646
Views
74
CrossRef citations to date
0
Altmetric
Review

Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics

&
Pages 611-619 | Published online: 09 Jan 2014

Keep up to date with the latest research on this topic with citation updates for this article.

Read on this site (6)

Maria-Linda Popa, Radu Albulescu, Monica Neagu, Mihail Eugen Hinescu & Cristiana Tanase. (2019) Multiplex assay for multiomics advances in personalized-precision medicine. Journal of Immunoassay and Immunochemistry 40:1, pages 3-25.
Read now
Kai Pong Law & Yoon Pin Lim. (2013) Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Review of Proteomics 10:6, pages 551-566.
Read now
Yansheng Liu, Ruth Hüttenhain, Ben Collins & Ruedi Aebersold. (2013) Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Review of Molecular Diagnostics 13:8, pages 811-825.
Read now
Oda Stoevesandt & Michael J Taussig. (2012) Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Review of Proteomics 9:4, pages 401-414.
Read now
Mikkel Nissum & Aude L Foucher. (2008) Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis. Expert Review of Proteomics 5:4, pages 571-587.
Read now
Praveen Govender, John A Baugh, Stephen R Pennington, Michael J Dunn & Seamas C Donnelly. (2007) Role of proteomics in the investigation of pulmonary fibrosis. Expert Review of Proteomics 4:3, pages 379-388.
Read now

Articles from other publishers (68)

Zhuhui Chen, Yue Xiong, Ranran Ma, Pei Chen, Le Duan, Shuying Yang, Ineza Urujeni Gisèle, Linjun You & Deli Xiao. (2023) A novel magnetic fluid for ultra-fast and highly efficient extraction of N 1 -methylnicotinamide in urine samples . New Journal of Chemistry 47:16, pages 7862-7872.
Crossref
Yaoran Liu, Zilong Wu, Daniel W. Armstrong, Herman Wolosker & Yuebing Zheng. (2023) Detection and analysis of chiral molecules as disease biomarkers. Nature Reviews Chemistry 7:5, pages 355-373.
Crossref
Christina Warinner, Kristine Korzow Richter & Matthew J. Collins. (2022) Paleoproteomics. Chemical Reviews 122:16, pages 13401-13446.
Crossref
Rivkah Rogawski & Michal Sharon. (2021) Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry. Chemical Reviews 122:8, pages 7386-7414.
Crossref
Rivkah Rogawski, Adi Rogel, Itai Bloch, Maayan Gal, Amnon Horovitz, Nir London & Michal Sharon. (2021) Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angewandte Chemie International Edition 60:36, pages 19637-19642.
Crossref
Rivkah Rogawski, Adi Rogel, Itai Bloch, Maayan Gal, Amnon Horovitz, Nir London & Michal Sharon. (2021) Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angewandte Chemie 133:36, pages 19789-19794.
Crossref
Nianrong Sun, Hailong Yu, Hao Wu, Xizhong Shen & Chunhui Deng. (2021) Advanced nanomaterials as sample technique for bio-analysis. TrAC Trends in Analytical Chemistry 135, pages 116168.
Crossref
Wolfgang Esser-Skala, Marius Segl, Therese Wohlschlager, Veronika Reisinger, Johann Holzmann & Christian G. Huber. (2020) Exploring sample preparation and data evaluation strategies for enhanced identification of host cell proteins in drug products of therapeutic antibodies and Fc-fusion proteins. Analytical and Bioanalytical Chemistry 412:24, pages 6583-6593.
Crossref
Daria N. Kashirina, Alexander G. Brzhozovskiy, Ludmila Kh. Pastushkova, Alexey S. Kononikhin, Christoph H. Borchers, Evgeny N. Nikolaev & Irina M. Larina. (2020) Semiquantitative Proteomic Research of Protein Plasma Profile of Volunteers in 21-Day Head-Down Bed Rest. Frontiers in Physiology 11.
