor and Product Ion Repository
    Konstantinos Thalassinos, Johannes P.C. Vissers, Stefan Tenzer, Yishai Levin, J. Will Thompson, David Daniel, Darrin Mann, Mark R. DeLong, Martin Arthur Moseley, Antoine H. P. America et al. · 2012 · Journal of the American Society for Mass Spectrometry
  11. Quality will determine the future of mass spectrometry imaging in clinical laboratories: the need for standardization
    Yasemin Uçal, Abdurrahman Coşkun, Aysel Özpınar · 2019 · Expert Review of Proteomics
  12. Synthetic Data Generation for the Development of 2D Gel Electrophoresis Protein Spot Models
    Dalius Matuzevičius · 2022 · Applied Sciences
  13. Working capital management practices and financial performance of tea processing firms in Kenya.
    Isaac Kibet Kiptoo, Samuel Nduati Kariuki, Maina E. Kimani · 2017
  14. Proteomics appending a complementary dimension to precision oncotherapy
    Zhaokai Zhou, Ruiqi Zhang, Aoyang Zhou, Jinxiang Lv, Shuang Chen, Haijiao Zou, Ge Zhang, Ting Lin, Zhan Wang, Yuyuan Zhang et al. · 2024 · Computational and Structural Biotechnology Journal
  15. A quality control of proteomic experiments based on multiple isotopologous internal standards
    Adèle Bourmaud, Sébastien Gallien, Bruno Domon · 2015 · EuPA Open Proteomics
  16. A gel-free approach in vascular smooth muscle cell proteome: perspectives for a better insight into activation
    Silvia Rocchiccioli, Lorenzo Citti, Claudia Boccardi, Nadia Ucciferri, Lorena Tedeschi, Caterina Lande, Maria Giovanna Trivella, Antonella Cecchettini · 2010 · Proteome Science
  17. Genetic regulation and the impact of omics in fruit ripening
    Railson Schreinert dos Santos, Luis Willian Pacheco Arge, Savana Irribarem Costa, Natã Dienes Machado, Paulo Mello-Farias, César Valmor Rombaldi, Antônio Costa de Oliveira · 2015 · Plant Omics
  18. Laser ionization mass spectrometry in oral squamous cell carcinoma
    Seema Saraswathy, Manu Krishnan, Arun Kumar Harith, Kavita Sahai, Satish R. Iyer, Vimal Arora, Rajendra Prashad Tripathi · 2013 · Journal of Oral Pathology and Medicine
  19. How to discover new proteins—translatome profiling
    Gong Zhang, Tong Wang, Qing‐Yu He · 2014 · Science China Life Sciences
  20. Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples
    Shiyong Ma, Ranjeeta Menon, Rebecca C. Poulos, Jason W.H. Wong · 2017 · Oncotarget
  21. A multi-omics dataset of human transcriptome and proteome stable reference
    Shaohua Lu, Hong Lü, Tingkai Zheng, Huiming Yuan, Hongli Du, Youhe Gao, Yongtao Liu, Xuanzhen Pan, Wenlu Zhang, Shuying Fu et al. · 2023 · Scientific Data
  22. Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens
    Oliver Kardell, Christine von Toerne, Juliane Merl‐Pham, Ann‐Christine König, Marcel Blindert, Teresa K. Barth, Julia Mergner, Christina Ludwig, Johanna Tüshaus, Stephan Eckert et al. · 2023 · Journal of Proteome Research
  23. Selected Works in Bioinformatics
    Xuhua Xia · 2011 · InTech eBooks
  24. Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment
    Shubham Gupta, Justin Sing, Hannes Luc Röst · 2023 · Communications Biology
  25. Acetylating Tryptic Peptides Enhances b Ion Intensity in MALDI TOF/TOF: Implications in Peptide Sequencing and Identification of Proteins in an Antarctic Bacterium Pseudomonas Syringae
    Heramb M. Kulkarni, V. Ramesh, Ragampetra Srinivas, Medicharla Venkata Jagannadham · 2010 · Proteomics Insights
