Selected reaction monitoring applied to proteomics

Mass spectrometry-based proteomics

Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683

Mass Spectrometry and Protein Analysis

Domon, B., & Aebersold, R. (2006) · Science · doi:10.1126/science.1124619 · Cited by 2,181

Protein biomarker discovery and validation: the long and uncertain path to clinical utility

Rifai, N., Gillette, M. A., & Carr, S. A. (2006) · Nature Biotechnology · doi:10.1038/nbt1235 · Cited by 1,867

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733

Selected reaction monitoring for quantitative proteomics: a tutorial

Lange, V., Picotti, P., Domon, B., & Aebersold, R. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.61 · Cited by 1,407

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins

Anderson, L., & Hunter, C. L. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500331-mcp200 · Cited by 1,230

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1546 · Cited by 1,037

Characterization of the Low Molecular Weight Human Serum Proteome

Tirumalai, R. S., Chan, K. C., Prieto, D. A., Issaq, H. J., Conrads, T. P., & Veenstra, T. D. (2003) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300031-mcp200 · Cited by 860

Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA)

Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., & Pearson, T. W. (2004) · Journal of Proteome Research · doi:10.1021/pr034086h · Cited by 804

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R. (2009) · Cell · doi:10.1016/j.cell.2009.05.051 · Cited by 744

Computational prediction of proteotypic peptides for quantitative proteomics

Mallick, P., Schirle, M., Chen, S. S., Flory, M. R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1275 · Cited by 695

Open Source System for Analyzing, Validating, and Storing Protein Identification Data

Craig, R., Cortens, J. P., & Beavis, R. C. (2004) · Journal of Proteome Research · doi:10.1021/pr049882h · Cited by 694

Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution

Keshishian, H., Addona, T., Burgess, M., Kuhn, E., & Carr, S. A. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700354-mcp200 · Cited by 684

Tandem Mass Spectrometry

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PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

Deutsch, E. W., Lam, H., & Aebersold, R. (2008) · EMBO reports · doi:10.1038/embor.2008.56 · Cited by 542

Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma

Kuzyk, M. A., Smith, D., Yang, J., Cross, T. J., Jackson, A. M., Hardie, D. B., Anderson, N. L., & Borchers, C. H. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800540-mcp200 · Cited by 515

Limit of detection (LQD)/limit of quantitation (LOQ): comparison of the empirical and the statistical methods exemplified with GC-MS assays of abused drugs

Armbruster, D. A., Tillman, M. D., & Hubbs, L. M. (1994) · Clinical Chemistry · doi:10.1093/clinchem/40.7.1233 · Cited by 483

Isotope-labeled Protein Standards

Brun, V., Dupuis, A., Adrait, A., Marcellin, M., Thomas, D., Court, M., Vandenesch, F., & Garin, J. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700163-mcp200 · Cited by 445

Quantification of C‐reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C‐labeled peptide standards

Kuhn, E., Wu, J., Karl, J., Liao, H., Zolg, W., & Guild, B. (2004) · PROTEOMICS · doi:10.1002/pmic.200300670 · Cited by 398

Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes

Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J., & Beynon, R. J. (2006) · Nature Protocols · doi:10.1038/nprot.2006.129 · Cited by 373

Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using18O-labeled internal standards

Mirgorodskaya, O. A., Kozmin, Y. P., Titov, M. I., K�rner, R., S�nksen, C. P., & Roepstorff, P. (2000) · Rapid Communications in Mass Spectrometry · doi:10.1002/1097-0231(20000730)14:14<1226::aid-rcm14>3.0.co;2-v · Cited by 368

Quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry: A study of ion suppression

Buhrman, D. L., Price, P. I., & Rudewiczcor, P. J. (1996) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(96)00072-4 · Cited by 364

High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites

Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K., Krek, W., Aebersold, R., & Domon, B. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700132-mcp200 · Cited by 361

Liquid chromatography/atmospheric pressure ionization–mass spectrometry in drug metabolism studies

Kostiainen, R., Kotiaho, T., Kuuranne, T., & Auriola, S. (2003) · Journal of Mass Spectrometry · doi:10.1002/jms.481 · Cited by 349

Isotope dilution--mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I

Barr, J. R., Maggio, V. L., Patterson, D. G., Cooper, G. R., Henderson, L. O., Turner, W. E., Smith, S. J., Hannon, W. H., Needham, L. L., & Sampson, E. J. (1996) · Clinical Chemistry · doi:10.1093/clinchem/42.10.1676 · Cited by 347

Triple quadrupole mass spectrometry for direct mixture analysis and structure elucidation

Yost, R. A., & Enke, C. G. (1979) · Analytical Chemistry · doi:10.1021/ac50048a002 · Cited by 337

An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers

Whiteaker, J. R., Zhao, L., Anderson, L., & Paulovich, A. G. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900254-mcp200 · Cited by 323

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

Fusaro, V. A., Mani, D. R., Mesirov, J. P., & Carr, S. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1524 · Cited by 293

Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution

Keshishian, H., Addona, T., Burgess, M., Mani, D. R., Shi, X., Kuhn, E., Sabatine, M. S., Gerszten, R. E., & Carr, S. A. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900140-mcp200 · Cited by 286

An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC

Krokhin, O. V., Craig, R., Spicer, V., Ens, W., Standing, K. G., Beavis, R. C., & Wilkins, J. A. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400031-mcp200 · Cited by 284

Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis

Liao, H., Wu, J., Kuhn, E., Chin, W., Chang, B., Jones, M. D., O'Neil, S., Clauser, K. R., Karl, J., Hasler, F., et al. (2004) · Arthritis & Rheumatism · doi:10.1002/art.20720 · Cited by 283

A Correlation Algorithm for the Automated Quantitative Analysis of Shotgun Proteomics Data

MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., & Yates, J. R. (2003) · Analytical Chemistry · doi:10.1021/ac034790h · Cited by 278

Electrospray Ionization High-Field Asymmetric Waveform Ion Mobility Spectrometry−Mass Spectrometry

Purves, R. W., & Guevremont, R. (1999) · Analytical Chemistry · doi:10.1021/ac981380y · Cited by 265

Mass spectrometric characterization of a high-field asymmetric waveform ion mobility spectrometer

Purves, R. W., Guevremont, R., Day, S., Pipich, C. W., & Matyjaszczyk, M. S. (1998) · Review of Scientific Instruments · doi:10.1063/1.1149255 · Cited by 265

Absolute Quantification of the Model Biomarker Prostate-Specific Antigen in Serum by LC−MS/MS Using Protein Cleavage and Isotope Dilution Mass Spectrometry

Barnidge, D. R., Goodmanson, M. K., Klee, G. G., & Muddiman, D. C. (2004) · Journal of Proteome Research · doi:10.1021/pr049963d · Cited by 253

Developing Multiplexed Assays for Troponin I and Interleukin-33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry

Kuhn, E., Addona, T., Keshishian, H., Burgess, M., Mani, D. R., Lee, R. T., Sabatine, M. S., Gerszten, R. E., & Carr, S. A. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2009.123935 · Cited by 247

Absolute Quantification of the G Protein-Coupled Receptor Rhodopsin by LC/MS/MS Using Proteolysis Product Peptides and Synthetic Peptide Standards

Barnidge, D. R., Dratz, E. A., Martin, T., Bonilla, L. E., Moran, L. B., & Lindall, A. (2003) · Analytical Chemistry · doi:10.1021/ac026154+ · Cited by 227

Atmospheric pressure ion focusing in a high-field asymmetric waveform ion mobility spectrometer

Guevremont, R., & Purves, R. W. (1999) · Review of Scientific Instruments · doi:10.1063/1.1149599 · Cited by 218

A database of mass spectrometric assays for the yeast proteome

Picotti, P., Lam, H., Campbell, D., Deutsch, E. W., Mirzaei, H., Ranish, J., Domon, B., & Aebersold, R. (2008) · Nature Methods · doi:10.1038/nmeth1108-913 · Cited by 211

Multiple Reaction Monitoring to Identify Sites of Protein Phosphorylation with High Sensitivity

Unwin, R. D., Griffiths, J. R., Leverentz, M. K., Grallert, A., Hagan, I. M., & Whetton, A. D. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500113-mcp200 · Cited by 208

Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry

Liu, T., Qian, W.-J., Mottaz, H. M., Gritsenko, M. A., Norbeck, A. D., Moore, R. J., Purvine, S. O., Camp, D. G., & Smith, R. D. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t600039-mcp200 · Cited by 208

Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring

Lange, V., Malmström, J. A., Didion, J., King, N. L., Johansson, B. P., Schäfer, J., Rameseder, J., Wong, C.-H., Deutsch, E. W., Brusniak, M.-Y., et al. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800032-mcp200 · Cited by 204

A modified protein precipitation procedure for efficient removal of albumin from serum

Chen, Y., Lin, S., Yeh, Y., Hsiao, H., Wu, C., Chen, S., & Wang, A. H. ‐. (2005) · ELECTROPHORESIS · doi:10.1002/elps.200410381 · Cited by 193

A computational approach toward label-free protein quantification using predicted peptide detectability

Tang, H., Arnold, R. J., Alves, P., Xun, Z., Clemmer, D. E., Novotny, M. V., Reilly, J. P., & Radivojac, P. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl237 · Cited by 178

Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomics

Kiyonami, R., Schoen, A., Prakash, A., Peterman, S., Zabrouskov, V., Picotti, P., Aebersold, R., Huhmer, A., & Domon, B. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002931 · Cited by 177

Clinical Quantitation of Prostate-specific Antigen Biomarker in the Low Nanogram/Milliliter Range by Conventional Bore Liquid Chromatography-Tandem Mass Spectrometry (Multiple Reaction Monitoring) Coupling and Correlation with ELISA Tests

Fortin, T., Salvador, A., Charrier, J. P., Lenz, C., Lacoux, X., Morla, A., Choquet-Kastylevsky, G., & Lemoine, J. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800238-mcp200 · Cited by 177

Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues

DeSouza, L. V., Taylor, A. M., Li, W., Minkoff, M. S., Romaschin, A. D., Colgan, T. J., & Siu, K. W. M. (2008) · Journal of Proteome Research · doi:10.1021/pr800312m · Cited by 172

Head-to-Head Comparison of Serum Fractionation Techniques

Whiteaker, J. R., Zhang, H., Eng, J. K., Fang, R., Piening, B. D., Feng, L.-C., Lorentzen, T. D., Schoenherr, R. M., Keane, J. F., Holzman, T., et al. (2007) · Journal of Proteome Research · doi:10.1021/pr0604920 · Cited by 165

Product ion scanning using a Q‐q‐Q linear ion trap (Q TRAP TM ) mass spectrometer

Hager, J. W., & Yves Le Blanc, J. C. (2003) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1020 · Cited by 161

Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biologic tissue

Desiderio, D. M., & Kai, M. (1983) · Biological Mass Spectrometry · doi:10.1002/bms.1200100806 · Cited by 158

Improved recovery of proteome‐informative, protein N‐terminal peptides by combined fractional diagonal chromatography (COFRADIC)

Staes, A., Van Damme, P., Helsens, K., Demol, H., Vandekerckhove, J., & Gevaert, K. (2008) · PROTEOMICS · doi:10.1002/pmic.200700950 · Cited by 158

Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum

Fortin, T., Salvador, A., Charrier, J., Lenz, C., Bettsworth, F., Lacoux, X., Choquet‐Kastylevsky, G., & Lemoine, J. (2009) · Analytical Chemistry · doi:10.1021/ac901447h · Cited by 151

Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes

Zhang, H., Yan, W., & Aebersold, R. H. (2003) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2003.12.001 · Cited by 148

Weighted Least-Squares Approach To Calculating Limits of Detection and Quantification by Modeling Variability as a Function of Concentration

Zorn, M. E., Gibbons, R. D., & Sonzogni, W. C. (1997) · Analytical Chemistry · doi:10.1021/ac970082i · Cited by 147

PRIDE: new developments and new datasets

Jones, P., Cote, R. G., Cho, S. Y., Klie, S., Martens, L., Quinn, A. F., Thorneycroft, D., & Hermjakob, H. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1021 · Cited by 137

Tandem Mass Spectrometry

Suder, P. (2019) · Mass Spectrometry · doi:10.1002/9781119377368.ch7 · Cited by 136

Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocolPreprint

Gallien, S., Perrodou, E., Carapito, C., Deshayes, C., Reyrat, J., DORSSELAER, A. V., Poch, O., Schaeffer‐Reiss, C., & Lecompte, O. (2008) · Genome Research · doi:10.1101/gr.081901.108 · Cited by 119

The mechanisms of collisional activation of ions in mass spectrometry

Mayer, P., & Poon, C. (2009) · Mass Spectrometry Reviews · doi:10.1002/mas.20225 · Cited by 102

A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme

Janecki, D. J., Bemis, K. G., Tegeler, T. J., Sanghani, P. C., Zhai, L., Hurley, T. D., BOSRON, W. F., & Wang, M. (2007) · Analytical Biochemistry · doi:10.1016/j.ab.2007.06.043 · Cited by 98

Selective binding and enrichment for low‐molecular weight biomarker molecules in human plasma after exposure to nanoporous silica particles

Terracciano, R., Gaspari, M., Testa, F., Pasqua, L., Tagliaferri, P., Cheng, M. M., Nijdam, A. J., Petricoin, E. F., Liotta, L. A., Cuda, G., et al. (2006) · PROTEOMICS · doi:10.1002/pmic.200500614 · Cited by 96

Prediction of peptides observable by mass spectrometry applied at the experimental set level

Sanders, W. S., Bridges, S. M., McCarthy, F., Nanduri, B., & Burgess, S. C. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s7-s23 · Cited by 83

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

Webb‐Robertson, B., Cannon, W. R., OEHMEN, C. S., Shah, A. R., Gurumoorthi, V., Lipton, M. S. W., & Waters, K. M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn218 · Cited by 82

Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem

Duncan, M. W., Yergey, A. L., & Patterson, S. D. (2009) · PROTEOMICS · doi:10.1002/pmic.200800739 · Cited by 78

A Synthetic Protein Approach toward Accurate Mass Spectrometric Quantification of Component Stoichiometry of Multiprotein Complexes

Kito, K., Ota, K., Fujita, T., & Ito, T. (2007) · Journal of Proteome Research · doi:10.1021/pr060447s · Cited by 76

Relative and absolute quantitative expression profiling of cytochromes P450 using isotope‐coded affinity tags

Jenkins, R. E., Kitteringham, N. R., Hunter, C. L., Webb, S., Hunt, T., Elsby, R., Watson, R. B., Williams, D. P., Pennington, S. R., & Park, B. K. (2006) · PROTEOMICS · doi:10.1002/pmic.200500432 · Cited by 71

Free computational resources for designing selected reaction monitoring transitions

Cham, J. A., Bianco, L., & Bessant, C. (2010) · PROTEOMICS · doi:10.1002/pmic.200900396 · Cited by 61

Validated quantitation method for a peptide in rat serum using liquid chromatography/high‐field asymmetric waveform ion mobility spectrometry

Klaassen, T., Szwandt, S., Kapron, J. T., & Römer, A. (2009) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.4147 · Cited by 59

Transformations in pharmaceutical research and development, driven by innovations in multidimensional mass spectrometry-based technologies

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Single and multiple ion recording techniques for the analysis of diphenylhydantoin and its major metabolite in plasma

Baty, J. D., & Robinson, P. R. (1977) · Journal of Mass Spectrometry · doi:10.1002/bms.1200040104 · Cited by 45

Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity

Sherman, J., McKay, M. J., Ashman, K., & Molloy, M. P. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800512-mcp200 · Cited by 45

Determination of serum cortisol by thermospray liquid chromatography/mass spectrometry: Comparison with gas chromatography/mass spectrometry

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Advances in analytical mass spectrometry to improve screening for inherited metabolic diseases

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Evaluation and Optimization of Ion-Current Ratio Measurements by Selected-Ion-Monitoring Mass Spectrometry

MacCoss, M. J., Toth, M. J., & Matthews, D. E. (2001) · Analytical Chemistry · doi:10.1021/ac010041t · Cited by 31

Targeted label-free quantitative analysis of secretory proteins from adipocytes in response to oxidative stress

Choi, S., Kim, J. J., Yea, K., Suh, P., Kim, J., & Ryu, S. H. (2010) · Analytical Biochemistry · doi:10.1016/j.ab.2010.03.006 · Cited by 25

What is the best means of estimating the detection and quantification limits of a chromatographic method?

Vial, J., Mapihan, K. L., & Jardy, A. (2003) · Chromatographia · doi:10.1007/bf02492120 · Cited by 21

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

Gallien, S., Duriez, E., Crone, C., Kellmann, M., Moehring, T., & Domon, B. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.019802 · Cited by 510

Mass spectrometry-based proteomics: existing capabilities and future directions

Angel, T. E., Aryal, U. K., Hengel, S. M., Baker, E. S., Kelly, R. T., Robinson, E. W., & Smith, R. D. (2012) · Chemical Society Reviews · doi:10.1039/c2cs15331a · Cited by 441

A review on mass spectrometry-based quantitative proteomics: targeted and data independent acquisition

Vidova, V., & Spacil, Z. (2017) · Analytica Chimica Acta · doi:10.1016/j.aca.2017.01.059 · Cited by 352

Multiplexed and data‐independent tandem mass spectrometry for global proteome profiling

Chapman, J. D., Goodlett, D. R., & Masselon, C. D. (2014) · Mass Spectrometry Reviews · doi:10.1002/mas.21400 · Cited by 259