Crossref
Menna El Demeiry, Ahmed Ali, Yasmine Abouleila, Yoshihiro Shimizu, Tsutomu Masujima, Randa Abdel Salam, Ghada Hadad & Samy Emara. (2020) Quantification and targeted detection of ciprofloxacin in dosage form and human urine by direct injection nano-electrospray ionization multi-stage mass spectrometry. Microchemical Journal 153, pages 104534.
Crossref
Shay Vimer, Gili Ben-Nissan & Michal Sharon. (2020) Direct characterization of overproduced proteins by native mass spectrometry. Nature Protocols 15:2, pages 236-265.
Crossref
Kasey M. Schalich, Anthony W. Herren & Vimal Selvaraj. (2020) Analysis of differential strategies to enhance detection of low‐abundance proteins in the bovine serum proteome. Animal Science Journal 91:1.
Crossref
Alexander G. Brzhozovskiy, Alexey S. Kononikhin, Lyudmila Ch. Pastushkova, Daria N. Kashirina, Maria I. Indeykina, Igor A. Popov, Marc-Antoine Custaud, Irina M. Larina & Evgeny N. Nikolaev. (2019) The Effects of Spaceflight Factors on the Human Plasma Proteome, Including Both Real Space Missions and Ground-Based Experiments. International Journal of Molecular Sciences 20:13, pages 3194.
Crossref
Kumar Yugandhar, Shagun Gupta & Haiyuan Yu. (2019) Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Computational and Structural Biotechnology Journal 17, pages 805-811.
Crossref
Donghwi Kim, Joonhee Lee, Byungjoo Kim & Sunghwan Kim. (2018) Optimization and Application of Paper-Based Spray Ionization Mass Spectrometry for Analysis of Natural Organic Matter. Analytical Chemistry 90:20, pages 12027-12034.
Crossref
Pietro Boccaletto, Mohammad Abdul Momin Siddique & Jacky Cosson. (2018) Proteomics: A valuable approach to elucidate spermatozoa post –testicular maturation in the endangered Acipenseridae family. Animal Reproduction Science 192, pages 18-27.
Crossref
Zhihong Chen & Xiangdong Wang. 2018. Genomic Approach to Asthma. Genomic Approach to Asthma 1 9 .
Carmine Savoia, Massimo Volpe, Guido Grassi, Claudio Borghi, Enrico Agabiti Rosei & Rhian M. Touyz. (2017) Personalized medicine—a modern approach for the diagnosis and management of hypertension. Clinical Science 131:22, pages 2671-2685.
Crossref
Keisuke Niikura, M. Shahanoor Alam, Masahiro Naruse, Mitsuru Jimbo, Hideaki Moriyama, Adrian Reich, Gary M. Wessel & Midori Matsumoto. (2017) Protein kinase A activity leads to the extension of the acrosomal process in starfish sperm. Molecular Reproduction and Development 84:7, pages 614-625.
Crossref
Liqing Gu, Adam R. Evans & Renã A. S. Robinson. (2015) Sample Multiplexing with Cysteine-Selective Approaches: cysDML and cPILOT. Journal of the American Society for Mass Spectrometry 26:4, pages 615-630.
Crossref
Batool Fatima, Fahmida Jabeen, Zahra Padashbarmchi & Muhammad Najam-ul-Haq. (2015) Enhanced enrichment performance of nickel oxide nanoparticles via fabrication of a nanocomposite with a graphene template. RSC Advances 5:30, pages 23658-23665.
Crossref
Fangjun WangFangjun Wang. 2014. Applications of Monolithic Column and Isotope Dimethylation Labeling in Shotgun Proteome Analysis. Applications of Monolithic Column and Isotope Dimethylation Labeling in Shotgun Proteome Analysis 7 33 .
Andrew J. Creese, Neil J. Shimwell, Katherine P. B. Larkins, John K. Heath & Helen J. Cooper. (2013) Probing the Complementarity of FAIMS and Strong Cation Exchange Chromatography in Shotgun Proteomics. Journal of the American Society for Mass Spectrometry 24:3, pages 431-443.
Crossref
John Y. Ng, Lies Boelen & Jason W. H. Wong. (2013) Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome. Open Biology 3:2, pages 120148.
Crossref
Rui Chen & Michael Snyder. (2012) Promise of personalized omics to precision medicine. WIREs Systems Biology and Medicine 5:1, pages 73-82.
Crossref
Albin Fontaine, Thierry Fusaï, Sébastien Briolant, Sylvain Buffet, Claude Villard, Emilie Baudelet, Mathieu Pophillat, Samuel Granjeaud, Christophe Rogier & Lionel Almeras. (2012) Anopheles salivary gland proteomes from major malaria vectors. BMC Genomics 13:1.
Crossref
P.C. Wright, J. Noirel, S.-Y. Ow & A. Fazeli. (2012) A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 77:4, pages 738-765.e52.
Crossref
Sylvain Bischof, Jonas Grossmann & Wilhelm Gruissem. 2012. Plant Biotechnology and Agriculture. Plant Biotechnology and Agriculture 55 65 .
Ján A. Miernyk & Mark L. Johnston. 2012. Seed Development: OMICS Technologies toward Improvement of Seed Quality and Crop Yield. Seed Development: OMICS Technologies toward Improvement of Seed Quality and Crop Yield 265 278 .
Rommel A. Mathias, Hong Ji & Richard J. Simpson. 2012. Difference Gel Electrophoresis (DIGE). Difference Gel Electrophoresis (DIGE) 269 286 .
Ching-Seng Ang, Steve Binos, Matthew I Knight, Peter J Moate, Benjamin G Cocks & Matthew B McDonagh. (2011) Global Survey of the Bovine Salivary Proteome: Integrating Multidimensional Prefractionation, Targeted, and Glycocapture Strategies. Journal of Proteome Research 10:11, pages 5059-5069.
Crossref
Diederick Duijvesz, Theo Luider, Chris H. Bangma & Guido Jenster. (2011) Exosomes as Biomarker Treasure Chests for Prostate Cancer. European Urology 59:5, pages 823-831.
Crossref
Franz D. Bergmann, Draženka Selesi & Rainer U. Meckenstock. (2011) Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47. Archives of Microbiology 193:4, pages 241-250.
Crossref
V. M. Govorun & V. T. Ivanov. (2011) Proteomics and peptidomics in fundamental and applied medical studies. Russian Journal of Bioorganic Chemistry 37:2, pages 176-190.
Crossref
Inez Finoulst, Martijn Pinkse, William Van Dongen & Peter Verhaert. (2011) Sample Preparation Techniques for the Untargeted LC-MS-Based Discovery of Peptides in Complex Biological Matrices. Journal of Biomedicine and Biotechnology 2011, pages 1-14.
Crossref
Agnes Rafalko, Othon Iliopoulos, Vincent A. Fusaro, William Hancock & Marina Hincapie. (2010) Immunoaffinity Enrichment and Liquid Chromatography-Selected Reaction Monitoring Mass Spectrometry for Quantitation of Carbonic Anhydrase 12 in Cultured Renal Carcinoma Cells. Analytical Chemistry 82:21, pages 8998-9005.
Crossref
Alexey I. Nesvizhskii. (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. Journal of Proteomics 73:11, pages 2092-2123.
Crossref
Rui Chen & Michael Snyder. (2010) Yeast proteomics and protein microarrays. Journal of Proteomics 73:11, pages 2147-2157.
Crossref
Meike Moschallski, Monika Hausmann, Anton Posch, Aran Paulus, Nancy Kunz, Thanh Tu Duong, Brigitte Angres, Kai Fuchsberger, Heiko Steuer, Dieter Stoll, Simon Werner, Britta Hagmeyer & Martin Stelzle. (2010) MicroPrep: Chip-based dielectrophoretic purification of mitochondria. ELECTROPHORESIS 31:15, pages 2655-2663.
Crossref
LiJuan Zhang, HaoJie Lu & PengYuan Yang. (2010) Recent developments of nanoparticle-based enrichment methods for mass spectrometric analysis in proteomics. Science China Chemistry 53:4, pages 695-703.
Crossref
Rommel A. Mathias, Yuan-Shou Chen, Bo Wang, Hong Ji, Eugene A. Kapp, Robert L. Moritz, Hong-Jian Zhu & Richard J. Simpson. (2010) Extracellular Remodelling During Oncogenic Ras-Induced Epithelial-Mesenchymal Transition Facilitates MDCK Cell Migration. Journal of Proteome Research 9:2, pages 1007-1019.
Crossref
I. A. Brewis & B. M. Gadella. (2009) Sperm surface proteomics: from protein lists to biological function. Molecular Human Reproduction 16:2, pages 68-79.
Crossref
Giuseppina Maccarrone, Christoph W. Turck & Daniel Martins-de-Souza. (2010) Shotgun Mass Spectrometry Workflow Combining IEF and LC-MALDI-TOF/TOF. The Protein Journal 29:2, pages 99-102.
Crossref
Marco F. L. Lemos, Amadeu M. V. M. Soares, António C. Correia & Ana C. Esteves. (2010) Proteins in ecotoxicology - How, why and why not?. PROTEOMICS 10:4, pages 873-887.
Crossref
Brent R. Reschke, Jarrod Schiffbauer, Boyd F. Edwards & Aaron T. Timperman. (2010) Simultaneous separation and detection of cations and anions on a microfluidic device with suppressed electroosmotic flow and a single injection point. The Analyst 135:6, pages 1351.
Crossref
Ian A. Brewis & P. Brennan. 2010. 1 44 .
Lijuang Zhang, Haojie Lu & Pengyuan Yang. (2009) Specific enrichment methods for glycoproteome research. Analytical and Bioanalytical Chemistry 396:1, pages 199-203.
Crossref
Mitchell Gross, Edward Macrohon Nepomuceno & David B. Agus. 2010. Drug Management of Prostate Cancer. Drug Management of Prostate Cancer 407 417 .
Jason WH Wong, Alexander B Schwahn & Kevin M Downard. (2009) ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics. BMC Bioinformatics 10:1.
Crossref
Lujian Liao, Daniel B. McClatchy & John R. Yates. (2009) Shotgun Proteomics in Neuroscience. Neuron 63:1, pages 12-26.
Crossref
Hong-Xia Dong, Hai-Xia Li, Guo-Sheng Xie & Han-Lai Zeng. (2009) Identification of Differentially Expressed Proteins Associated with Chlorophyll-Deficient Mutant Rice. Asian Journal of Plant Sciences 8:5, pages 344-352.
Crossref
MH Han & L Steinman. (2009) Systems biology for identification of molecular networks in multiple sclerosis. Multiple Sclerosis Journal 15:5, pages 529-530.
Crossref
Daniel Martins-de-Souza, Giuseppina Maccarrone, Stefan Reckow, Peter Falkai, Andrea Schmitt & Christoph W. Turck. (2009) Shotgun mass spectrometry analysis of the human thalamus proteome. Journal of Separation Science 32:8, pages 1231-1236.
Crossref
J.M. Robinson, D.D. Vandré & W.E. AckermanIVIV. (2009) Placental Proteomics: A Shortcut to Biological Insight. Placenta 30, pages 83-89.
Crossref
Weiwei Wu, Heidi Slåstad, Daniel de la Rosa Carrillo, Tom Frey, Geir Tjønnfjord, Eva Boretti, Hans-Christian Aasheim, Vaclav Horejsi & Fridtjof Lund-Johansen. (2009) Antibody Array Analysis with Label-based Detection and Resolution of Protein Size. Molecular & Cellular Proteomics 8:2, pages 245-257.
Crossref
Nitin Agarwal & Eric V. Shusta. (2009) Multiplex expression cloning of blood–brain barrier membrane proteins. PROTEOMICS 9:4, pages 1099-1108.
Crossref
Jennifer J. Hill, Maria J. Moreno, Jean C. Y. Lam, Arsalan S. Haqqani & John F. Kelly. (2009) Identification of secreted proteins regulated by cAMP in glioblastoma cells using glycopeptide capture and label-free quantification. PROTEOMICS 9:3, pages 535-549.
Crossref
Brent R. Reschke, Hao Luo, Jarrod Schiffbauer, Boyd F. Edwards & Aaron T. Timperman. (2009) A theoretical and experimental study of the electrophoretic extraction of ions from a pressure driven flow in a microfluidic device. Lab on a Chip 9:15, pages 2203.
Crossref
Jacqueline Burré, Ilka Wittig & Hermann Schägger. 2009. Proteomics. Proteomics 33 57 .
Victor J. Nesatyy & Marc J.-F. Suter. (2008) Analysis of environmental stress response on the proteome level. Mass Spectrometry Reviews 27:6, pages 556-574.
Crossref
Johannes A. Hewel & Andrew Emili. (2008) High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates. PROTEOMICS - CLINICAL APPLICATIONS 2:10-11, pages 1422-1434.
Crossref
Wilma Dormeyer, Dennis van Hoof, Christine L. Mummery, Jeroen Krijgsveld & Albert J. R. Heck. (2008) A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. PROTEOMICS 8:19, pages 4036-4053.
Crossref
Daniel Martins-de-Souza, Wagner F. Gattaz, Andrea Schmitt, Christiane Rewerts, Giuseppina Maccarrone, Emmanuel Dias-Neto & Christoph W. Turck. (2008) Proteome analysis of human dorsolateral prefrontal cortex using shotgun mass spectrometry. Journal of Separation Science 31:16-17, pages 3122-3126.
Crossref
D. Martins de Souza, B. M. Oliveira, E. Castro-Dias, F. V. Winck, R. S. O. Horiuchi, P. A. Baldasso, H. T. Caetano, N. K. D. Pires, S. Marangoni & J. C. Novello. (2008) The untiring search for the most complete proteome representation: reviewing the methods. Briefings in Functional Genomics and Proteomics 7:4, pages 312-321.
Crossref
Jason D. Hoffert & Mark A. Knepper. (2008) Taking aim at shotgun phosphoproteomics. Analytical Biochemistry 375:1, pages 1-10.
Crossref
Stanley M. StevensJr.Jr., R. Scott Duncan, Peter Koulen & Laszlo Prokai. (2008) Proteomic Analysis of Mouse Brain Microsomes: Identification and Bioinformatic Characterization of Endoplasmic Reticulum Proteins in the Mammalian Central Nervous System. Journal of Proteome Research 7:3, pages 1046-1054.
Crossref
Mikkel Nissum, Sabine Kuhfuss, Monika Hauptmann, Christian Obermaier, Ute Sukop, Robert Wildgruber, Gerhard Weber, Christoph Eckerskorn & Johan Malmström. (2007) Two‐dimensional separation of human plasma proteins using iterative free‐flow electrophoresis. PROTEOMICS 7:23, pages 4218-4227.
Crossref
Linfeng Wu, Sun-Il Hwang, Karim Rezaul, Long J. Lu, Viveka Mayya, Mark Gerstein, Jimmy K. Eng, Deborah H. Lundgren & David K. Han. (2007) Global Survey of Human T Leukemic Cells by Integrating Proteomics and Transcriptomics Profiling. Molecular & Cellular Proteomics 6:8, pages 1343-1353.
Crossref

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.