  26. Assessing the validity and reproducibility of genome-scale predictions
    Lauren A. Sugden, Michael Tackett, Yiannis A. Savva, William A. Thompson, Charles E. Lawrence · 2013 · Bioinformatics
  27. Reproducible Cancer Biomarker Discovery in SELDI-TOF MS Using Different Pre-Processing Algorithms
    Jinfeng Zou, Guini Hong, Xinwu Guo, Lin Zhang, Chen Yao, Jing Wang, Zheng Guo · 2011 · PLoS ONE
  28. Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice
    Anna M. Nia, Tianlong Chen, Brooke L. Barnette, Kamil Khanipov, Robert L. Ullrich, Suresh K. Bhavnani, Mark R. Emmett · 2020 · BMC Bioinformatics
  29. Oligonucleotide aptamers: emerging affinity probes for bioanalytical mass spectrometry and biomarker discovery
    Basri Gülbakan · 2015 · Analytical Methods
  30. New Strategies and Paradigm for Drug Target Discovery: A Special Focus on Infectious Diseases Tuberculosis, Malaria, Leishmaniasis, Trypanosomiasis and Gastritis
    Nageswara Rao Reddy Neelapu, Ravi C P. K. Srimath-Tirumala-Peddinti, Deepthi Nammi, Amita Martin Corolina Pasupuleti · 2014 · Infectious Disorders - Drug Targets
  31. Design considerations for proteomic reference materials
    David M. Bunk · 2010 · PROTEOMICS
  32. Big Data in Computational Toxicology: Challenges and Opportunities
    Linlin Zhao, Hao Zhu · 2018 · Computational Toxicology
  33. Decoding the impact of neighboring amino acids on ESI-MS intensity output through deep learning
    Naim Abdul-Khalek, Reinhard Wimmer, Michael Toft Overgaard, Simon Gregersen Echers · 2024 · Journal of Proteomics
  34. Spatial Bias in Antibody Microarrays May Be an Underappreciated Source of Variability
    Frédéric Normandeau, Andy Ng, Maïwenn Beaugrand, David Juncker · 2021 · ACS Sensors
  35. Prognostic Value of IGF2 mRNA-Binding Protein 3 (IGF2BP3) Intratumoral Expression in Melanoma Patients at the Time of Diagnosis: Comparative Analysis of RT-qPCR Versus Immunohistochemistry
    Beatriz Sánchez‐Sendra, Silvia Pérez‐Debén, José González, Amelia Murgui, Carlos Couceiro Monteagudo · 2022 · Cancers
  36. A comparative study of data‐dependent acquisition and data‐independent acquisition in proteomics analysis of clinical lung cancer tissues constrained by blood contamination
    Tao Su, Yi Zhong, Weibiao Zeng, Yong Zhang, Shisheng Wang, Jingqiu Cheng, Hao Yang, Yiping Wei, Meng Gong · 2021 · PROTEOMICS - CLINICAL APPLICATIONS
  37. Production of Ethanol from Hardwood
    Jay Mitchell · 2006 · DigitalCommons (California Polytechnic State University)
  38. Top-down proteomics-a near-future technique for clinical diagnosis?
    Li-Dong He, A. Rockwood, Archana M. Agarwal, Lissa C. Anderson, Chad R. Weisbrod, C. Hendrickson, A. Marshall · 2020 · Annals of Translational Medicine
  39. A report on the ESF workshop on quality control in proteomics
    Lennart Martens · 2010 · Molecular BioSystems
  40. Implementation of Clinical Phosphoproteomics and Proteomics for Personalized Medicine
    Pedro Casado, Maruan Hijazi, Henry Gerdes, Pedro R. Cutillas · 2021 · Methods in molecular biology
  41. A flexible statistical model for alignment of label-free proteomics data - incorporating ion mobility and product ion information
    Ashlee M. Benjamin, J. Will Thompson, Erik J. Soderblom, Scott J. Geromanos, Ricardo Henao, Virginia B. Kraus, Martin Arthur Moseley, Joseph E. Lucas · 2013 · BMC Bioinformatics
