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

Open Mass Spectrometry Search Algorithm

View Author Information
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, and the Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892
Cite this: Journal of Proteome Research 2004, 3, 5, 958–964
Publication Date (Web):July 2, 2004
https://doi.org/10.1021/pr0499491
Copyright © 2004 American Chemical Society

    Article Views

    5979

    Altmetric

    -

    Citations

    LEARN ABOUT THESE METRICS
    Other access options

    Abstract

    Abstract Image

    Large numbers of MS/MS peptide spectra generated in proteomics experiments require efficient, sensitive and specific algorithms for peptide identification. In the Open Mass Spectrometry Search Algorithm (OMSSA), specificity is calculated by a classic probability score using an explicit model for matching experimental spectra to sequences. At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets.

    Keywords: protein identification • algorithm • bioinformatics • mass spectrometry • proteomics • significance testing

    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.

    Recommended

    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.

    *

     To whom correspondence should be addressed. E-mail:  lewisg@ mail.nih.gov.

     National Center for Biotechnology Information.

     Laboratory of Neurotoxicology.

    Cited By

    This article is cited by 1173 publications.

    1. Eduardo A. De La Toba, Krishna D. B. Anapindi, Jonathan V. Sweedler. Assessment and Comparison of Database Search Engines for Peptidomic Applications. Journal of Proteome Research 2023, 22 (10) , 3123-3134. https://doi.org/10.1021/acs.jproteome.2c00307
    2. 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, 34 (10) , 2232-2246. https://doi.org/10.1021/jasms.3c00187
    3. Jamie Canderan, Moses Stamboulian, Yuzhen Ye. MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of Proteome Research 2023, 22 (2) , 442-453. https://doi.org/10.1021/acs.jproteome.2c00614
    4. 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
    5. Kenneth W. Lee, Trenton M. Peters-Clarke, Keaton L. Mertz, Graeme C. McAlister, John E. P. Syka, Michael S. Westphall, Joshua J. Coon. Infrared Photoactivation Boosts Reporter Ion Yield in Isobaric Tagging. Analytical Chemistry 2022, 94 (7) , 3328-3334. https://doi.org/10.1021/acs.analchem.1c05398
    6. Trenton M. Peters-Clarke, Nicholas M. Riley, Michael S. Westphall, Joshua J. Coon. Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics. Journal of the American Society for Mass Spectrometry 2022, 33 (1) , 100-110. https://doi.org/10.1021/jasms.1c00284
    7. Yehia Mokhtar Farag, Carlos Horro, Marc Vaudel, Harald Barsnes. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data. Journal of Proteome Research 2021, 20 (12) , 5419-5423. https://doi.org/10.1021/acs.jproteome.1c00678
    8. 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
    9. Xiaoyu Yang, Pedatsur Neta, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Concepcion A. Remoroza, Meghan C. Burke, Yuxue Liang, Sanford P. Markey, Stephen E. Stein. MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides. Journal of Proteome Research 2021, 20 (9) , 4603-4609. https://doi.org/10.1021/acs.jproteome.1c00324
    10. 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
    11. 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
    12. Axel Broman, Andreas Lenshof, Mikael Evander, Lotta Happonen, Anson Ku, Johan Malmström, Thomas Laurell. Multinodal Acoustic Trapping Enables High Capacity and High Throughput Enrichment of Extracellular Vesicles and Microparticles in miRNA and MS Proteomics Studies. Analytical Chemistry 2021, 93 (8) , 3929-3937. https://doi.org/10.1021/acs.analchem.0c04772
    13. 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
    14. 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
    15. 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
    16. Johra Muhammad Moosa, Shenheng Guan, Michael F. Moran, Bin Ma. Repeat-Preserving Decoy Database for False Discovery Rate Estimation in Peptide Identification. Journal of Proteome Research 2020, 19 (3) , 1029-1036. https://doi.org/10.1021/acs.jproteome.9b00555
    17. Balakrishnan Ramesh, Shaza Abnouf, Sujina Mali, Wilna J. Moree, Ujwal Patil, Steven J. Bark, Navin Varadarajan. Engineered ChymotrypsiN for Mass Spectrometry-Based Detection of Protein Glycosylation. ACS Chemical Biology 2019, 14 (12) , 2616-2628. https://doi.org/10.1021/acschembio.9b00506
    18. Samaneh Azari, Bing Xue, Mengjie Zhang, Lifeng Peng. Preprocessing Tandem Mass Spectra Using Genetic Programming for Peptide Identification. Journal of the American Society for Mass Spectrometry 2019, 30 (7) , 1294-1307. https://doi.org/10.1007/s13361-019-02196-5
    19. Suruchi Aggarwal, Narayan C. Talukdar, Amit K. Yadav. Advances in Higher Order Multiplexing Techniques in Proteomics. Journal of Proteome Research 2019, 18 (6) , 2360-2369. https://doi.org/10.1021/acs.jproteome.9b00228
    20. Uri Keich, Kaipo Tamura, William Stafford Noble. Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate. Journal of Proteome Research 2019, 18 (2) , 585-593. https://doi.org/10.1021/acs.jproteome.8b00802
    21. Luis Felipe Clemente, María Luisa Hernáez, Antonio Ramos-Fernández, Gertrudis Ligero, Concha Gil, Fernando José Corrales, Miguel Marcilla. Identification of the Missing Protein Hyaluronan Synthase 1 in Human Mesenchymal Stem Cells Derived from Adipose Tissue or Umbilical Cord. Journal of Proteome Research 2018, 17 (12) , 4325-4328. https://doi.org/10.1021/acs.jproteome.8b00384
    22. Ekaterina V. Ilgisonis, Arthur T. Kopylov, Elena A. Ponomarenko, Ekaterina V. Poverennaya, Olga V. Tikhonova, Tatiana E. Farafonova, Svetlana Novikova, Andrey V. Lisitsa, Victor G. Zgoda, Alexander I. Archakov. Increased Sensitivity of Mass Spectrometry by Alkaline Two-Dimensional Liquid Chromatography: Deep Cover of the Human Proteome in Gene-Centric Mode. Journal of Proteome Research 2018, 17 (12) , 4258-4266. https://doi.org/10.1021/acs.jproteome.8b00754
    23. Swantje Lenz, Sven H. Giese, Lutz Fischer, Juri Rappsilber. In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides. Journal of Proteome Research 2018, 17 (11) , 3923-3931. https://doi.org/10.1021/acs.jproteome.8b00600
    24. Viktoria Dorfer, Sergey Maltsev, Stephan Winkler, Karl Mechtler. CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction. Journal of Proteome Research 2018, 17 (8) , 2581-2589. https://doi.org/10.1021/acs.jproteome.7b00836
    25. Lev I. Levitsky, Mark V. Ivanov, Anna A. Lobas, Julia A. Bubis, Irina A. Tarasova, Elizaveta M. Solovyeva, Marina L. Pridatchenko, Mikhail V. Gorshkov. IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics. Journal of Proteome Research 2018, 17 (7) , 2249-2255. https://doi.org/10.1021/acs.jproteome.7b00640
    26. Harald Barsnes, Marc Vaudel. SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines. Journal of Proteome Research 2018, 17 (7) , 2552-2555. https://doi.org/10.1021/acs.jproteome.8b00175
    27. Sebastian Dorl, Stephan Winkler, Karl Mechtler, and Viktoria Dorfer . PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search. Journal of Proteome Research 2018, 17 (1) , 290-295. https://doi.org/10.1021/acs.jproteome.7b00563
    28. Amanda E. Starr, Shelley A. Deeke, Leyuan Li, Xu Zhang, Rachid Daoud, James Ryan, Zhibin Ning, Kai Cheng, Linh V. H. Nguyen, Elias Abou-Samra, Mathieu Lavallée-Adam, and Daniel Figeys . Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Analytical Chemistry 2018, 90 (1) , 86-109. https://doi.org/10.1021/acs.analchem.7b04340
    29. Elizabeth Guruceaga, Alba Garin-Muga, Gorka Prieto, Bartolomé Bejarano, Miguel Marcilla, Consuelo Marín-Vicente, Yasset Perez-Riverol, J. Ignacio Casal, Juan Antonio Vizcaíno, Fernando J. Corrales, and Victor Segura . Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach. Journal of Proteome Research 2017, 16 (12) , 4374-4390. https://doi.org/10.1021/acs.jproteome.7b00388
    30. Panpan Zhao, Jiayong Zhong, Wanting Liu, Jing Zhao, and Gong Zhang . Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage. Journal of Proteome Research 2017, 16 (12) , 4446-4454. https://doi.org/10.1021/acs.jproteome.7b00463
    31. Lisa E. Kilpatrick and Eric L. Kilpatrick . Optimizing High-Resolution Mass Spectrometry for the Identification of Low-Abundance Post-Translational Modifications of Intact Proteins. Journal of Proteome Research 2017, 16 (9) , 3255-3265. https://doi.org/10.1021/acs.jproteome.7b00244
    32. Matthew J. P. Rush, Nicholas M. Riley, Michael S. Westphall, John E. P. Syka, Joshua J. Coon. Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry 2017, 28 (7) , 1324-1332. https://doi.org/10.1007/s13361-017-1600-8
    33. Nicholas M. Riley, Michael S. Westphall, Alexander S. Hebert, and Joshua J. Coon . Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer. Analytical Chemistry 2017, 89 (12) , 6358-6366. https://doi.org/10.1021/acs.analchem.7b00213
    34. Olivier Langella, Benoît Valot, Thierry Balliau, Mélisande Blein-Nicolas, Ludovic Bonhomme, and Michel Zivy . X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. Journal of Proteome Research 2017, 16 (2) , 494-503. https://doi.org/10.1021/acs.jproteome.6b00632
    35. Sander Willems, Maarten Dhaenens, Elisabeth Govaert, Laura De Clerck, Paulien Meert, Christophe Van Neste, Filip Van Nieuwerburgh, and Dieter Deforce . Flagging False Positives Following Untargeted LC–MS Characterization of Histone Post-Translational Modification Combinations. Journal of Proteome Research 2017, 16 (2) , 655-664. https://doi.org/10.1021/acs.jproteome.6b00724
    36. Meena Choi, Zeynep F. Eren-Dogu, Christopher Colangelo, John Cottrell, Michael R. Hoopmann, Eugene A. Kapp, Sangtae Kim, Henry Lam, Thomas A. Neubert, Magnus Palmblad, Brett S. Phinney, Susan T. Weintraub, Brendan MacLean, and Olga Vitek . ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments. Journal of Proteome Research 2017, 16 (2) , 945-957. https://doi.org/10.1021/acs.jproteome.6b00881
    37. Brynne E. Lycette, Jacob W. Glickman, Samuel J. Roth, Abigail E. Cram, Tae Hee Kim, Danny Krizanc, and Michael P. Weir . N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries. Journal of Proteome Research 2016, 15 (9) , 2891-2899. https://doi.org/10.1021/acs.jproteome.5b00996
    38. Johannes Veit, Timo Sachsenberg, Aleksandar Chernev, Fabian Aicheler, Henning Urlaub, and Oliver Kohlbacher . LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein–RNA Cross-Linking Integrated into Proteome Discoverer. Journal of Proteome Research 2016, 15 (9) , 3441-3448. https://doi.org/10.1021/acs.jproteome.6b00407
    39. Ruth A. Fuhrman-Luck, Scott H. Stansfield, Carson R. Stephens, Daniela Loessner, and Judith A. Clements . Prostate Cancer-Associated Kallikrein-Related Peptidase 4 Activates Matrix Metalloproteinase-1 and Thrombospondin-1. Journal of Proteome Research 2016, 15 (8) , 2466-2478. https://doi.org/10.1021/acs.jproteome.5b01148
    40. John T. Halloran, Jeff A. Bilmes, and William S. Noble . Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra. Journal of Proteome Research 2016, 15 (8) , 2749-2759. https://doi.org/10.1021/acs.jproteome.6b00290
    41. Nicholas M. Riley, Marshall Bern, Michael S. Westphall, and Joshua J. Coon . Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation. Journal of Proteome Research 2016, 15 (8) , 2768-2776. https://doi.org/10.1021/acs.jproteome.6b00319
    42. Anita Saraf, Serena Cervantes, Evelien M. Bunnik, Nadia Ponts, Mihaela E. Sardiu, Duk-Won D. Chung, Jacques Prudhomme, Joseph M. Varberg, Zhihui Wen, Michael P. Washburn, Laurence Florens, and Karine G. Le Roch . Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite. Journal of Proteome Research 2016, 15 (8) , 2787-2801. https://doi.org/10.1021/acs.jproteome.6b00366
    43. Chuan-Yih Yu, Anoop Mayampurath, Rui Zhu, Lauren Zacharias, Ehwang Song, Lei Wang, Yehia Mechref, and Haixu Tang . Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides. Analytical Chemistry 2016, 88 (11) , 5725-5732. https://doi.org/10.1021/acs.analchem.5b04858
    44. Şule Yılmaz, Bjorn Victor, Niels Hulstaert, Elien Vandermarliere, Harald Barsnes, Sven Degroeve, Surya Gupta, Adriaan Sticker, Sarah Gabriël, Pierre Dorny, Magnus Palmblad, and Lennart Martens . A Pipeline for Differential Proteomics in Unsequenced Species. Journal of Proteome Research 2016, 15 (6) , 1963-1970. https://doi.org/10.1021/acs.jproteome.6b00140
    45. Janet E. McCombs and Jennifer J. Kohler . Pneumococcal Neuraminidase Substrates Identified through Comparative Proteomics Enabled by Chemoselective Labeling. Bioconjugate Chemistry 2016, 27 (4) , 1013-1022. https://doi.org/10.1021/acs.bioconjchem.6b00050
    46. Matthias Schittmayer, Katarina Fritz, Laura Liesinger, Johannes Griss, and Ruth Birner-Gruenberger . Cleaning out the Litterbox of Proteomic Scientists’ Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts. Journal of Proteome Research 2016, 15 (4) , 1222-1229. https://doi.org/10.1021/acs.jproteome.5b01105
    47. Kai-Ting Fan, Aaron K. Rendahl, Wen-Ping Chen, Dana M. Freund, William M. Gray, Jerry D. Cohen, and Adrian D. Hegeman . Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants. Journal of Proteome Research 2016, 15 (3) , 851-867. https://doi.org/10.1021/acs.jproteome.5b00772
    48. Chris Bielow, Guido Mastrobuoni, and Stefan Kempa . Proteomics Quality Control: Quality Control Software for MaxQuant Results. Journal of Proteome Research 2016, 15 (3) , 777-787. https://doi.org/10.1021/acs.jproteome.5b00780
    49. Lukas P. M. Kremer, Johannes Leufken, Purevdulam Oyunchimeg, Stefan Schulze, and Christian Fufezan . Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis. Journal of Proteome Research 2016, 15 (3) , 788-794. https://doi.org/10.1021/acs.jproteome.5b00860
    50. Jennifer S. Brodbelt . Ion Activation Methods for Peptides and Proteins. Analytical Chemistry 2016, 88 (1) , 30-51. https://doi.org/10.1021/acs.analchem.5b04563
    51. Jin-Young Cho, Hyoung-Joo Lee, Seul-Ki Jeong, Kwang-Youl Kim, Kyung-Hoon Kwon, Jong Shin Yoo, Gilbert S. Omenn, Mark S. Baker, William S. Hancock, and Young-Ki Paik . Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project. Journal of Proteome Research 2015, 14 (12) , 4959-4966. https://doi.org/10.1021/acs.jproteome.5b00578
    52. Dhirendra Kumar, Aradhya Jain, and Debasis Dash . Probing the Missing Human Proteome: A Computational Perspective. Journal of Proteome Research 2015, 14 (12) , 4949-4958. https://doi.org/10.1021/acs.jproteome.5b00728
    53. Bruce D. Pascal, Graham M. West, Catherina Scharager-Tapia, Ricardo Flefil, Tina Moroni, Pablo Martinez-Acedo, Patrick R. Griffin, Anthony C. Carvalloza. Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications. Journal of the American Society for Mass Spectrometry 2015, 26 (12) , 2133-2140. https://doi.org/10.1007/s13361-015-1229-4
    54. Chengjian Tu, Quanhu Sheng, Jun Li, Danjun Ma, Xiaomeng Shen, Xue Wang, Yu Shyr, Zhengping Yi, and Jun Qu . Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data. Journal of Proteome Research 2015, 14 (11) , 4662-4673. https://doi.org/10.1021/acs.jproteome.5b00536
    55. Mathieu Lavallée-Adam, Sung Kyu Robin Park, Salvador Martínez-Bartolomé, Lin He, John R. Yates, III. From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics. Journal of the American Society for Mass Spectrometry 2015, 26 (11) , 1820-1826. https://doi.org/10.1007/s13361-015-1161-7
    56. Christopher M. Rose, Matthew J. P. Rush, Nicholas M. Riley, Anna E. Merrill, Nicholas W. Kwiecien, Dustin D. Holden, Christopher Mullen, Michael S. Westphall, Joshua J. Coon. A Calibration Routine for Efficient ETD in Large-Scale Proteomics. Journal of the American Society for Mass Spectrometry 2015, 26 (11) , 1848-1857. https://doi.org/10.1007/s13361-015-1183-1
    57. Rovshan G. Sadygov. Using SEQUEST with Theoretically Complete Sequence Databases. Journal of the American Society for Mass Spectrometry 2015, 26 (11) , 1858-1864. https://doi.org/10.1007/s13361-015-1228-5
    58. Nicholas B. Borotto, Yuping Zhou, Stephen R. Hollingsworth, John E. Hale, Eric M. Graban, Robert C. Vaughan, and Richard W. Vachet . Investigating Therapeutic Protein Structure with Diethylpyrocarbonate Labeling and Mass Spectrometry. Analytical Chemistry 2015, 87 (20) , 10627-10634. https://doi.org/10.1021/acs.analchem.5b03180
    59. Petar Žuvela, J. Jay Liu, Katarzyna Macur, and Tomasz Bączek . Molecular Descriptor Subset Selection in Theoretical Peptide Quantitative Structure–Retention Relationship Model Development Using Nature-Inspired Optimization Algorithms. Analytical Chemistry 2015, 87 (19) , 9876-9883. https://doi.org/10.1021/acs.analchem.5b02349
    60. Attila Kertesz-Farkas , Uri Keich , William Stafford Noble . Tandem Mass Spectrum Identification via Cascaded Search. Journal of Proteome Research 2015, 14 (8) , 3027-3038. https://doi.org/10.1021/pr501173s
    61. Jianqi Wang, Yajie Zhang, Yonghao Yu. Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra. Journal of the American Society for Mass Spectrometry 2015, 26 (7) , 1077-1084. https://doi.org/10.1007/s13361-015-1120-3
    62. Giulia Gonnelli, Michiel Stock, Jan Verwaeren, Davy Maddelein, Bernard De Baets, Lennart Martens, and Sven Degroeve . A Decoy-Free Approach to the Identification of Peptides. Journal of Proteome Research 2015, 14 (4) , 1792-1798. https://doi.org/10.1021/pr501164r
    63. René B. H. Braakman, Karel Bezstarosti, Anieta M. Sieuwerts, Vanja de Weerd, Anne M. van Galen, Christoph Stingl, Theo M. Luider, Mieke A. M. Timmermans, Marcel Smid, John W. M. Martens, John A. Foekens, Jeroen A. A. Demmers, and Arzu Umar . Integrative Analysis of Genomics and Proteomics Data on Clinical Breast Cancer Tissue Specimens Extracted with Acid Guanidinium Thiocyanate–Phenol–Chloroform. Journal of Proteome Research 2015, 14 (3) , 1627-1636. https://doi.org/10.1021/acs.jproteome.5b00046
    64. Thilo Muth, Alexander Behne, Robert Heyer, Fabian Kohrs, Dirk Benndorf, Marcus Hoffmann, Miro Lehtevä, Udo Reichl, Lennart Martens, and Erdmann Rapp . The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation. Journal of Proteome Research 2015, 14 (3) , 1557-1565. https://doi.org/10.1021/pr501246w
    65. Timo Sachsenberg, Florian-Alexander Herbst, Martin Taubert, René Kermer, Nico Jehmlich, Martin von Bergen, Jana Seifert, and Oliver Kohlbacher . MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics. Journal of Proteome Research 2015, 14 (2) , 619-627. https://doi.org/10.1021/pr500245w
    66. Uri Keich and William Stafford Noble . On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra. Journal of Proteome Research 2015, 14 (2) , 1147-1160. https://doi.org/10.1021/pr5010983
    67. Wenzhou Li Hua Xu Oleg Borisov . Informatics for Mass Spectrometry-Based Protein Characterization. 2015, 189-225. https://doi.org/10.1021/bk-2015-1202.ch007
    68. Zuo-Fei Yuan, Shu Lin, Rosalynn C. Molden, and Benjamin A. Garcia . Evaluation of Proteomic Search Engines for the Analysis of Histone Modifications. Journal of Proteome Research 2014, 13 (10) , 4470-4478. https://doi.org/10.1021/pr5008015
    69. Viktoria Dorfer, Peter Pichler, Thomas Stranzl, Johannes Stadlmann, Thomas Taus, Stephan Winkler, and Karl Mechtler . MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra. Journal of Proteome Research 2014, 13 (8) , 3679-3684. https://doi.org/10.1021/pr500202e
    70. Peng Wu, Hongyu Zhang, Weiran Lin, Yunwei Hao, Liangliang Ren, Chengpu Zhang, Ning Li, Handong Wei, Ying Jiang, and Fuchu He . Discovery of Novel Genes and Gene Isoforms by Integrating Transcriptomic and Proteomic Profiling from Mouse Liver. Journal of Proteome Research 2014, 13 (5) , 2409-2419. https://doi.org/10.1021/pr4012206
    71. Mark V. Ivanov, Lev I. Levitsky, Anna A. Lobas, Tanja Panic, Ünige A. Laskay, Goran Mitulovic, Rainer Schmid, Marina L. Pridatchenko, Yury O. Tsybin, and Mikhail V. Gorshkov . Empirical Multidimensional Space for Scoring Peptide Spectrum Matches in Shotgun Proteomics. Journal of Proteome Research 2014, 13 (4) , 1911-1920. https://doi.org/10.1021/pr401026y
    72. Miin S. Lin, Justin J. Cherny, Claire T. Fournier, Samuel J. Roth, Danny Krizanc, and Michael P. Weir . Assessment of MS/MS Search Algorithms with Parent-Protein Profiling. Journal of Proteome Research 2014, 13 (4) , 1823-1832. https://doi.org/10.1021/pr401090d
    73. Derek J. Bailey, Molly T. McDevitt, Michael S. Westphall, David J. Pagliarini, and Joshua J. Coon . Intelligent Data Acquisition Blends Targeted and Discovery Methods. Journal of Proteome Research 2014, 13 (4) , 2152-2161. https://doi.org/10.1021/pr401278j
    74. Xiaofen Liu, Yingwei Hu, Pei-Jing Pai, Daijie Chen, and Henry Lam . Label-Free Quantitative Proteomics Analysis of Antibiotic Response in Staphylococcus aureus to Oxacillin. Journal of Proteome Research 2014, 13 (3) , 1223-1233. https://doi.org/10.1021/pr400669d
    75. Heike Wiese, Katja Kuhlmann, Sebastian Wiese, Nadine S. Stoepel, Magdalena Pawlas, Helmut E. Meyer, Christian Stephan, Martin Eisenacher, Friedel Drepper, and Bettina Warscheid . Comparison of Alternative MS/MS and Bioinformatics Approaches for Confident Phosphorylation Site Localization. Journal of Proteome Research 2014, 13 (2) , 1128-1137. https://doi.org/10.1021/pr400402s
    76. Thilo Muth, Lisa Weilnböck, Erdmann Rapp, Christian G. Huber, Lennart Martens, Marc Vaudel, and Harald Barsnes . DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra. Journal of Proteome Research 2014, 13 (2) , 1143-1146. https://doi.org/10.1021/pr4008078
    77. Bruce R. Southey, Ji Eun Lee, Leonid Zamdborg, Norman Atkins, Jr., Jennifer W. Mitchell, Mingxi Li, Martha U. Gillette, Neil L. Kelleher, and Jonathan V. Sweedler . Comparing Label-Free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus. Analytical Chemistry 2014, 86 (1) , 443-452. https://doi.org/10.1021/ac4023378
    78. Roger Higdon, Elizabeth Stewart, Larissa Stanberry, Winston Haynes, John Choiniere, Elizabeth Montague, Nathaniel Anderson, Gregory Yandl, Imre Janko, William Broomall, Simon Fishilevich, Doron Lancet, Natali Kolker, and Eugene Kolker. MOPED Enables Discoveries through Consistently Processed Proteomics Data. Journal of Proteome Research 2014, 13 (1) , 107-113. https://doi.org/10.1021/pr400884c
    79. Arne Ulbrich, Anna E. Merrill, Alexander S. Hebert, Michael S. Westphall, Mark P. Keller, Alan D. Attie, Joshua J. Coon. Neutron-Encoded Protein Quantification by Peptide Carbamylation. Journal of the American Society for Mass Spectrometry 2014, 25 (1) , 6-9. https://doi.org/10.1007/s13361-013-0765-z
    80. Eisuke Hayakawa, Gerben Menschaert, Pieter-Jan De Bock, Walter Luyten, Kris Gevaert, Geert Baggerman, and Liliane Schoofs . Improving the Identification Rate of Endogenous Peptides Using Electron Transfer Dissociation and Collision-Induced Dissociation. Journal of Proteome Research 2013, 12 (12) , 5410-5421. https://doi.org/10.1021/pr400446z
    81. Yingwei Hu and Henry Lam . Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications. Journal of Proteome Research 2013, 12 (12) , 5971-5977. https://doi.org/10.1021/pr4007443
    82. Scott A. Robotham, Christien Kluwe, Joe R. Cannon, Andrew Ellington, and Jennifer S. Brodbelt . De Novo Sequencing of Peptides Using Selective 351 nm Ultraviolet Photodissociation Mass Spectrometry. Analytical Chemistry 2013, 85 (20) , 9832-9838. https://doi.org/10.1021/ac402309h
    83. Brian A. Risk, Nathan J. Edwards, and Morgan C. Giddings . A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities. Journal of Proteome Research 2013, 12 (9) , 4240-4247. https://doi.org/10.1021/pr400286p
    84. Xin Huang, Lin Huang, Hong Peng, Ashu Guru, Weihua Xue, Sang Yong Hong, Miao Liu, Seema Sharma, Kai Fu, Adam P. Caprez, David R. Swanson, Zhixin Zhang, and Shi-Jian Ding . ISPTM: An Iterative Search Algorithm for Systematic Identification of Post-translational Modifications from Complex Proteome Mixtures. Journal of Proteome Research 2013, 12 (9) , 3831-3842. https://doi.org/10.1021/pr4003883
    85. Zhikai Zhu, Xiaomeng Su, Daniel F. Clark, Eden P. Go, and Heather Desaire . Characterizing O-Linked Glycopeptides by Electron Transfer Dissociation: Fragmentation Rules and Applications in Data Analysis. Analytical Chemistry 2013, 85 (17) , 8403-8411. https://doi.org/10.1021/ac401814h
    86. Anastasia Kalli, Geoffrey T. Smith, Michael J. Sweredoski, and Sonja Hess . Evaluation and Optimization of Mass Spectrometric Settings during Data-dependent Acquisition Mode: Focus on LTQ-Orbitrap Mass Analyzers. Journal of Proteome Research 2013, 12 (7) , 3071-3086. https://doi.org/10.1021/pr3011588
    87. Wenguang Shao and Henry Lam . Denoising Peptide Tandem Mass Spectra for Spectral Libraries: A Bayesian Approach. Journal of Proteome Research 2013, 12 (7) , 3223-3232. https://doi.org/10.1021/pr400080b
    88. S. Farshid Moussavi-Harami, Douglas S. Annis, Wenjiang Ma, Scott M. Berry, Emma E. Coughlin, Lindsay N. Strotman, Lisa M. Maurer, Michael S. Westphall, Joshua J. Coon, Deane F. Mosher, and David J. Beebe . Characterization of Molecules Binding to the 70K N-Terminal Region of Fibronectin by IFAST Purification Coupled with Mass Spectrometry. Journal of Proteome Research 2013, 12 (7) , 3393-3404. https://doi.org/10.1021/pr400225p
    89. Dennis Linke, Chien-Wen Hung, Liam Cassidy, and Andreas Tholey . Optimized Fragmentation Conditions for iTRAQ-labeled Phosphopeptides. Journal of Proteome Research 2013, 12 (6) , 2755-2763. https://doi.org/10.1021/pr400113n
    90. Christopher M. Rose, Anna E. Merrill, Derek J. Bailey, Alexander S. Hebert, Michael S. Westphall, and Joshua J. Coon . Neutron Encoded Labeling for Peptide Identification. Analytical Chemistry 2013, 85 (10) , 5129-5137. https://doi.org/10.1021/ac400476w
    91. Thomas Fannes, Elien Vandermarliere, Leander Schietgat, Sven Degroeve, Lennart Martens, and Jan Ramon . Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles. Journal of Proteome Research 2013, 12 (5) , 2253-2259. https://doi.org/10.1021/pr4001114
    92. Chad P. Satori, Michelle M. Henderson, Elyse A. Krautkramer, Vratislav Kostal, Mark M. Distefano, and Edgar A. Arriaga . Bioanalysis of Eukaryotic Organelles. Chemical Reviews 2013, 113 (4) , 2733-2811. https://doi.org/10.1021/cr300354g
    93. Hosein Mohimani, Sangtae Kim, and Pavel A. Pevzner . A New Approach to Evaluating Statistical Significance of Spectral Identifications. Journal of Proteome Research 2013, 12 (4) , 1560-1568. https://doi.org/10.1021/pr300453t
    94. Hendrik Weisser, Sven Nahnsen, Jonas Grossmann, Lars Nilse, Andreas Quandt, Hendrik Brauer, Marc Sturm, Erhan Kenar, Oliver Kohlbacher, Ruedi Aebersold, and Lars Malmström . An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics. Journal of Proteome Research 2013, 12 (4) , 1628-1644. https://doi.org/10.1021/pr300992u
    95. Yasset Perez-Riverol, Aniel Sánchez, Jesus Noda, Diogo Borges, Paulo Costa Carvalho, Rui Wang, Juan Antonio Vizcaíno, Lázaro Betancourt, Yassel Ramos, Gabriel Duarte, Fabio C.S. Nogueira, Luis J. González, Gabriel Padrón, David L. Tabb, Henning Hermjakob, Gilberto B. Domont, and Vladimir Besada . HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions. Analytical Chemistry 2013, 85 (7) , 3515-3520. https://doi.org/10.1021/ac303239g
    96. Andrew B. Dykstra, Miguel Rodriguez, Jr., Babu Raman, Kelsey D. Cook, and Robert L. Hettich . Characterizing the Range of Extracellular Protein Post-Translational Modifications in a Cellulose-Degrading Bacteria Using a Multiple Proteolyic Digestion/Peptide Fragmentation Approach. Analytical Chemistry 2013, 85 (6) , 3144-3151. https://doi.org/10.1021/ac3032838
    97. Catherine E. Vincent, Gregory K. Potts, Arne Ulbrich, Michael S. Westphall, James A. Atwood, III, Joshua J. Coon, and D. Brent Weatherly . Segmentation of Precursor Mass Range Using “Tiling” Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification. Analytical Chemistry 2013, 85 (5) , 2825-2832. https://doi.org/10.1021/ac303352n
    98. Craig D. Wenger and Joshua J. Coon . A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra. Journal of Proteome Research 2013, 12 (3) , 1377-1386. https://doi.org/10.1021/pr301024c
    99. Richard S. L. Stein, Nan Li, Wei He, Elizabeth Komives, and Wei Wang . Recognition of Methylated Peptides by Drosophila melanogaster Polycomb Chromodomain. Journal of Proteome Research 2013, 12 (3) , 1467-1477. https://doi.org/10.1021/pr3011205
    100. Ji Eun Lee, Leonid Zamdborg, Bruce R. Southey, Norman Atkins, Jr., Jennifer W. Mitchell, Mingxi Li, Martha U. Gillette, Neil L. Kelleher, and Jonathan V. Sweedler . Quantitative Peptidomics for Discovery of Circadian-Related Peptides from the Rat Suprachiasmatic Nucleus. Journal of Proteome Research 2013, 12 (2) , 585-593. https://doi.org/10.1021/pr300605p
    Load more 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.

    MENDELEY PAIRING EXPIRED
    Your Mendeley pairing has expired. Please reconnect