ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter

View Author Information
Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
Department of Communication Engineering, National Central University, 300 Jung-da Road, Jung-li City, Taoyuan 32001, Taiwan
*Tel: +1 (858) 784-8862. Fax: +1 (858) 784-8883. E-mail: [email protected]
Cite this: Anal. Chem. 2015, 87, 22, 11361–11367
Publication Date (Web):October 26, 2015
Copyright © 2015 American Chemical Society

    Article Views





    Other access options


    Abstract Image

    Extraction of data from the proprietary RAW files generated by Thermo Fisher mass spectrometers is the primary step for subsequent data analysis. High resolution and high mass accuracy data obtained by state-of-the-art mass spectrometers (e.g., Orbitraps) can significantly improve both peptide/protein identification and quantification. We developed RawConverter, a stand-alone software tool, to improve data extraction on RAW files from high-resolution Thermo Fisher mass spectrometers. RawConverter extracts full scan and MSn data from RAW files like its predecessor RawXtract; most importantly, it associates the accurate precursor mass-to-charge (m/z) value with the tandem mass spectrum. RawConverter accepts RAW data generated by either data-dependent acquisition (DDA) or data-independent acquisition (DIA). It generates output into MS1/MS2/MS3, MGF, or mzXML file formats, which fulfills the format requirements for most data identification and quantification tools. Using the tandem mass spectra extracted by RawConverter with corrected m/z values, 32.8%, 27.1%, and 84.1%, peptide spectra matches (PSMs) produce 17.4% (13.0%), 14.4% (11.5%), and 45.7% (36.2%) more peptide (protein) identifications than ProteoWizard, pXtract, and RawXtract, respectively. RawConverter is implemented in C# and is freely accessible at

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.


    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Cited By

    This article is cited by 192 publications.

    1. Lauren Fields, Nhu Q. Vu, Tina C. Dang, Hsu-Ching Yen, Min Ma, Wenxin Wu, Mitchell Gray, Lingjun Li. EndoGenius: Optimized Neuropeptide Identification from Mass Spectrometry Datasets. Journal of Proteome Research 2024, Article ASAP.
    2. Ching Tarn, Yu-Zhuo Wu, Kai-Fei Wang. PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors. Journal of Proteome Research 2024, 23 (2) , 574-584.
    3. Madeline Isom, Eden P. Go, Heather Desaire. Enabling Lipidomic Biomarker Studies for Protected Populations by Combining Noninvasive Fingerprint Sampling with MS Analysis and Machine Learning. Journal of Proteome Research 2024, Article ASAP.
    4. Antonio F. M. Pinto, Jolene K. Diedrich, James J. Moresco, John R. Yates, III. Differential Precipitation of Proteins: A Simple Protein Fractionation Strategy to Gain Biological Insights with Proteomics. Journal of the American Society for Mass Spectrometry 2023, 34 (9) , 2025-2033.
    5. Huan Tang, Guogeng Jia, Jinjun Gao, Fan Yang, Ziyao Tang, Yuan Liu, Chu Wang. Quantifying Turnover Dynamics of Selenoproteome by Isotopic Perturbation. Analytical Chemistry 2022, 94 (27) , 9636-9647.
    6. Frederico G. Pinto, Iqbal Mahmud, Vanessa Y. Rubio, Ademar Domingos Viagem Máquina, Anízia Fausta Furtado Durans, Waldomiro Borges Neto, Timothy J. Garrett. Data-Driven Soft Independent Modeling of Class Analogy in Paper Spray Ionization Mass Spectrometry-Based Metabolomics for Rapid Detection of Prostate Cancer. Analytical Chemistry 2022, 94 (4) , 1925-1931.
    7. Sabyasachi Baboo, Jolene K. Diedrich, Salvador Martínez-Bartolomé, Xiaoning Wang, Torben Schiffner, Bettina Groschel, William R. Schief, James C. Paulson, John R. Yates, III. DeGlyPHER: An Ultrasensitive Method for the Analysis of Viral Spike N-Glycoforms. Analytical Chemistry 2021, 93 (40) , 13651-13657.
    8. Xiaobo Tian, Marcel P. de Vries, Hjalmar P. Permentier, Rainer Bischoff. The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode. Analytical Chemistry 2021, 93 (23) , 8196-8202.
    9. Casimir Bamberger, Sandra Pankow, Salvador Martínez-Bartolomé, Michelle Ma, Jolene Diedrich, Robert A. Rissman, John R. Yates, III. Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer’s Disease. Journal of Proteome Research 2021, 20 (5) , 2762-2771.
    10. Joshua J. Hamey, Amy Nguyen, Marc R. Wilkins. Discovery of Arginine Methylation, Phosphorylation, and Their Co-occurrence in Condensate-Associated Proteins in Saccharomyces cerevisiae. Journal of Proteome Research 2021, 20 (5) , 2420-2434.