  42. Gene expression as a quantitative trait: what about translation?
    Constantin Polychronakos · 2012 · Journal of Medical Genetics
  43. Challenges Facing Complete Human Proteome Analysis
    Mio Iwasaki, Yasushi Ishihama · 2014 · Chromatography
  44. Epigenetics to proteomics: From yeast to brain
    Purnima Bhargava · 2009 · PROTEOMICS
  45. Proteomics and Precision Medicine
    Chen Ding, Zhaoyu Qin, Yan Li, Wenhao Shi, Lingling Li, Dongdong Zhan, Wenjun Yang · 2019 · Small Methods
  46. Design and Initial Characterization of the SC-200 Proteomics Standard Mixture
    Andrew Bauman, Roger Higdon, Sean Rapson, Brenton Loiue, Jason M. Hogan, Robin Stacy, Alberto J. Napuli, Wenjin Guo, Wesley C. Van Voorhis A, Jared C. Roach et al. · 2011 · OMICS A Journal of Integrative Biology
  47. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
    Natalie Stanford, Martin Scharm, Paul D. Dobson, Martin Golebiewski, Michael Hucka, Varun B. Kothamachu, David Phillip Nickerson, Stuart Owen, Jürgen Pahle, Ulrike Wittig et al. · 2019 · Methods in molecular biology
  48. Mining proteomic data for biomedical research
    Laura L. Elo, Benno Schwikowski · 2011 · Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery
  49. Quantum chemical mass spectrometry: Ab initio study of b 2 ‐ion formation mechanisms for the singly protonated Gln‐His‐Ser tripeptide
    Julie Cautereels, Julien Giribaldi, Christine Enjalbal, Frank Blockhuys · 2020 · Rapid Communications in Mass Spectrometry
  50. New advances in quantitative proteomics research and current applications in asthma
    Yanting Lan, Xiaoyin Zeng, Jing Xiao, Longbo Hu, Long Tan, Mengdi Liang, Xufei Wang, Shaohua Lu, Fei Long, Tao Peng · 2021 · Expert Review of Proteomics
  51. The Role of Proteomics in the Study of Kidney Diseases and in the Development of Diagnostic Tools
    Uwe Christians, Stephanie McCrery, Jost Klawitter, Jelena Klawitter · 2010 · Elsevier eBooks
  52. Editorial: From Data to Results
    Ruedi H. Aebersold · 2011 · Molecular & Cellular Proteomics
  53. Fragmentation Characteristics and Utility of Immonium Ions for Peptide Identification by MALDI-TOF/TOF-Mass Spectrometry
    Wang Yong, Shui-Ming Li, Manwen He · 2014 · Chinese Journal of Analytical Chemistry
  54. Consistency of a two clinical site sample collection: A proteomics study
    Cedric Wiesner, Charles H. Hannum, Karen L. Reckamp, Robert A. Figlin, Robert B. DuBridge, Sushmita Mimi Roy, Shanhua Lin, Christopher H. Becker, Ted Jones, Jordan Hiller et al. · 2010 · PROTEOMICS - CLINICAL APPLICATIONS
  55. Scaling Proteome-Wide Reactions of Activity-Based Probes
    Song Li, Pamela Ann Diego, Bekim Bajrami, Santosh K. Keshipeddy, Ying‐Wai Lam, Bin Deng, Vahid Farrokhi, Adam J. McShane, Reza Nemati, Amy R. Howell et al. · 2017 · Analytical Chemistry
  56. QCMS2 as a new method for providing insight into peptide fragmentation: The influence of the side‐chain and inter–side‐chain interactions
    Julie Cautereels, Nils Van Hee, Sneha Chatterjee, Christian Van Alsenoy, Filip Lemière, Frank Blockhuys · 2019 · Journal of Mass Spectrometry
