ACS Publications. Most Trusted. Most Cited. Most Read

OR SEARCH CITATIONS

My Activity
Publications
CONTENT TYPES

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Am. Soc. Mass Spectrom. 1994, 5, 11, 976-989
RETURN TO ISSUEPREVResearch ArticleNEXT

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

  • Jimmy K. Eng
    Jimmy K. Eng
    Department of Molecular Biotechnology, University of Washington, 98185, Seattle, WA, USA
    More by Jimmy K. Eng
  • , 
  • Ashley L. McCormack
    Ashley L. McCormack
    Department of Molecular Biotechnology, University of Washington, 98185, Seattle, WA, USA
    More by Ashley L. McCormack
  • , and 
  • John R. Yates
    John R. Yates
    Department of Molecular Biotechnology, University of Washington, 98185, Seattle, WA, USA
    More by John R. Yates
Cite this: J Am Soc Mass Spectrom 1994, 5, 11, 976–989
Publication Date (Print):November 1, 1994
https://doi.org/10.1016/1044-0305(94)80016-2
Request reuse permissions

    Article Views

    1248

    Altmetric

    -

    Citations

    5245
    LEARN ABOUT THESE METRICS
    PDF (1 MB)

    Abstract

    A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (10–50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mass tolerance of ±1 u of the precursor ion molecular weight A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions of the first- and second-ranked search results indicates a successful match between sequence and spectrum. Searches of species-specific protein databases with tandem mass spectra acquired from peptides obtained from the enzymatically digested total proteins of E. coli and S. cerevisiae cells allowed matching of the spectra to amino acid sequences within proteins of these organisms. The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.

    KEYWORDS:

    Cited By

    This article is cited by 5245 publications.