    11. Elizaveta M. Solovyeva, Sergei A. Moshkovskii, Mikhail V. Gorshkov. Identification-Free Control over the Precursor Isotopic Mass Misassignment in Orbitrap-Based Proteomics. Journal of the American Society for Mass Spectrometry 2021, 32 (1) , 218-224.
    12. Ramin Rad, Jiaming Li, Julian Mintseris, Jeremy O’Connell, Steven P. Gygi, Devin K. Schweppe. Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage. Journal of Proteome Research 2021, 20 (1) , 591-598.
    13. Xiaobo Tian, Marcel P. de Vries, Hjalmar P. Permentier, Rainer Bischoff. A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes. Analytical Chemistry 2020, 92 (24) , 16149-16157.
    14. Dong-Gi Mun, Santosh Renuse, Mayank Saraswat, Anil Madugundu, Savita Udainiya, Hokeun Kim, Sung-Kyu Robin Park, Hui Zhao, Raja Sekhar Nirujogi, Chan Hyun Na, Nagarajan Kannan, John R. Yates, III, Sang-Won Lee, Akhilesh Pandey. PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies. Analytical Chemistry 2020, 92 (21) , 14466-14475.
    15. Xiaobo Tian, Marcel P. de Vries, Hjalmar P. Permentier, Rainer Bischoff. A Collision-Induced Dissociation Cleavable Isobaric Tag for Peptide Fragment Ion-Based Quantification in Proteomics. Journal of Proteome Research 2020, 19 (9) , 3817-3824.
    16. Carolina Fernández-Costa, Salvador Martínez-Bartolomé, Daniel B. McClatchy, Anthony J. Saviola, Nam-Kyung Yu, John R. Yates, III. Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results. Journal of Proteome Research 2020, 19 (8) , 3153-3161.
    17. Devin K. Schweppe, Jimmy K. Eng, Qing Yu, Derek Bailey, Ramin Rad, Jose Navarrete-Perea, Edward L. Huttlin, Brian K. Erickson, Joao A. Paulo, Steven P. Gygi. Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. Journal of Proteome Research 2020, 19 (5) , 2026-2034.
    18. Maria K. Andersen, Sebastian Krossa, Therese S. Høiem, Rebecca Buchholz, Britt S. R. Claes, Benjamin Balluff, Shane R. Ellis, Elin Richardsen, Helena Bertilsson, Ron M. A. Heeren, Tone F. Bathen, Uwe Karst, Guro F. Giskeødegård, May-Britt Tessem. Simultaneous Detection of Zinc and Its Pathway Metabolites Using MALDI MS Imaging of Prostate Tissue. Analytical Chemistry 2020, 92 (4) , 3171-3179.
    19. Vanessa Y. Rubio, Joy G. Cagmat, Gary P. Wang, Richard A. Yost, Timothy J. Garrett. Analysis of Tryptophan Metabolites in Serum Using Wide-Isolation Strategies for UHPLC–HRMS/MS. Analytical Chemistry 2020, 92 (3) , 2550-2557.
    20. Carolina Fernández-Costa, Salvador Martínez-Bartolomé, Daniel McClatchy, John R. Yates, III. Improving Proteomics Data Reproducibility with a Dual-Search Strategy. Analytical Chemistry 2020, 92 (2) , 1697-1701.
    21. Soo Youn Lee, Heeyoun Hwang, Young-Mook Kang, Hyejin Kim, Dong Geun Kim, Ji Eun Jeong, Jin Young Kim, Jong Shin Yoo. SAAVpedia: Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation. Journal of Proteome Research 2019, 18 (12) , 4133-4142.
    22. Benjamin D. Stein, Sébastien Herzig, Salvador Martínez-Bartolomé, Mathieu Lavallée-Adam, Reuben J. Shaw, John R. Yates, III. Comparison of CRISPR Genomic Tagging for Affinity Purification and Endogenous Immunoprecipitation Coupled with Quantitative Mass Spectrometry To Identify the Dynamic AMPKα2 Interactome. Journal of Proteome Research 2019, 18 (10) , 3703-3714.
    23. Carrie Miranda, Quanle Xu, Nathan W. Oehrle, Nazrul Islam, Wesley M. Garrett, Savithiry S. Natarajan, Jason D. Gillman, Hari B. Krishnan. Proteomic Comparison of Three Extraction Methods Reveals the Abundance of Protease Inhibitors in the Seeds of Grass Pea, a Unique Orphan Legume. Journal of Agricultural and Food Chemistry 2019, 67 (37) , 10296-10305.
    24. Jie Luo, Jacob Bassett, Jeff Ranish. Identification of Cross-linked Peptides Using Isotopomeric Cross-linkers. Journal of the American Society for Mass Spectrometry 2019, 30 (9) , 1643-1653.
    25. Michael Götze, Claudio Iacobucci, Christian H. Ihling, Andrea Sinz. A Simple Cross-Linking/Mass Spectrometry Workflow for Studying System-wide Protein Interactions. Analytical Chemistry 2019, 91 (15) , 10236-10244.