  57. Detection of Doping with Recombinant Human Growth Hormone
    Chun‐Ting He, Moutian Wu · 2009 · Bioanalysis
  58. Analytical Proteomics: An emerging field?
    Hugo Miguel Santos, Carlos Lodeiro, José Luís Capelo · 2010 · Journal of Proteomics
  59. MiS-MALDI: microgel-selected detection ofproteinbiomarkers by MALDI-ToFmass spectrometry
    Eleonora Cerasoli, Paulina D. Rakowska, Adrian M. Horgan, Jascindra Ravi, Melanie Bradley, Brian Vincent, Maxim G. Ryadnov · 2010 · Molecular BioSystems
  60. Publishing confirming and non-confirming data
    Bruce Alberts, Alexander Kamb · 2016 · F1000Research
  61. Power analysis of transcriptome-wide association study: implications for practical protocol choice
    Chen Cao, Bowei Ding, Qing Li, Devin Kwok, Jingjing Wu, Quan Long · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  62. Reproducible Computational Workflows with Continuous Analysis
    Beaulieu-Jones, Brett K., Greene, Casey S. · 2016
  63. Discovery of Amphoteric Fingerprints of Amino Acids With Field-Effect Transistors
    Naveen Kumar, Rakshita Pritam Singh Dhar, Janwa El‐Maiss, Vihar Georgiev, César Pascual García · 2024 · IEEE Access
  64. The Moscow HUPO Human Proteome Project Workshop
    Alexander I. Archakov, John J.M. Bergeron, Alexander Khlunov, А.В. Лисица, Young‐Ki Paik · 2009 · Molecular & Cellular Proteomics
  65. Statistical Assessment of QC Metrics on Raw LC-MS/MS Data
    Xia Wang · 2016 · Methods in molecular biology
  66. The Role of Proteomics in the Study of Kidney Diseases and in the Development of Diagnostic Tools
    Uwe Christians, Jelena Klawitter, Jacek Klepacki, Jelena Klawitter · 2016 · Elsevier eBooks
  67. Proteomics of Toxoplasma gondii
    Jonathan M. Wastling, Dong Xia · 2013 · Elsevier eBooks
  68. Discovery of Amino Acid fingerprints transducing their amphoteric signatures by field-effect transistors
    Naveen Kumar, Rakshita Pritam Singh Dhar, César Pascual García, Vihar Georgiev · 2022 · ChemRxiv
  69. Lithium in felsic magmas: a volcanological perspective
    Maylis Dupont de Dinechin, Hélène Balcone‐Boissard, Caroline Martel, Monika K. Rusiecka · 2023 · Frontiers in Earth Science
  70. Limitation of predictive 2‐ D liquid chromatography in reducing the database search space in shotgun proteomics: In silico studies
    Eugene V. Moskovets, Anton A. Goloborodko, Alexander V. Gorshkov, Mikhail V. Gorshkov · 2012 · Journal of Separation Science
  71. Mass Spectral Analysis of Synthetic Peptides: Implications in Proteomics
    Medicharla Venkata Jagannadham, Pratap Gayatri, Taniya Mary Binny, Bathisaran Raman, Duvvuri Butchi Kameshwari, Ramakrishnan Nagaraj · 2020 · Journal of Biomolecular Techniques JBT
  72. Precision Medicine in Asthma Therapy
    Stefania Principe, Susanne J. H. Vijverberg, Mahmoud I. Abdel‐Aziz, Nicola Scichilone, Anke H. Maitland‐van der Zee · 2022 · Handbook of experimental pharmacology
  73. Use of Proteomics Tools to Investigate Protein Expression in Azospirillum brasilense
    Gurusahai Khalsa-Moyers · 2010
  74. Slow Off-Rate Modified Aptamer Arrays for Biomarker Discovery and Diagnostic Applications
    Jeffrey J. Walker, Edward N. Brody, Larry Gold · 2012 · Springer eBooks
  75. Sperm Proteomics: Thinking Outside the Collision Cell
    Senga K. Oxenham · 2010 · Journal of Andrology
  76. The Advent of Mass Spectrometry-Based Proteomics in Systems Biology Research
    Peter Blattmann, Ruedi H. Aebersold · 2015 · Elsevier eBooks
  77. Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines
    Claudio Iacobucci, Christine Piotrowski, Ruedi H. Aebersold, Bruno C. Amaral, Philip Andrews, Christoph H. Borchers, Nicolas I. Brodie, James E. Bruce, Stéphane Chaignepain, Juan D. Chavez et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Non-target Identification. Chromatography and Spectrometry
    Boris L. Milman · 2010 · Springer eBooks
  79. Altered Mascot search results by changing the m/z range of MS/MS spectra: analysis and potential applications
    Thomas Köcher, Peter Pichler, Michael Mazanek, Remco Swart, Karl Mechtler · 2010 · Analytical and Bioanalytical Chemistry
  80. QSAR facilitating safety evaluation and risk assessment
    Rebecca L. Kusko, Huixiao Hong · 2023 · Elsevier eBooks
  81. Role of proteomics in nutrigenomics and nutrigenetics
    Martin Kussmann · 2009 · Expert Review of Proteomics
  82. FPGA-Accelerated Isotope Pattern Calculator for Use in Simulated Mass Spectrometry Peptide and Protein Chemistry
    Carlo Pascoe, David Box, Herman X. Lam, Alan D. George · 2012 · Symposium on Application Accelerators in High-Performance Computing (SAAHPC)
  83. Using semantic workflows to disseminate best practices and accelerate discoveries in multi-omic data analysis
    Yolanda Gil, Shannon K. McWeeney, Christopher E. Mason · 2013 · National Conference on Artificial Intelligence
  84. Characterization of acetylated histidine b 1 -ion structure: A competition between oxazolone and side chain imidazole moiety
    Kranthikumar Yadav, J. Laxmikanth Rao, Ragampeta Srinivas, Ramakrishnan Nagaraj, Medicharla Venkata Jagannadham · 2018 · European Journal of Mass Spectrometry
  85. Impact of Whole Genome Protein Analysis on Gene Discovery of Disease Models
    Sheng Zhang, Yong Yang, Theodore W. Thannhauser · 2011 · Wiley eBooks
  86. Environmental Metabolomics
    Daniel W. Bearden · 1996 · Encyclopedia of Magnetic Resonance
  87. Discovery of Amino Acid fingerprints transducing their amphoteric signatures by field-effect transistors
    César Pascual García, Naveen Kumar, Rakshita Pritam Singh Dhar, Vihar Georgiev · 2022 · Research Square
  88. Rethinking analytical approaches to nanoparticles protein corona heterogeneity: a call for innovation
    Ali Akbar Ashkarran · 2025 · Nanomedicine
  89. Adding a spatial dimension to the proteome
    Kay Grünewald · 2009 · Nature Methods
  90. Evaluation of empirical rule of linearly correlated peptide selection (ERLPS) for proteotypic peptide‐based quantitative proteomics
    Kehui Liu, Jiyang Zhang, Bin Fu, Hongwei Xie, Yingchun Wang, Xiaohong Qian · 2014 · PROTEOMICS
  91. Report on the Barbados Workshop
    Sylvie Ouellette, Alexander W. Bell, Jan van Oostrum, John J.M. Bergeron · 2009 · Molecular & Cellular Proteomics
  92. System-driven Research: Legitimate Experimental Design for Biological/biomedical Research
    Eve A. Roberts · 2015 · DalSpace (Dalhousie University)
  93. Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms
    Congcong Lu, Tina Glisovic‐Aplenc, Kathrin Maria Bernt, Kevin A. Nestler, Joseph Cesare, Lusha Cao, Hyoungjoo Lee, Hossein Fazelinia, Asif Chinwalla, Yang Xu et al. · 2021 · Journal of Proteome Research
  94. 怎样发现未知蛋白质——翻译组测序
    庆瑜 何, 通 王, 弓 张 · 2014 · Scientia Sinica Vitae
  95. Transcriptomics and Proteomics
    Jeremy J. Ramsden · 2023 · Computational biology
  96. Sequence Protein Identification by Randomized Sequence Database and Transcriptome Mass Spectrometry (SPIDER-TMS): From Manual to Automatic Application of a ‘ de Novo Sequencing’ Approach
    Raffaella Pascale, Gerarda Grossi, Gabriele Cruciani, Giansalvatore Mecca, Donatello Santoro, Renzo Sarli Calace, Patrizia Falabella, Giuliana Lo Bianco · 2016 · European Journal of Mass Spectrometry
  97. Multi-laboratory analysis of the variability of shipped samples for proteomics following non-cooled international transport
    Pascal Steffen, Christoph Krisp, Yi Wang, Pengyuan Yang, Mark P. Molloy, Hartmut Schlüter · 2018 · Analytical Biochemistry
  98. High-resolution antibody array analysis of proteins from primary human keratinocytes and leukocytes
    Daniel de la Rosa Carrillo, Krzysztof Sikorski, Denis Khnykin, Weiwei Wu, Fridtjof Lund‐Johansen · 2018 · PLoS ONE
  99. RT-Tranformer: Retention Time Predictionfor Metabolite Annotation to Assist inMetabolite Identification
    jun xue, Bingyi Wang, Weihua Li · 2023 · ChemRxiv
  100. Proteomic Approaches to Study Immunity in Infection
    Gustavo A. de Souza, Harald Gotten Wiker · 2010 · Methods in microbiology