    1. Georg Wallmann, Andrew Leduc, Nikolai Slavov. Data-Driven Optimization of DIA Mass Spectrometry by DO-MS. Journal of Proteome Research 2023, Article ASAP.
    2. Chris D. McGann, William D. Barshop, Jesse D. Canterbury, Chuwei Lin, Wassim Gabriel, Jingjing Huang, David Bergen, Vlad Zabrouskov, Rafael D. Melani, Mathias Wilhelm, Graeme C. McAlister, Devin K. Schweppe. Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics. Journal of Proteome Research 2023, 22 (9) , 2836-2846. https://doi.org/10.1021/acs.jproteome.3c00085
    3. Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler, Viktoria Dorfer. MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity. Journal of Proteome Research 2023, 22 (9) , 3009-3021. https://doi.org/10.1021/acs.jproteome.3c00325
    4. Fanny C. Liu, Mark E. Ridgeway, Christopher A. Wootton, Alina Theisen, Erin M. Panczyk, Florian Meier, Melvin A. Park, Christian Bleiholder. Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis. Journal of the American Society for Mass Spectrometry 2023, Article ASAP.
    5. Cagdas Tasoglu, Alper Arslanoglu, Talat Yalcin. Gas Phase Fragmentation Behavior of Proline in Macrocyclic b7 Ions. Journal of the American Society for Mass Spectrometry 2023, 34 (8) , 1576-1583. https://doi.org/10.1021/jasms.3c00049
    6. Dimitris Korovesis, Vanessa P. Gaspar, Hester A. Beard, Suyuan Chen, René P. Zahédi, Steven H. L. Verhelst. Mapping Peptide–Protein Interactions by Amine-Reactive Cleavable Photoaffinity Reagents. ACS Omega 2023, 8 (28) , 25487-25495. https://doi.org/10.1021/acsomega.3c03064
    7. Lewis Y. Geer, Joel Lapin, Douglas J. Slotta, Tytus D. Mak, Stephen E. Stein. AIomics: Exploring More of the Proteome Using Mass Spectral Libraries Extended by Artificial Intelligence. Journal of Proteome Research 2023, 22 (7) , 2246-2255. https://doi.org/10.1021/acs.jproteome.2c00807
    8. Steven R. Shuken. An Introduction to Mass Spectrometry-Based Proteomics. Journal of Proteome Research 2023, 22 (7) , 2151-2171. https://doi.org/10.1021/acs.jproteome.2c00838
    9. Tehmina Bharucha, Bevin Gangadharan, Abhinav Kumar, Ashleigh C. Myall, Nazli Ayhan, Boris Pastorino, Anisone Chanthongthip, Manivanh Vongsouvath, Mayfong Mayxay, Onanong Sengvilaipaseuth, Ooyanong Phonemixay, Sayaphet Rattanavong, Darragh P. O’Brien, Iolanda Vendrell, Roman Fischer, Benedikt Kessler, Lance Turtle, Xavier de Lamballerie, Audrey Dubot-Pérès, Paul N. Newton, Nicole Zitzmann, SEAe Consortium. Deep Proteomics Network and Machine Learning Analysis of Human Cerebrospinal Fluid in Japanese Encephalitis Virus Infection. Journal of Proteome Research 2023, 22 (6) , 1614-1629. https://doi.org/10.1021/acs.jproteome.2c00563
    10. Yuanfang Sun, Dongliang Song, Xin Zhang, Qinglan Zhang, Baoyun Li, Kuangcai Chen, Ning Fang. Correlation and Autocorrelation Analysis of Nanoscale Rotational Dynamics. The Journal of Physical Chemistry C 2023, 127 (15) , 7327-7334. https://doi.org/10.1021/acs.jpcc.3c00286
    11. Dominik Madej, Henry Lam. Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics. Journal of Proteome Research 2023, 22 (4) , 1159-1171. https://doi.org/10.1021/acs.jproteome.2c00604
    12. Milan A. Clasen, Marlon D. M. Santos, Louise Ulrich Kurt, Juliana Fischer, Amanda C. Camillo-Andrade, Lucas Albuquerque Sales, Tatiana de Arruda Campos Brasil de Souza, Diogo Borges Lima, Fabio C. Gozzo, Richard Hemmi Valente, Rosario Duran, Valmir C. Barbosa, Paulo C. Carvalho. PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification. Journal of the American Society for Mass Spectrometry 2023, 34 (4) , 794-796. https://doi.org/10.1021/jasms.3c00063
    13. Emilia Christofi, Perdita Barran. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chemical Reviews 2023, 123 (6) , 2902-2949. https://doi.org/10.1021/acs.chemrev.2c00600
    14. Senhan Xu, Kejun Yin, Ronghu Wu. Combining Selective Enrichment and a Boosting Approach to Globally and Site-Specifically Characterize Protein Co-translational O-GlcNAcylation. Analytical Chemistry 2023, 95 (9) , 4371-4380. https://doi.org/10.1021/acs.analchem.2c04779
    15. Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaíno, Mathias Wilhelm, Magnus Palmblad. Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research 2023, 22 (3) , 681-696. https://doi.org/10.1021/acs.jproteome.2c00711
    16. Nikolai Slavov. Great Gains in Mass Spectrometry Data Interpretation. Journal of Proteome Research 2023, 22 (3) , 659-659. https://doi.org/10.1021/acs.jproteome.3c00099
    17. Anton N. Kozhinov, Alex Johnson, Konstantin O. Nagornov, Michael Stadlmeier, Warham Lance Martin, Loïc Dayon, John Corthésy, Martin Wühr, Yury O. Tsybin. Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly Multiplexed Proteomics at the MS2 Level. Analytical Chemistry 2023, 95 (7) , 3712-3719. https://doi.org/10.1021/acs.analchem.2c04742
    18. Jonathon J. O’Brien, Meagan Gadzuk-Shea, Phillip M. Seitzer, Ramin Rad, Fiona E. McAllister, Devin K. Schweppe. Conditional Fragment Ion Probabilities Improve Database Searching for Nonmonoisotopic Precursors. Journal of Proteome Research 2023, 22 (2) , 334-342. https://doi.org/10.1021/acs.jproteome.2c00247
    19. Hui-Yin Chang, Sarah E. Haynes, Fengchao Yu, Alexey I. Nesvizhskii. Implementing the MSFragger Search Engine as a Node in Proteome Discoverer. Journal of Proteome Research 2023, 22 (2) , 520-525. https://doi.org/10.1021/acs.jproteome.2c00485
    20. Nhu Q. Vu, Hsu-Ching Yen, Lauren Fields, Weifeng Cao, Lingjun Li. HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search. Journal of Proteome Research 2023, 22 (2) , 420-431. https://doi.org/10.1021/acs.jproteome.2c00597
    21. Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, Robert L. Moritz. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of Proteome Research 2023, 22 (2) , 615-624. https://doi.org/10.1021/acs.jproteome.2c00624
    22. Brian C. Searle, Ariana E. Shannon, Damien Beau Wilburn. Scribe: Next Generation Library Searching for DDA Experiments. Journal of Proteome Research 2023, 22 (2) , 482-490. https://doi.org/10.1021/acs.jproteome.2c00672
    23. Moustafa R. K. Ali, Paige E. Warner, Anthony M. Yu, Ming Tong, Tiegang Han, Yan Tang. Preventing Metastasis Using Gold Nanorod-Assisted Plasmonic Photothermal Therapy in Xenograft Mice. Bioconjugate Chemistry 2022, 33 (12) , 2320-2331. https://doi.org/10.1021/acs.bioconjchem.2c00011
    24. Yuling Dai, Robert J. Millikin, Zach Rolfs, Michael R. Shortreed, Lloyd M. Smith. A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis. Journal of Proteome Research 2022, 21 (11) , 2609-2618. https://doi.org/10.1021/acs.jproteome.2c00305
    25. Kejun Yin, Ming Tong, Fangxu Sun, Ronghu Wu. Quantitative Structural Proteomics Unveils the Conformational Changes of Proteins under the Endoplasmic Reticulum Stress. Analytical Chemistry 2022, 94 (38) , 13250-13260. https://doi.org/10.1021/acs.analchem.2c03076
    26. Christina Warinner, Kristine Korzow Richter, Matthew J. Collins. Paleoproteomics. Chemical Reviews 2022, 122 (16) , 13401-13446. https://doi.org/10.1021/acs.chemrev.1c00703
    27. Tamara Reyes-Robles, Aleksandra K. Olow, Tyler J. Bechtel, Scott A. Lesley, Olugbeminiyi O. Fadeyi, Rob C. Oslund. Nanoscale Mapping of EGFR and c-MET Protein Environments on Lung Cancer Cell Surfaces via Therapeutic Antibody Photocatalyst Conjugates. ACS Chemical Biology 2022, 17 (8) , 2304-2314. https://doi.org/10.1021/acschembio.2c00409
    28. Yang Zhang, Benjamin Dreyer, Natalia Govorukhina, Alexander M. Heberle, Saša Končarević, Christoph Krisp, Christiane A. Opitz, Pauline Pfänder, Rainer Bischoff, Hartmut Schlüter, Marcel Kwiatkowski, Kathrin Thedieck, Peter L. Horvatovich. Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics. Analytical Chemistry 2022, 94 (31) , 10893-10906. https://doi.org/10.1021/acs.analchem.2c01036
    29. Joon-Yong Lee, Hugh D. Mitchell, Meagan C. Burnet, Ruonan Wu, Sarah C. Jenson, Eric D. Merkley, Ernesto S. Nakayasu, Carrie D. Nicora, Janet K. Jansson, Kristin E. Burnum-Johnson, Samuel H. Payne. Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics. Journal of Proteome Research 2022, 21 (8) , 2023-2035. https://doi.org/10.1021/acs.jproteome.2c00334