    26. Dong-Gi Mun, Dowoon Nam, Hokeun Kim, Akhilesh Pandey, Sang-Won Lee. Accurate Precursor Mass Assignment Improves Peptide Identification in Data-Independent Acquisition Mass Spectrometry. Analytical Chemistry 2019, 91 (13) , 8453-8460.
    27. Casey A. Chamberlain, Vanessa Y. Rubio, Timothy J. Garrett. Strain-Level Differentiation of Bacteria by Paper Spray Ionization Mass Spectrometry. Analytical Chemistry 2019, 91 (8) , 4964-4968.
    28. Paul D. Veith, Michelle D. Glew, Dhana G. Gorasia, Dina Chen, Neil M. O’Brien-Simpson, Eric C. Reynolds. Localization of Outer Membrane Proteins in Treponema denticola by Quantitative Proteome Analyses of Outer Membrane Vesicles and Cellular Fractions. Journal of Proteome Research 2019, 18 (4) , 1567-1581.
    29. Daniel B. McClatchy, Nam-Kyung Yu, Salvador Martínez-Bartolomé, Reesha Patel, Alexander R. Pelletier, Mathieu Lavalle-Adam, Susan B. Powell, Marisa Roberto, John R. Yates. Structural Analysis of Hippocampal Kinase Signal Transduction. ACS Chemical Neuroscience 2018, 9 (12) , 3072-3085.
    30. Joshua J. Hamey, Ryan J. Separovich, Marc R. Wilkins. MT-MAMS: Protein Methyltransferase Motif Analysis by Mass Spectrometry. Journal of Proteome Research 2018, 17 (10) , 3485-3491.
    31. Christoph U. Schräder, Shaun Moore, Aaron A. Goodarzi, David C. Schriemer. Lysine Propionylation To Boost Sequence Coverage and Enable a “Silent SILAC” Strategy for Relative Protein Quantification. Analytical Chemistry 2018, 90 (15) , 9077-9084.
    32. Zuo-Fei Yuan, Simone Sidoli, Dylan M. Marchione, Johayra Simithy, Kevin A. Janssen, Mary R. Szurgot, Benjamin A. Garcia. EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. Journal of Proteome Research 2018, 17 (7) , 2533-2541.
    33. Heeyoun Hwang, Gun Wook Park, Ji Yeong Park, Hyun Kyoung Lee, Ju Yeon Lee, Ji Eun Jeong, Sung-Kyu Robin Park, John R. Yates, III, Kyung-Hoon Kwon, Young Mok Park, Hyoung-Joo Lee, Young-Ki Paik, Jin Young Kim, and Jong Shin Yoo . Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases. Journal of Proteome Research 2017, 16 (12) , 4425-4434.
    34. Matthieu David, Guillaume Fertin, Hélène Rogniaux, and Dominique Tessier . SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes. Journal of Proteome Research 2017, 16 (8) , 3030-3038.
    35. Thomas N. Lawson, Ralf J. M. Weber, Martin R. Jones, Andrew J. Chetwynd, Giovanny Rodrı́guez-Blanco, Riccardo Di Guida, Mark R. Viant, and Warwick B. Dunn . msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics. Analytical Chemistry 2017, 89 (4) , 2432-2439.
    36. Ju-Wan Kim, Heeyoun Hwang, Jong-Sun Lim, Hyoung-Joo Lee, Seul-Ki Jeong, Jong Shin Yoo, and Young-Ki Paik . gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides. Journal of Proteome Research 2016, 15 (11) , 4116-4125.
    37. Dominique Tessier, Virginie Lollier, Colette Larré, and Hélène Rogniaux . Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines. Journal of Proteome Research 2016, 15 (10) , 3481-3488.
    38. Leonie F. Schrӧder, Wesley Peng, Ge Gao, Yvette C. Wong, Michael Schwake, Dimitri Krainc. VPS13C regulates phospho-Rab10-mediated lysosomal function in human dopaminergic neurons. Journal of Cell Biology 2024, 223 (5)
    39. Andrea L. Rocha, Victor Pai, Guy Perkins, Tina Chang, Jiao Ma, Qian Chu, Joan M. Vaughan, Jolene K. Diedrich, Mark H. Ellisman, Alan Saghatelian. An inner mitochondrial membrane microprotein from the SLC35A4 upstream ORF regulates cellular metabolism. Journal of Molecular Biology 2024, 106 , 168559.
    40. Benjamin M. Lewis, Chae Yun Cho, Hsuan-Lin Her, Orel Mizrahi, Tony Hunter, Gene W. Yeo. LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function. RNA 2024, 30 (3) , 223-239.
    41. Travis Nemkov, Francesca Cendali, Monika Dzieciatkowska, Daniel Stephenson, Kirk C. Hansen, Catherine M. Jankowski, Angelo D’Alessandro, Ryan J. Marker. A Multiomics Assessment of Preoperative Exercise in Pancreatic Cancer Survivors Receiving Neoadjuvant Therapy: A Case Series. Pathophysiology 2024, 31 (1) , 166-182.
    42. Tingpeng Yang, Tianze Ling, Boyan Sun, Zhendong Liang, Fan Xu, Xiansong Huang, Linhai Xie, Yonghong He, Leyuan Li, Fuchu He, Yu Wang, Cheng Chang. Introducing π-HelixNovo for practical large-scale de novo peptide sequencing. Briefings in Bioinformatics 2024, 25 (2)
    43. Erik J. Quiroz, Seongjae Kim, Lalit K. Gautam, Zea Borok, Christopher Kintner, Amy L. Ryan. RBL2 represses the transcriptional activity of Multicilin to inhibit multiciliogenesis. Cell Death & Disease 2024, 15 (1)
    44. Wenxin Wu, Lauren Fields, Kellen DeLaney, Amanda R. Buchberger, Lingjun Li. An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome. 2024, 255-289.
    45. Francesco Greco, Luca Fidia Pardini, Asia Botto, Liam Andrew McDonnell. Low-melting point agarose as embedding medium for MALDI mass spectrometry imaging and laser-capture microdissection-based proteomics. Scientific Reports 2023, 13 (1)
    46. Kaisa E. Happonen, Patrick G. Burrola, Greg Lemke. Regulation of brain endothelial cell physiology by the TAM receptor tyrosine kinase Mer. Communications Biology 2023, 6 (1)
    47. Corina E. Antal, Tae Gyu Oh, Stefan Aigner, En-Ching Luo, Brian A. Yee, Tania Campos, Hervé Tiriac, Katherine L. Rothamel, Zhang Cheng, Henry Jiao, Allen Wang, Nasun Hah, Elizabeth Lenkiewicz, Jan C. Lumibao, Morgan L. Truitt, Gabriela Estepa, Ester Banayo, Senada Bashi, Edgar Esparza, Ruben M. Munoz, Jolene K. Diedrich, Nicole M. Sodir, Jasmine R. Mueller, Cory R. Fraser, Erkut Borazanci, David Propper, Daniel D. Von Hoff, Christopher Liddle, Ruth T. Yu, Annette R. Atkins, Haiyong Han, Andrew M. Lowy, Michael T. Barrett, Dannielle D. Engle, Gerard I. Evan, Gene W. Yeo, Michael Downes, Ronald M. Evans. A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. Nature Communications 2023, 14 (1)
    48. Pingping Song, Wesley Peng, Veronique Sauve, Rayan Fakih, Zhong Xie, Daniel Ysselstein, Talia Krainc, Yvette C. Wong, Niccolò E. Mencacci, Jeffrey N. Savas, D. James Surmeier, Kalle Gehring, Dimitri Krainc. Parkinson’s disease-linked parkin mutation disrupts recycling of synaptic vesicles in human dopaminergic neurons. Neuron 2023, 111 (23) , 3775-3788.e7.
    49. Andreea Manole, Thomas Wong, Amanda Rhee, Sammy Novak, Shao-Ming Chin, Katya Tsimring, Andres Paucar, April Williams, Traci Fang Newmeyer, Simon T. Schafer, Idan Rosh, Susmita Kaushik, Rene Hoffman, Songjie Chen, Guangwen Wang, Michael Snyder, Ana Maria Cuervo, Leo Andrade, Uri Manor, Kevin Lee, Jeffrey R. Jones, Shani Stern, Maria C. Marchetto, Fred H. Gage. NGLY1 mutations cause protein aggregation in human neurons. Cell Reports 2023, 42 (12) , 113466.
    50. Wellington J. Rody, Nathan G. Reuter, Shannen E. Brooks, Lina I. Hammadi, Macey L. Martin, Joy G. Cagmat, Timothy J. Garrett, L. Shannon Holliday. Metabolomic signatures distinguish extracellular vesicles from osteoclasts and odontoclasts. Orthodontics & Craniofacial Research 2023, 26 (4) , 632-641.
    51. Yan Ma, Yang Cao, Xiaocui Song, Weichen Xu, Zichen Luo, Jinjun Shan, Jingjie Zhou. Integration of semi-empirical MS/MS library with characteristic features for the annotation of novel amino acid-conjugated bile acids. The Analyst 2023, 148 (21) , 5380-5389.
    52. Konstantinos Tsioras, Kevin C. Smith, Seby L. Edassery, Mehraveh Garjani, Yichen Li, Chloe Williams, Elizabeth D. McKenna, Wenxuan Guo, Anika P. Wilen, Timothy J. Hark, Stefan L. Marklund, Lyle W. Ostrow, Jonathan D. Gilthorpe, Justin K. Ichida, Robert G. Kalb, Jeffrey N. Savas, Evangelos Kiskinis. Analysis of proteome-wide degradation dynamics in ALS SOD1 iPSC-derived patient neurons reveals disrupted VCP homeostasis. Cell Reports 2023, 42 (10) , 113160.
    53. Ukrae H Cho, Martin W Hetzer. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife 2023, 12
    54. Ukrae H Cho, Martin W Hetzer. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife 2023, 12
    55. Abir Mukherjee, Divya Bezwada, Francesco Greco, Malu Zandbergen, Tong Shen, Chun-Yi Chiang, Medine Tasdemir, Johannes Fahrmann, Dmitry Grapov, Michael R. La Frano, Hieu S. Vu, Brandon Faubert, John W. Newman, Liam A. McDonnell, Luigi Nezi, Oliver Fiehn, Ralph J. DeBerardinis, Ernst Lengyel. Adipocytes reprogram cancer cell metabolism by diverting glucose towards glycerol-3-phosphate thereby promoting metastasis. Nature Metabolism 2023, 5 (9) , 1563-1577.
    56. Hongliang Wang, Yubei Wang, Tian Sang, Zhen Lin, Rongxia Li, Weiwei Ren, Xin Shen, Bing Zhao, Xiao Wang, Xuebin Zhang, Shaoqun Zhou, Shaojun Dai, Honghong Hu, Chun‐Peng Song, Pengcheng Wang. Cell type‐specific proteomics uncovers a RAF15‐SnRK2.6/OST1 kinase cascade in guard cells. Journal of Integrative Plant Biology 2023, 65 (9) , 2122-2137.
    57. Li-Chun Cheng, Xi Zhang, Sabyasachi Baboo, Julie A Nguyen, Salvador Martinez-Bartolomé, Esther Loose, Jolene Diedrich, John R Yates, Larry Gerace. Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. Life Science Alliance 2023, 6 (9) , e202301998.
    58. Alexander Eckersley, Mychel RPT Morais, Matiss Ozols, Rachel Lennon. Peptide location fingerprinting identifies structural alterations within basement membrane components in ageing kidney. Matrix Biology 2023, 121 , 167-178.
    59. Erik A. Koppes, Marie A. Johnson, James J. Moresco, Patrizia Luppi, Dale W. Lewis, Donna B. Stolz, Jolene K. Diedrich, John R. Yates, Ronald C. Wek, Simon C. Watkins, Susanne M. Gollin, Hyun Jung Park, Peter Drain, Robert D. Nicholls, . Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones. PLOS Genetics 2023, 19 (4) , e1010710.
    60. Chang-ki Oh, Tomohiro Nakamura, Nathan Beutler, Xu Zhang, Juan Piña-Crespo, Maria Talantova, Swagata Ghatak, Dorit Trudler, Lauren N. Carnevale, Scott R. McKercher, Malina A. Bakowski, Jolene K. Diedrich, Amanda J. Roberts, Ashley K. Woods, Victor Chi, Anil K. Gupta, Mia A. Rosenfeld, Fiona L. Kearns, Lorenzo Casalino, Namir Shaabani, Hejun Liu, Ian A. Wilson, Rommie E. Amaro, Dennis R. Burton, John R. Yates, Cyrus Becker, Thomas F. Rogers, Arnab K. Chatterjee, Stuart A. Lipton. Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nature Chemical Biology 2023, 19 (3) , 275-283.
    61. Sabyasachi Baboo, Jolene K. Diedrich, Salvador Martínez-Bartolomé, Xiaoning Wang, Torben Schiffner, Bettina Groschel, William R. Schief, James C. Paulson, John R. Yates. DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins. 2023, 137-185.
    62. Carlos Pérez-López, Antoni Ginebreda, Damia Barcelo, Roma Tauler. SigSel: A MATLAB package for the pre and post-treatment of high-resolution mass spectrometry signals using the ROIMCR methodology. MethodsX 2023, 10 , 102199.
    63. Carlos Pérez-López, Sara Rodríguez-Mozaz, Albert Serra-Compte, Diana Alvarez-Muñoz, Antoni Ginebreda, Damià Barceló, Romà Tauler. Effects of sulfamethoxazole exposure on mussels (Mytilus galloprovincialis) metabolome using retrospective non-target high-resolution mass spectrometry and chemometric tools. Talanta 2023, 252 , 123804.
    64. Alexander Eckersley, Matiss Ozols, Peikai Chen, Vivian Tam, Liam J. Ward, Judith A. Hoyland, Andrew Trafford, Xi-Ming Yuan, Herbert B. Schiller, Danny Chan, Michael J. Sherratt. Peptide location fingerprinting identifies species- and tissue-conserved structural remodelling of proteins as a consequence of ageing and disease. Matrix Biology 2022, 114 , 108-137.
    65. Klemens Engelberg, Tyler Bechtel, Cynthia Michaud, Eranthie Weerapana, Marc-Jan Gubbels. Proteomic characterization of the Toxoplasma gondii cytokinesis machinery portrays an expanded hierarchy of its assembly and function. Nature Communications 2022, 13 (1)
    66. Hyejin Kim, Geul Bang, Ye Eun Park, Moonhee Park, Jung Hoon Choi, Myung Jin Oh, Hyun Joo An, Jong Shin Yoo, Youngja Hwang Park, Jin Young Kim, Heeyoun Hwang. Advanced assessment through intact glycopeptide analysis of Infliximab’s biologics and biosimilar. Frontiers in Molecular Biosciences 2022, 9
    67. Jordan R. Willis, Zachary T. Berndsen, Krystal M. Ma, Jon M. Steichen, Torben Schiffner, Elise Landais, Alessia Liguori, Oleksandr Kalyuzhniy, Joel D. Allen, Sabyasachi Baboo, Oluwarotimi Omorodion, Jolene K. Diedrich, Xiaozhen Hu, Erik Georgeson, Nicole Phelps, Saman Eskandarzadeh, Bettina Groschel, Michael Kubitz, Yumiko Adachi, Tina-Marie Mullin, Nushin B. Alavi, Samantha Falcone, Sunny Himansu, Andrea Carfi, Ian A. Wilson, John R. Yates, James C. Paulson, Max Crispin, Andrew B. Ward, William R. Schief. Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors. Immunity 2022, 55 (11) , 2149-2167.e9.
    68. Brendan Miller, Su-Jeong Kim, Hemal H. Mehta, Kevin Cao, Hiroshi Kumagai, Neehar Thumaty, Naphada Leelaprachakul, Regina Gonzalez Braniff, Henry Jiao, Joan Vaughan, Jolene Diedrich, Alan Saghatelian, Thalida E. Arpawong, Eileen M. Crimmins, Nilüfer Ertekin-Taner, Meral A. Tubi, Evan T. Hare, Meredith N. Braskie, Léa Décarie-Spain, Scott E. Kanoski, Francine Grodstein, David A. Bennett, Lu Zhao, Arthur W. Toga, Junxiang Wan, Kelvin Yen, Pinchas Cohen, . Mitochondrial DNA variation in Alzheimer’s disease reveals a unique microprotein called SHMOOSE. Molecular Psychiatry 2022, 11
    69. Shan Lu, Jiaojiao Hu, Olubankole Aladesuyi Arogundade, Alexander Goginashvili, Sonia Vazquez-Sanchez, Jolene K. Diedrich, Jinge Gu, Jacob Blum, Spencer Oung, Qiaozhen Ye, Haiyang Yu, John Ravits, Cong Liu, John R. Yates, Don W. Cleveland. Heat-shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition. Nature Cell Biology 2022, 24 (9) , 1378-1393.
    70. Larissa Traxler, Joseph R. Herdy, Davide Stefanoni, Sophie Eichhorner, Silvia Pelucchi, Attila Szücs, Alice Santagostino, Yongsung Kim, Ravi K. Agarwal, Johannes C.M. Schlachetzki, Christopher K. Glass, Jessica Lagerwall, Douglas Galasko, Fred H. Gage, Angelo D’Alessandro, Jerome Mertens. Warburg-like metabolic transformation underlies neuronal degeneration in sporadic Alzheimer’s disease. Cell Metabolism 2022, 34 (9) , 1248-1263.e6.
    71. Leah D. Pfeifer, Milani W. Patabandige, Heather Desaire. Leveraging R (LevR) for fast processing of mass spectrometry data and machine learning: Applications analyzing fingerprints and glycopeptides. Frontiers in Analytical Science 2022, 2
    72. Martins Jansons, Deniss Fedorenko, Romans Pavlenko, Zane Berzina, Vadims Bartkevics. Nanoflow liquid chromatography mass spectrometry method for quantitative analysis and target ion screening of pyrrolizidine alkaloids in honey, tea, herbal tinctures, and milk. Journal of Chromatography A 2022, 1676 , 463269.
    73. Timothy B. Rowe, Thomas W. Stafford, Daniel C. Fisher, Jan J. Enghild, J. Michael Quigg, Richard A. Ketcham, J. Chris Sagebiel, Romy Hanna, Matthew W. Colbert. Human Occupation of the North American Colorado Plateau ∼37,000 Years Ago. Frontiers in Ecology and Evolution 2022, 10
    74. Rucha Patel, Anna Santoro, Peter Hofer, Dan Tan, Monika Oberer, Andrew T. Nelson, Srihari Konduri, Dionicio Siegel, Rudolf Zechner, Alan Saghatelian, Barbara B. Kahn. ATGL is a biosynthetic enzyme for fatty acid esters of hydroxy fatty acids. Nature 2022, 606 (7916) , 968-975.
    75. Søren Fjelstrup, Daniel M Dupont, Claus Bus, Jan J Enghild, Jørgen B Jensen, Karin Birkenkamp-Demtröder, Lars Dyrskjøt, Jørgen Kjems. Differential RNA aptamer affinity profiling on plasma as a potential diagnostic tool for bladder cancer. NAR Cancer 2022, 4 (3)
    76. Terra Marie M. Jouaneh, Neil Motta, Christine Wu, Cole Coffey, Christopher W. Via, Riley D. Kirk, Matthew J. Bertin. Analysis of botanicals and botanical supplements by LC-MS/MS-based molecular networking: Approaches for annotating plant metabolites and authentication. Fitoterapia 2022, 159 , 105200.
    77. Smitha Pillai, Iqbal Mahmud, Rohit Mahar, Crystal Griffith, Michael Langsen, Jonathan Nguyen, Jonathan W. Wojtkowiak, Pawel Swietach, Robert A. Gatenby, Marilyn M. Bui, Matthew E. Merritt, Patricia McDonald, Timothy J. Garrett, Robert J. Gillies. Lipogenesis mediated by OGR1 regulates metabolic adaptation to acid stress in cancer cells via autophagy. Cell Reports 2022, 39 (6) , 110796.
    78. Zehra Yildirim, Sabyasachi Baboo, Syed M Hamid, Asli E Dogan, Ozlem Tufanli, Sabrina Robichaud, Christina Emerton, Jolene K Diedrich, Hasan Vatandaslar, Fotis Nikolos, Yanghong Gu, Takao Iwawaki, Elizabeth Tarling, Mireille Ouimet, David L Nelson, John R Yates, Peter Walter, Ebru Erbay. Intercepting IRE1 kinase‐FMRP signaling prevents atherosclerosis progression. EMBO Molecular Medicine 2022, 14 (4)
    79. Vinay Dahiya, Daniel Andreas Rutz, Patrick Moessmer, Moritz Mühlhofer, Jannis Lawatscheck, Matthias Rief, Johannes Buchner. The switch from client holding to folding in the Hsp70/Hsp90 chaperone machineries is regulated by a direct interplay between co-chaperones. Molecular Cell 2022, 82 (8) , 1543-1556.e6.
    80. Dale S. George, Sandra Hackelberg, Nirupa D. Jayaraj, Dongjun Ren, Seby L. Edassery, Craig A. Rathwell, Rachel E. Miller, Anne-Marie Malfait, Jeffrey N. Savas, Richard J. Miller, Daniela M. Menichella. Mitochondrial calcium uniporter deletion prevents painful diabetic neuropathy by restoring mitochondrial morphology and dynamics. Pain 2022, 163 (3) , 560-578.
    81. M. Dolores Martín-de-Saavedra, Marc Dos Santos, Lorenza Culotta, Olga Varea, Benjamin P. Spielman, Euan Parnell, Marc P. Forrest, Ruoqi Gao, Sehyoun Yoon, Emmarose McCoig, Hiba A. Jalloul, Kristoffer Myczek, Natalia Khalatyan, Elizabeth A. Hall, Liam S. Turk, Antonio Sanz-Clemente, Davide Comoletti, Stefan F. Lichtenthaler, Jeffrey S. Burgdorf, Maria V. Barbolina, Jeffrey N. Savas, Peter Penzes. Shed CNTNAP2 ectodomain is detectable in CSF and regulates Ca2+ homeostasis and network synchrony via PMCA2/ATP2B2. Neuron 2022, 110 (4) , 627-643.e9.
    82. Guogeng Jia, Jinjun Gao, Fan Yang, Tianyu Feng, Chu Wang. An accelerated and optimized algorithm of selenium-encoded isotopic signature targeted profiling for global selenoproteome analysis. 2022, 241-258.
    83. Sandra Donkervoort, Niklas Krause, Mykola Dergai, Pomi Yun, Judith Koliwer, Svetlana Gorokhova, Janelle Geist Hauserman, Beryl B Cummings, Ying Hu, Rosemarie Smith, Prech Uapinyoying, Vijay S Ganesh, Partha S Ghosh, Kristin G Monaghan, Seby L Edassery, Pia E Ferle, Sarah Silverstein, Katherine R Chao, Molly Snyder, Sara Ellingwood, Diana Bharucha‐Goebel, Susan T Iannaccone, Matteo Dal Peraro, A Reghan Foley, Jeffrey N Savas, Véronique Bolduc, Dirk Fasshauer, Carsten G Bönnemann, Michael Schwake. BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy. EMBO Molecular Medicine 2021, 13 (12)
    84. Jorge Urresti, Pan Zhang, Patricia Moran-Losada, Nam-Kyung Yu, Priscilla D. Negraes, Cleber A. Trujillo, Danny Antaki, Megha Amar, Kevin Chau, Akula Bala Pramod, Jolene Diedrich, Leon Tejwani, Sarah Romero, Jonathan Sebat, John R. Yates III, Alysson R. Muotri, Lilia M. Iakoucheva. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism. Molecular Psychiatry 2021, 26 (12) , 7560-7580.
    85. Kwang-eun Kim, Isaac Park, Jeesoo Kim, Myeong-Gyun Kang, Won Gun Choi, Hyemi Shin, Jong-Seo Kim, Hyun-Woo Rhee, Jae Myoung Suh. Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice. Nature Communications 2021, 12 (1)
    86. Jong Woo Bae, Sangtae Kim, V. Narry Kim, Jong-Seo Kim. Photoactivatable ribonucleosides mark base-specific RNA-binding sites. Nature Communications 2021, 12 (1)
    87. Navratan Bagwan, Henrik H. El Ali, Alicia Lundby. Proteome-wide profiling and mapping of post translational modifications in human hearts. Scientific Reports 2021, 11 (1)
    88. Roberta Noberini, Evelyn Oliva Savoia, Stefania Brandini, Francesco Greco, Francesca Marra, Giovanni Bertalot, Giancarlo Pruneri, Liam A. McDonnell, Tiziana Bonaldi. Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clinical Epigenetics 2021, 13 (1)
    89. Dieter Waschbüsch, Kerryn Berndsen, Pawel Lis, Axel Knebel, Yuko PY Lam, Dario R Alessi, Amir R Khan. Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. EMBO reports 2021, 22 (11)
    90. Jade Sales-Lee, Daniela S. Perry, Bradley A. Bowser, Jolene K. Diedrich, Beiduo Rao, Irene Beusch, John R. Yates, Scott W. Roy, Hiten D. Madhani. Coupling of spliceosome complexity to intron diversity. Current Biology 2021, 31 (22) , 4898-4910.e4.
    91. Shefali Krishna, Rafael Arrojo e Drigo, Juliana S. Capitanio, Ranjan Ramachandra, Mark Ellisman, Martin W. Hetzer. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Developmental Cell 2021, 56 (21) , 2952-2965.e9.
    92. Elisabeth Scheer, Jie Luo, Andrea Bernardini, Frank Ruffenach, Jean-Marie Garnier, Isabelle Kolb-Cheynel, Kapil Gupta, Imre Berger, Jeff Ranish, László Tora. TAF8 regions important for TFIID lobe B assembly or for TAF2 interactions are required for embryonic stem cell survival. Journal of Biological Chemistry 2021, 297 (5) , 101288.
    93. Priscilla D. Negraes, Cleber A. Trujillo, Nam-Kyung Yu, Wei Wu, Hang Yao, Nicholas Liang, Jonathan D. Lautz, Ellius Kwok, Daniel McClatchy, Jolene Diedrich, Salvador Martinez de Bartolome, Justin Truong, Ryan Szeto, Timothy Tran, Roberto H. Herai, Stephen E. P. Smith, Gabriel G. Haddad, John R. Yates, Alysson R. Muotri. Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy. Molecular Psychiatry 2021, 26 (11) , 7047-7068.
    94. Nam-Kyung Yu, Daniel B. McClatchy, Jolene K. Diedrich, Sarah Romero, Jun-Hyeok Choi, Salvador Martínez-Bartolomé, Claire M. Delahunty, Alysson R. Muotri, John R. Yates. Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. iScience 2021, 24 (11) , 103321.
    95. Szu-Hsueh Lai, Sem Tamara, Albert J.R. Heck. Single-particle mass analysis of intact ribosomes by mass photometry and Orbitrap-based charge detection mass spectrometry. iScience 2021, 24 (11) , 103211.
    96. Alexander Eckersley, Matiss Ozols, Peikai Chen, Vivian Tam, Judith A. Hoyland, Andrew Trafford, Danny Chan, Michael J. Sherratt. Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ. International Journal of Molecular Sciences 2021, 22 (19) , 10408.
    97. Martina Klünemann, Sergej Andrejev, Sonja Blasche, Andre Mateus, Prasad Phapale, Saravanan Devendran, Johanna Vappiani, Bernd Simon, Timothy A. Scott, Eleni Kafkia, Dimitrios Konstantinidis, Katharina Zirngibl, Eleonora Mastrorilli, Manuel Banzhaf, Marie-Therese Mackmull, Felix Hövelmann, Leo Nesme, Ana Rita Brochado, Lisa Maier, Thomas Bock, Vinita Periwal, Manjeet Kumar, Yongkyu Kim, Melanie Tramontano, Carsten Schultz, Martin Beck, Janosch Hennig, Michael Zimmermann, Daniel C. Sévin, Filipe Cabreiro, Mikhail M. Savitski, Peer Bork, Athanasios Typas, Kiran R. Patil. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 2021, 597 (7877) , 533-538.
    98. Matthew A. Tancos, Michael B. McMahon, Wesley M. Garrett, Douglas G. Luster, Elizabeth E. Rogers. Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species. Phytopathology® 2021, 111 (9) , 1530-1540.
    99. Megha Amar, Akula Bala Pramod, Nam-Kyung Yu, Victor Munive Herrera, Lily R. Qiu, Patricia Moran-Losada, Pan Zhang, Cleber A. Trujillo, Jacob Ellegood, Jorge Urresti, Kevin Chau, Jolene Diedrich, Jiaye Chen, Jessica Gutierrez, Jonathan Sebat, Dhakshin Ramanathan, Jason P. Lerch, John R. Yates, Alysson R. Muotri, Lilia M. Iakoucheva. Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling. Molecular Psychiatry 2021, 26 (7) , 3586-3613.
    100. Casey A. Chamberlain, Marguerite Hatch, Timothy J. Garrett. Extracellular Vesicle Analysis by Paper Spray Ionization Mass Spectrometry. Metabolites 2021, 11 (5) , 308.
    Load all citations

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect