Quantitative multiple reaction monitoring analysis of synaptic proteins from human brain

Journal of Neuroscience Methods

Volumn 227, Issue , 2014, Pages 189-210

  Chang, Rachel Yoon Kyung ^a   Etheridge, Naomi ^a   Dodd, Peter ^a   Nouwens, Amanda ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Alzheimer's disease; Human autopsy brain; Neurodegeneration; Sample enrichment; Synapse

Indexed keywords

ALPHA TUBULIN; CATHEPSIN D; ENOLASE; FLUORESCENT DYE; SYNAPTOTAGMIN I; SYNTHETIC PEPTIDE; TRYPSIN; TUBULIN ALPHA 1A CHAIN; UNCLASSIFIED DRUG; PEPTIDE; TUBA1A PROTEIN, HUMAN; TUBULIN;

ANALYSIS; ANIMAL TISSUE; ARTICLE; AUTOPSY; BRAIN SYNAPTOSOME; CELL FRACTIONATION; COMPARATIVE STUDY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN TISSUE; ION TRAP MASS SPECTROMETRY; MULTIPLE REACTION MONITORING ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUADRUPOLE MASS SPECTROMETRY; QUANTITATIVE ANALYSIS; SEROTYPE; STREPTOCOCCUS PYOGENES; BRAIN; CHEMISTRY; CYTOLOGY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; MOLECULAR GENETICS; PROCEDURES; PROTEOMICS;

BRAIN; CATHEPSIN D; CHROMATOGRAPHY, LIQUID; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; PHOSPHOPYRUVATE HYDRATASE; PROTEOMICS; SUBCELLULAR FRACTIONS; SYNAPTOTAGMIN I; TUBULIN;

EID: 84896447933     PISSN: 01650270     EISSN: 1872678X     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2014.02.016     Document Type: Article

References (32)

1. Ackermann B.L., Berna M.J. Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomics 2007, 4:175-186.
2. Addona T.A., Abbatiello S.E., Schilling B., Skates S.J., Mani D.R., Bunk D.M., et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009, 27:633-641.
3. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
4. Altschul S.F., Wootton J.C., Gertz E.M., Agarwala R., Morgulis A., Schaffer A.A., et al. Protein database searches using compositionally adjusted substitution matrices. FASEB J 2005, 272:5101-5109.
5. Barnidge D.R., Goodmanson M.K., Klee G.G., Muddiman D.C. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-MS/MS using protein cleavage and isotope dilution mass spectrometry. J Proteome Res 2004, 3:644-652.
6. Chang R.Y., Nouwens A.S., Dodd P.R., Etheridge N. The synaptic proteome in Alzheimer's disease. Alzheimers Dement 2012, 9:499-511.
7. Chen J., Wang M., Turko I.V. Mass spectrometry quantification of clusterin in the human brain. Mol Neurodegener 2012, 7:41.
8. Choi S., Kim J., Yea K., Suh P.G., Kim J., Ryu S.H. Targeted label-free quantitative analysis of secretory proteins from adipocytes in response to oxidative stress. Anal Biochem 2010, 401:196-202.
9. Choi S.W., Gerencser A.A., Ng R., Flynn J.M., Melov S., Danielson S.R., et al. No consistent bioenergetic defects in presynaptic nerve terminals isolated from mouse models of Alzheimer's disease. J Neurosci 2012, 32:16775-16784.
10. Eissler C.L., Bremmer S.C., Martinez J.S., Parker L.L., Charbonneau H., Hall M.C. A general strategy for studying multisite protein phosphorylation using label-free selected reaction monitoring mass spectrometry. Anal Biochem 2011, 418:267-275.
11. Etheridge N., Lewohl J.M., Mayfield R.D., Harris R.A., Dodd P.R. Synaptic proteome changes in the superior frontal gyrus and occipital cortex of the alcoholic brain. Proteomics Clin Appl 2009, 3:730-742.
12. Grant S.G. The synapse proteome and phosphoproteome: a new paradigm for synapse biology. Biochem Soc Trans 2006, 34:59-63.
13. Gredilla R., Weissman L., Yang J.L., Bohr V.A., Stevnsner T. Mitochondrial base excision repair in mouse synaptosomes during normal aging and in a model of Alzheimer's disease. Neurobiol Aging 2012, 33:694-707.
14. Grimm M.O., Grosgen S., Riemenschneider M., Tanila H., Grimm H.S., Hartmann T. From brain to food: analysis of phosphatidylcholins, lyso-phosphatidylcholins and phosphatidylcholin-plasmalogens derivates in Alzheimer's disease human post mortem brains and mice model via mass spectrometry. J Chromatogr A 2011, 1218:7713-7722.
15. Hansson E., Ronnback L. Glial neuronal signaling in the central nervous system. FASEB J 2003, 17:341-348.
16. Hoofnagle A.N., Becker J.O., Oda M.N., Cavigiolio G., Mayer P., Vaisar T. Multiple-reaction monitoring-mass spectrometric assays can accurately measure the relative protein abundance in complex mixtures. Clin Chem 2012, 58:777-781.
17. Kondrat R.W., McClusky G.A., Cooks R.G. Multiple reaction monitoring in mass spectrometry/mass spectrometry for direct analysis of complex mixtures. Anal Chem 1978, 50:2017-2021.
18. Krapfenbauer K., Fountoulakis M., Lubec G. A rat brain protein expression map including cytosolic and enriched mitochondrial and microsomal fractions. Electrophoresis 2003, 24:1847-1870.
19. Lange V., Picotti P., Domon B., Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008, 4:222.
20. MacLean B., Tomazela D.M., Shulman N., Chambers M., Finney G.L., Frewen B., et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26:966-968.
21. Shah I., James R., Barker J., Petroczi A., Naughton D.P. Misleading measures in Vitamin D analysis: a novel LC-MS/MS assay to account for epimers and isobars. Nutr J 2011, 10:46.
22. Shi M., Bradner J., Bammler T.K., Eaton D.L., Zhang J., Ye Z., et al. Identification of glutathione S-transferase pi as a protein involved in Parkinson disease progression. Am J Pathol 2009, 175:54-65.
23. Shilov I.V., Seymour S.L., Patel A.A., Loboda A., Tang W.H., Keating S.P., et al. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 2007, 6:1638-1655.
24. Tang H.Y., Beer L.A., Barnhart K.T., Speicher D.W. Rapid verification of candidate serological biomarkers using gel-based, label-free multiple reaction monitoring. J Proteome Res 2011, 10:4005-4017.
25. Toyama A., Nakagawa H., Matsuda K., Ishikawa N., Kohno N., Daigo Y., et al. Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer. Proteome Sci 2011, 9:18.
26. Valencia A., Sapp E., Kimm J.S., McClory H., Reeves P.B., Alexander J., et al. Elevated NADPH oxidase activity contributes to oxidative stress and cell death in Huntington's disease. Hum Mol Genet 2013, 22:1112-1131.
27. Wang M., Turko I.V. Mass spectrometry quantification revealed accumulation of C-terminal fragment of apolipoprotein E in the Alzheimer's frontal cortex. PloS ONE 2013, 8:e61498.
28. Williams R.W., Herrup K. The control of neuron number. Annu Rev Neurosci 1988, 11:423-453.
29. Wolf-Yadlin A., Hautaniemi S., Lauffenburger D.A., White F.M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci USA 2007, 104:5860-5865.
30. Yang H., Qiao H., Tian X. Proteomic analysis of cerebral synaptosomes isolated from rat model of Alzheimer's disease. Indian J Exp Biol 2011, 49:118-124.
31. Zeng X., Hood B.L., Zhao T., Conrads T.P., Sun M., Gopalakrishnan V., et al. Lung cancer serum biomarker discovery using label-free liquid chromatography-tandem mass spectrometry. J Thorac Oncol 2011, 6:725-734.
32. Zhou J., Jones D.R., Duong D.M., Levey A.I., Lah J.J., Peng J. Proteomic analysis of postsynaptic density in Alzheimer's disease. Clin Chim Acta 2013, 420:62-68.