    30. Lilian R. Heil, William E. Fondrie, Christopher D. McGann, Alexander J. Federation, William S. Noble, Michael J. MacCoss, Uri Keich. Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data. Journal of Proteome Research 2022, 21 (6) , 1382-1391. https://doi.org/10.1021/acs.jproteome.1c00895
    31. Chang Yoon Doh, Katherine L. Dominic, Caitlin E. Swanberg, Nikhil Bharambe, Belinda B. Willard, Ling Li, Rajesh Ramachandran, Julian E. Stelzer. Identification of Phosphorylation and Other Post-Translational Modifications in the Central C4C5 Domains of Murine Cardiac Myosin Binding Protein C. ACS Omega 2022, 7 (16) , 14189-14202. https://doi.org/10.1021/acsomega.2c00799
    32. Tianyang Yan, Andrew B. Palmer, Daniel J. Geiszler, Daniel A. Polasky, Lisa M. Boatner, Nikolas R. Burton, Ernest Armenta, Alexey I. Nesvizhskii, Keriann M. Backus. Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation. Analytical Chemistry 2022, 94 (9) , 3800-3810. https://doi.org/10.1021/acs.analchem.1c04402
    33. Crystal L. Pace, Jared Simmons, Ryan T. Kelly, David C. Muddiman. Multimodal Mass Spectrometry Imaging of Rat Brain Using IR-MALDESI and NanoPOTS-LC-MS/MS. Journal of Proteome Research 2022, 21 (3) , 713-720. https://doi.org/10.1021/acs.jproteome.1c00641
    34. Dominik Madej, Long Wu, Henry Lam. Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics. Journal of Proteome Research 2022, 21 (2) , 339-348. https://doi.org/10.1021/acs.jproteome.1c00600
    35. Hannah Boekweg, Daisha Van Der Watt, Thy Truong, S. Madisyn Johnston, Amanda J. Guise, Edward D. Plowey, Ryan T. Kelly, Samuel H. Payne. Features of Peptide Fragmentation Spectra in Single-Cell Proteomics. Journal of Proteome Research 2022, 21 (1) , 182-188. https://doi.org/10.1021/acs.jproteome.1c00670
    36. Daniel Abegg, Martin Tomanik, Nan Qiu, Dany Pechalrieu, Anton Shuster, Bruno Commare, Antonio Togni, Seth B. Herzon, Alexander Adibekian. Chemoproteomic Profiling by Cysteine Fluoroalkylation Reveals Myrocin G as an Inhibitor of the Nonhomologous End Joining DNA Repair Pathway. Journal of the American Chemical Society 2021, 143 (48) , 20332-20342. https://doi.org/10.1021/jacs.1c09724
    37. Paul Ka Po To, Long Wu, Chak Ming Chan, Ayman Hoque, Henry Lam. ClusterSheep: A Graphics Processing Unit-Accelerated Software Tool for Large-Scale Clustering of Tandem Mass Spectra from Shotgun Proteomics. Journal of Proteome Research 2021, 20 (12) , 5359-5367. https://doi.org/10.1021/acs.jproteome.1c00485
    38. Taran Driver, Nikhil Bachhawat, Rüdiger Pipkorn, Leszek J. Frasiński, Jon P. Marangos, Marina Edelson-Averbukh, Vitali Averbukh. Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry. Analytical Chemistry 2021, 93 (45) , 14946-14954. https://doi.org/10.1021/acs.analchem.1c00895
    39. Jingchuan Xue, Rico J. E. Derks, Linh Hoang, Martin Giera, Gary Siuzdak. Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification. Journal of the American Society for Mass Spectrometry 2021, 32 (11) , 2644-2654. https://doi.org/10.1021/jasms.1c00188
    40. Polina Kudriavtseva, Matvey Kashkinov, Attila Kertész-Farkas. Deep Convolutional Neural Networks Help Scoring Tandem Mass Spectrometry Data in Database-Searching Approaches. Journal of Proteome Research 2021, 20 (10) , 4708-4717. https://doi.org/10.1021/acs.jproteome.1c00315
    41. Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang. CIMAGE2.0: An Expanded Tool for Quantitative Analysis of Activity-Based Protein Profiling (ABPP) Data. Journal of Proteome Research 2021, 20 (10) , 4893-4900. https://doi.org/10.1021/acs.jproteome.1c00455
    42. Benjamin A. Neely, Magnus Palmblad. Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics. Journal of Proteome Research 2021, 20 (10) , 4640-4645. https://doi.org/10.1021/acs.jproteome.1c00528
    43. Fangxu Sun, Suttipong Suttapitugsakul, Ronghu Wu. An Azo Coupling-Based Chemoproteomic Approach to Systematically Profile the Tyrosine Reactivity in the Human Proteome. Analytical Chemistry 2021, 93 (29) , 10334-10342. https://doi.org/10.1021/acs.analchem.1c01935
    44. Xiangyuan Zeng, Bin Ma. MSTracer: A Machine Learning Software Tool for Peptide Feature Detection from Liquid Chromatography–Mass Spectrometry Data. Journal of Proteome Research 2021, 20 (7) , 3455-3462. https://doi.org/10.1021/acs.jproteome.0c01029
    45. Karel Stejskal, Jeff Op de Beeck, Gerhard Dürnberger, Paul Jacobs, Karl Mechtler. Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO. Analytical Chemistry 2021, 93 (25) , 8704-8710. https://doi.org/10.1021/acs.analchem.1c00990
    46. Ricardo M. Borges, Sean M. Colby, Susanta Das, Arthur S. Edison, Oliver Fiehn, Tobias Kind, Jesi Lee, Amy T. Merrill, Kenneth M. Merz, Jr., Thomas O. Metz, Jamie R. Nunez, Dean J. Tantillo, Lee-Ping Wang, Shunyang Wang, Ryan S. Renslow. Quantum Chemistry Calculations for Metabolomics. Chemical Reviews 2021, 121 (10) , 5633-5670. https://doi.org/10.1021/acs.chemrev.0c00901
    47. Pasrawin Taechawattananant, Kazuyoshi Yoshii, Yasushi Ishihama. Peak Identification and Quantification by Proteomic Mass Spectrogram Decomposition. Journal of Proteome Research 2021, 20 (5) , 2291-2298. https://doi.org/10.1021/acs.jproteome.0c00819
    48. Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, Viktoria Dorfer. MS Annika: A New Cross-Linking Search Engine. Journal of Proteome Research 2021, 20 (5) , 2560-2569. https://doi.org/10.1021/acs.jproteome.0c01000
    49. Shanshan Guan, Benjamin J. Bythell. Size Dependent Fragmentation Chemistry of Short Doubly Protonated Tryptic Peptides. Journal of the American Society for Mass Spectrometry 2021, 32 (4) , 1020-1032. https://doi.org/10.1021/jasms.1c00009
    50. Paolo Cifani, Zhi Li, Danmeng Luo, Mark Grivainis, Andrew M. Intlekofer, David Fenyö, Alex Kentsis. Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. Journal of Proteome Research 2021, 20 (4) , 1835-1848. https://doi.org/10.1021/acs.jproteome.0c00638
    51. Kyle Lucke, Jake Pennington, Patrick Kreitzberg, Lukas Käll, Oliver Serang. Performing Selection on a Monotonic Function in Lieu of Sorting Using Layer-Ordered Heaps. Journal of Proteome Research 2021, 20 (4) , 1849-1854. https://doi.org/10.1021/acs.jproteome.0c00711
    52. Benjamin A. Neely. Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments. Journal of Proteome Research 2021, 20 (4) , 2076-2082. https://doi.org/10.1021/acs.jproteome.0c00920
    53. Damien B. Wilburn, Alicia L. Richards, Danielle L. Swaney, Brian C. Searle. CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. Journal of Proteome Research 2021, 20 (4) , 1951-1965. https://doi.org/10.1021/acs.jproteome.0c00964
    54. William E. Fondrie, William S. Noble. mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. Journal of Proteome Research 2021, 20 (4) , 1966-1971. https://doi.org/10.1021/acs.jproteome.0c01010
    55. Fanni Bugyi, Dániel Szabó, Győző Szabó, Ágnes Révész, Veronika F. S. Pape, Eszter Soltész-Katona, Eszter Tóth, Orsolya Kovács, Tamás Langó, Károly Vékey, László Drahos. Influence of Post-Translational Modifications on Protein Identification in Database Searches. ACS Omega 2021, 6 (11) , 7469-7477. https://doi.org/10.1021/acsomega.0c05997
    56. Zinan Zhang, Dominic Ortega, Anthony Rush, Lauren R. Blankenship, Zi Jun Cheng, Rebecca E. Moore, Minh L. N. Tran, Lucero G. Sandoval, Kareem Aboulhosn, Seiichiro Watanabe, Kendra S. Cortez, David H. Perlman, Martin F. Semmelhack, Laura C. Miller Conrad. Antibiotic Adjuvant Activity Revealed in a Photoaffinity Approach to Determine the Molecular Target of Antipyocyanin Compounds. ACS Infectious Diseases 2021, 7 (3) , 535-543. https://doi.org/10.1021/acsinfecdis.0c00160
    57. Vinícius Marquioni, Francis Morais Franco Nunes, Maria Teresa Marques Novo-Mansur. Protein Identification by Database Searching of Mass Spectrometry Data in the Teaching of Proteomics. Journal of Chemical Education 2021, 98 (3) , 812-823. https://doi.org/10.1021/acs.jchemed.0c00853
    58. Ayako Takemori, Jun Ishizaki, Kenji Nakashima, Takeshi Shibata, Hidemasa Kato, Yoshio Kodera, Tetsuro Suzuki, Hitoshi Hasegawa, Nobuaki Takemori. BAC-DROP: Rapid Digestion of Proteome Fractionated via Dissolvable Polyacrylamide Gel Electrophoresis and Its Application to Bottom-Up Proteomics Workflow. Journal of Proteome Research 2021, 20 (3) , 1535-1543. https://doi.org/10.1021/acs.jproteome.0c00749
    59. Linda Berg Luecke, Rebekah L. Gundry. Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies. Journal of Proteome Research 2021, 20 (2) , 1153-1164. https://doi.org/10.1021/acs.jproteome.0c00772
    60. Suttipong Suttapitugsakul, Ming Tong, Fangxu Sun, Ronghu Wu. Enhancing Comprehensive Analysis of Secreted Glycoproteins from Cultured Cells without Serum Starvation. Analytical Chemistry 2021, 93 (4) , 2694-2705. https://doi.org/10.1021/acs.analchem.0c05126
    61. Mak A. Saito, Jaclyn K. Saunders, Michael Chagnon, David A. Gaylord, Adam Shepherd, Noelle A. Held, Christopher Dupont, Nicholas Symmonds, Amber York, Matthew Charron, Danie B. Kinkade. Development of an Ocean Protein Portal for Interactive Discovery and Education. Journal of Proteome Research 2021, 20 (1) , 326-336. https://doi.org/10.1021/acs.jproteome.0c00382
    62. Theo Sturm, Benedikt Sautter, Tobias P. Wörner, Stefan Stevanović, Hans-Georg Rammensee, Oliver Planz, Albert J. R. Heck, Ruedi Aebersold. Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome. Journal of Proteome Research 2021, 20 (1) , 289-304. https://doi.org/10.1021/acs.jproteome.0c00386
    63. Lichao Zhang, Patrick L. McAlpine, Marlene L. Heberling, Joshua E. Elias. Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass Spectrometry. Journal of Proteome Research 2021, 20 (1) , 393-408. https://doi.org/10.1021/acs.jproteome.0c00464
    64. 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. https://doi.org/10.1021/acs.jproteome.0c00563
    65. Manuel David Peris-Díaz, Roman Guran, Ondrej Zitka, Vojtech Adam, Artur Krężel. Mass Spectrometry-Based Structural Analysis of Cysteine-Rich Metal-Binding Sites in Proteins with MetaOdysseus R Software. Journal of Proteome Research 2021, 20 (1) , 776-785. https://doi.org/10.1021/acs.jproteome.0c00651
    66. Casey A. Schmidt, David T. Wilson, Ira Cooke, Jeremy Potriquet, Katie Tungatt, Visai Muruganandah, Chloë Boote, Felicity Kuek, John J. Miles, Andreas Kupz, Stephanie Ryan, Alex Loukas, Paramjit S. Bansal, Rozita Takjoo, David J. Miller, Steve Peigneur, Jan Tytgat, Norelle L. Daly. Identification and Characterization of a Peptide from the Stony Coral Heliofungia actiniformis. Journal of Natural Products 2020, 83 (11) , 3454-3463. https://doi.org/10.1021/acs.jnatprod.0c00981
    67. 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. https://doi.org/10.1021/acs.analchem.0c02513
    68. Christopher J. Thompson, Matthias Witt, Sara Forcisi, Franco Moritz, Nikolas Kessler, Frank H. Laukien, Philippe Schmitt-Kopplin. An Enhanced Isotopic Fine Structure Method for Exact Mass Analysis in Discovery Metabolomics: FIA-CASI-FTMS. Journal of the American Society for Mass Spectrometry 2020, 31 (10) , 2025-2034. https://doi.org/10.1021/jasms.0c00047
    69. Julia A. Bubis, Vladimir Gorshkov, Mikhail V. Gorshkov, Frank Kjeldsen. PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety. Journal of the American Society for Mass Spectrometry 2020, 31 (10) , 2053-2060. https://doi.org/10.1021/jasms.0c00171
    70. Jos Oomens, Lisanne J. M. Kempkes, Thijs P. J. Geurts, Luuk van Dijk, Jonathan Martens, Giel Berden, P. B. Armentrout. Water Loss from Protonated XxxSer and XxxThr Dipeptides Gives Oxazoline—Not Oxazolone—Product Ions. Journal of the American Society for Mass Spectrometry 2020, 31 (10) , 2111-2123. https://doi.org/10.1021/jasms.0c00239
    71. Joseph M. Dobbs, Meredith L. Jenkins, John E. Burke. Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. Journal of the American Society for Mass Spectrometry 2020, 31 (10) , 2202-2209. https://doi.org/10.1021/jasms.0c00283
    72. Chad R. Weisbrod, Lissa C. Anderson, Joseph B. Greer, Caroline J. DeHart, Christopher L. Hendrickson. Increased Single-Spectrum Top-Down Protein Sequence Coverage in Trapping Mass Spectrometers with Chimeric Ion Loading. Analytical Chemistry 2020, 92 (18) , 12193-12200. https://doi.org/10.1021/acs.analchem.0c01064
    73. James E. Keating, Chris Chung, Shengjie Chai, Jans F. Prins, Benjamin G. Vincent, Sally A. Hunsucker, Paul M. Armistead, Gary L. Glish. Alkali Metal Cationization of Tumor-associated Antigen Peptides for Improved Dissociation and Measurement by Differential Ion Mobility-Mass Spectrometry. Journal of Proteome Research 2020, 19 (8) , 3176-3183. https://doi.org/10.1021/acs.jproteome.0c00157
    74. Naiping Dong, Daniel M. Spencer, Quan Quan, J. C. Yves Le Blanc, Jinwen Feng, Mengzhu Li, K. W. Michael Siu, Ivan K. Chu. rPTMDetermine: A Fully Automated Methodology for Endogenous Tyrosine Nitration Validation, Site-Localization, and Beyond. Analytical Chemistry 2020, 92 (15) , 10768-10776. https://doi.org/10.1021/acs.analchem.0c02148
    75. Ming Tong, Suttipong Suttapitugsakul, Ronghu Wu. Effective Method for Accurate and Sensitive Quantitation of Rapid Changes of Newly Synthesized Proteins. Analytical Chemistry 2020, 92 (14) , 10048-10057. https://doi.org/10.1021/acs.analchem.0c01823
    76. Kellen DeLaney, Weifeng Cao, Yadi Ma, Mingming Ma, Yuzhuo Zhang, Lingjun Li. PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1358-1371. https://doi.org/10.1021/jasms.0c00013
    77. Matthew Waas, Jack Littrell, Rebekah L. Gundry. CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1389-1397. https://doi.org/10.1021/jasms.0c00021
    78. Ashley N. Ives, Taojunfeng Su, Kenneth R. Durbin, Bryan P. Early, Henrique dos Santos Seckler, Ryan T. Fellers, Richard D. LeDuc, Luis F. Schachner, Steven M. Patrie, Neil L. Kelleher. Using 10,000 Fragment Ions to Inform Scoring in Native Top-down Proteomics. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1398-1409. https://doi.org/10.1021/jasms.0c00026
    79. Jeremy P. Gygi, Ramin Rad, Jose Navarrete-Perea, Simon Younesi, Steven P. Gygi, Joao A. Paulo. A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1344-1349. https://doi.org/10.1021/jasms.0c00029
    80. Michelle A. Kennedy, William A. Hofstadter, Ileana M. Cristea. TRANSPIRE: A Computational Pipeline to Elucidate Intracellular Protein Movements from Spatial Proteomics Data Sets. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1422-1439. https://doi.org/10.1021/jasms.0c00033
    81. Alexander R. Pelletier, Yun-En Chung, Zhibin Ning, Nora Wong, Daniel Figeys, Mathieu Lavallée-Adam. MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1459-1472. https://doi.org/10.1021/jasms.0c00064
    82. John R. Yates, III. The Journey Is the Reward, a Taoist Proverb: John B. Fenn Award for Distinguished Contribution in Mass Spectrometry Lecture. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1327-1336. https://doi.org/10.1021/jasms.0c00073
    83. Jennifer S. Brodbelt, (Associate Editor, JASMS)Gavin E. Reid (Associate Editor, JASMS). Special Focus: Honoring John Yates for Receiving the 2019 John B. Fenn Award for a Distinguished Contribution in Mass Spectrometry. Journal of the American Society for Mass Spectrometry 2020, 31 (7) , 1326-1326. https://doi.org/10.1021/jasms.0c00219
    84. Xiang Yu, Arthur Fridman, Ansuman Bagchi, Shiyao Xu, Kristen A. Kwasnjuk, Ping Lu, Mark T. Cancilla. Metabolite Identification of Therapeutic Peptides and Proteins by Top-down Differential Mass Spectrometry and Metabolite Database Matching. Analytical Chemistry 2020, 92 (12) , 8298-8305. https://doi.org/10.1021/acs.analchem.0c00652
    85. Sangeetha Ramachandran, Tessamma Thomas. A Frequency-Based Approach to Predict the Low-Energy Collision-Induced Dissociation Fragmentation Spectra. ACS Omega 2020, 5 (22) , 12615-12622. https://doi.org/10.1021/acsomega.9b03935
    86. Viveka Perera, Baku Acharya, Amanda L. Patrick, Deb Mlsna. Hands-On Electrospray Ionization Mass Spectrometry for Undergraduate Biochemistry Students: Peptide Identification by Ladder Sequencing. Journal of Chemical Education 2020, 97 (5) , 1437-1442. https://doi.org/10.1021/acs.jchemed.9b00800
    87. 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. https://doi.org/10.1021/acs.jproteome.9b00860
    88. Daniel A. Polasky, Sugyan M. Dixit, Michael F. Keating, Varun V. Gadkari, Philip C. Andrews, Brandon T. Ruotolo. Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data. Journal of the American Chemical Society 2020, 142 (14) , 6750-6760. https://doi.org/10.1021/jacs.0c01076
    89. Pavel Sulimov, Attila Kertész-Farkas. Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics. Journal of Proteome Research 2020, 19 (4) , 1481-1490. https://doi.org/10.1021/acs.jproteome.9b00736
    90. Xi Wang, Adam C. Swensen, Tong Zhang, Paul D. Piehowski, Matthew J. Gaffrey, Matthew E. Monroe, Ying Zhu, Hailiang Dong, Wei-Jun Qian. Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy. Journal of Proteome Research 2020, 19 (4) , 1863-1872. https://doi.org/10.1021/acs.jproteome.9b00766
    91. Liangyong Mei, Maureen R. Montoya, Guy M. Quanrud, Minh Tran, Athena Villa-Sharma, Ming Huang, Joseph C. Genereux. Bait Correlation Improves Interactor Identification by Tandem Mass Tag-Affinity Purification-Mass Spectrometry. Journal of Proteome Research 2020, 19 (4) , 1565-1573. https://doi.org/10.1021/acs.jproteome.9b00825
    92. Adithi R. Varadarajan, Sandra Goetze, Maria P. Pavlou, Virginie Grosboillot, Yang Shen, Martin J. Loessner, Christian H. Ahrens, Bernd Wollscheid. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype–Proteotype–Phenotype Relationships. Journal of Proteome Research 2020, 19 (4) , 1647-1662. https://doi.org/10.1021/acs.jproteome.9b00842
    93. Thomas Aumer, Sébastien N. Voisin, Thomas Knobloch, Céline Landon, Philippe Bulet. Impact of an Antifungal Insect Defensin on the Proteome of the Phytopathogenic Fungus Botrytis cinerea. Journal of Proteome Research 2020, 19 (3) , 1131-1146. https://doi.org/10.1021/acs.jproteome.9b00638
    94. Marie Locard-Paulet, David Bouyssié, Carine Froment, Odile Burlet-Schiltz, Lars J. Jensen. Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization. Journal of Proteome Research 2020, 19 (3) , 1338-1345. https://doi.org/10.1021/acs.jproteome.9b00679
    95. William E. Fondrie, William S. Noble. Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. Journal of Proteome Research 2020, 19 (3) , 1267-1274. https://doi.org/10.1021/acs.jproteome.9b00780
    96. Nikhil Madhusudhan, Bin Hu, Prashant Mishra, Josè F. Calva-Moreno, Khushbu Patel, Richard Boriack, Joseph M. Ready, Deepak Nijhawan. Target Discovery of Selective Non-Small-Cell Lung Cancer Toxins Reveals Inhibitors of Mitochondrial Complex I. ACS Chemical Biology 2020, 15 (1) , 158-170. https://doi.org/10.1021/acschembio.9b00734
    97. Naoaki Arima, Yusuke Sasaki, Lang Ho Lee, Hengmin Zhang, Jose-Luiz Figueiredo, Andrew K. Mlynarchik, Jiao Qiao, Iwao Yamada, Hideyuki Higashi, Anna H. Ha, Arda Halu, Ken Mizuno, Sasha A. Singh, Yukiyoshi Yamazaki, Masanori Aikawa. Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery. Journal of Proteome Research 2020, 19 (1) , 129-143. https://doi.org/10.1021/acs.jproteome.9b00441
    98. Yuanliang Zhang, Zhilong Lin, Yifan Tan, Fanyu Bu, Piliang Hao, Keren Zhang, Huanming Yang, Siqi Liu, Yan Ren. Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines. Journal of Proteome Research 2020, 19 (1) , 401-408. https://doi.org/10.1021/acs.jproteome.9b00590
    99. Fernanda Negrão, Jolene K. Diedrich, Selma Giorgio, Marcos N. Eberlin, John R. Yates III. Tandem Mass Tag Proteomic Analysis of in Vitro and in Vivo Models of Cutaneous Leishmaniasis Reveals Parasite-Specific and Nonspecific Modulation of Proteins in the Host. ACS Infectious Diseases 2019, 5 (12) , 2136-2147. https://doi.org/10.1021/acsinfecdis.9b00275
    100. David D. Shteynberg, Eric W. Deutsch, David S. Campbell, Michael R. Hoopmann, Ulrike Kusebauch, Dave Lee, Luis Mendoza, Mukul K. Midha, Zhi Sun, Anthony D. Whetton, Robert L. Moritz. PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. Journal of Proteome Research 2019, 18 (12) , 4262-4272. https://doi.org/10.1021/acs.jproteome.9b00205
    Load more citations
    Download PDF

    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.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect