Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery

Frontiers in Biology

Volumn 7, Issue 4, 2012, Pages 313-335

  Cunningham, Robert ^a   Ma, Di ^a   Li, Lingjun ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

bioinformatics; biomarker discovery; fragmentation; mass spectrometry; peptidomics; post translational modifications; protein quantitation; proteomics; review; sample preparation; separation; validation

Indexed keywords

EID: 85027926759     PISSN: 16747984     EISSN: 16747992     Source Type: Journal    
DOI: 10.1007/s11515-012-1218-y     Document Type: Review

References (246)

1. Acosta-Martin A E, Panchaud A, Chwastyniak M, Dupont A, Juthier F, Gautier C, Jude B, Amouyel P, Goodlett D R, Pinet F (2011). Quantitative mass spectrometry analysis using PAcIFIC for the identification of plasma diagnostic biomarkers for abdominal aortic aneurysm. PLoS ONE, 6(12): e28698.
2. Addona T A, Shi X, Keshishian H, Mani D R, Burgess M, Gillette M A, Clauser K R, Shen D, Lewis G D, Farrell L A, Fifer MA, Sabatine M S, Gerszten R E, Carr S A (2011). A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat Biotechnol, 29(7): 635-643.
3. Ahmed F E (2009a). The role of capillary electrophoresis-mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci, 877(22): 1963-1981.
4. Ahmed F E (2009b). Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci, 32(5-6): 771-798.
5. Al-Tarawneh S K, Border MB, Dibble C F, Bencharit S (2011). Defining salivary biomarkers using mass spectrometry-based proteomics: a systematic review. OMICS, 15(6): 353-361.
6. Albalat A, Mischak H, Mullen W (2011a). Clinical application of urinary proteomics/peptidomics. Expert Rev Proteomics, 8(5): 615-629.
7. Albalat A, Mischak H, Mullen W (2011b). Urine proteomics in clinical applications: technologies, principal considerations and clinical implementation. Prilozi, 32(1): 13-44.
8. Alpert A J (1990). Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J Chromatogr A, 499: 177-196.
9. Alpert A J (2008). Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem, 80(1): 62-76.
10. Altelaar A F, Mohammed S, Brans M A, Adan R A, Heck A J (2009). Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. J Proteome Res, 8(2): 870-876.
11. Altelaar AM, Heck A J (2012), Trends in ultrasensitive proteomics. Curr Opin Chem Biol, DOI: 10. 1016/j. cbpa. 2011. 12. 011.
12. Bandura D R, Baranov V I, Ornatsky O I, Antonov A, Kinach R, Lou X, Pavlov S, Vorobiev S, Dick J E, Tanner S D (2009). Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem, 81(16): 6813-6822.
13. Barbara J E, Castro-Perez J M (2011). High-resolution chromatography/time-of-flight MSE with in silico data mining is an information-rich approach to reactive metabolite screening. Rapid Commun Mass Spectrom, 25(20): 3029-3040.
14. Beausoleil S A, Villén J, Gerber S A, Rush J, Gygi S P (2006). A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol, 24(10): 1285-1292.
15. Belda-Iniesta C, de Castro J, Perona R (2011). Translational proteomics: what can you do for true patients?. J Proteome Res, 10(1): 101-104.
16. Belov ME, Prasad S, Prior D C, Danielson WF 3rd, Weitz K, Ibrahim Y M, Smith R D (2011). Pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer. Anal Chem, 83(6): 2162-2171.
17. Bermejo-Pareja F, Antequera D, Vargas T, Molina J A, Carro E (2010). Saliva levels of Abeta1-42 as potential biomarker of Alzheimer's disease: a pilot study. BMC Neurol, 10(1): 108.
18. Bondarenko P V, Chelius D, Shaler T A (2002). Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem, 74(18): 4741-4749.
19. Brechlin P, Jahn O, Steinacker P, Cepek L, Kratzin H, Lehnert S, Jesse S, Mollenhauer B, Kretzschmar H A, Wiltfang J, Otto M (2008). Cerebrospinal fluid-optimized two-dimensional difference gel electrophoresis (2-D DIGE) facilitates the differential diagnosis of Creutzfeldt-Jakob disease. Proteomics, 8(20): 4357-4366.
20. Burke T W, Mant C T, Black J A, Hodges R S (1989). Strong cationexchange high-performance liquid chromatography of peptides. Effect of non-specific hydrophobic interactions and linearization of peptide retention behaviour. J Chromatogr, 476: 377-389.
21. Butterfield D A, Owen J B (2011). Lectin-affinity chromatography brain glycoproteomics and Alzheimer disease: insights into protein alterations consistent with the pathology and progression of this dementing disorder. Proteomics Clin Appl, 5(1-2): 50-56.
22. Caprioli R M, Farmer T B, Gile J (1997). Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem, 69(23): 4751-4760.
23. Castagnola M, Cabras T, Vitali A, Sanna M T, Messana I (2011). Biotechnological implications of the salivary proteome. Trends Biotechnol, 29(8): 409-418.
24. Cazares L H, Troyer D A, Wang B, Drake R R, Semmes O J (2011). MALDI tissue imaging: from biomarker discovery to clinical applications. Anal Bioanal Chem, 401(1): 17-27.
25. Chakraborty A B, Berger S J, Gebler J C (2007). Use of an integrated MS-multiplexed MS/MS data acquisition strategy for high-coverage peptide mapping studies. Rapid Commun Mass Spectrom, 21(5): 730-744.
26. Chaurand P, Schwartz S A, Caprioli R M (2002). Imaging mass spectrometry: a new tool to investigate the spatial organization of peptides and proteins in mammalian tissue sections. Curr Opin Chem Biol, 6(5): 676-681.
27. Chaurand P, Stoeckli M, Caprioli R M (1999). Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. Anal Chem, 71(23): 5263-5270.
28. Che F Y, Fricker L D (2005). Quantitative peptidomics of mouse pituitary: comparison of different stable isotopic tags. J Mass Spectrom, 40(2): 238-249.
29. Chelius D, Bondarenko P V (2002). Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res, 1(4): 317-323.
30. Chen J, Balgley B M, DeVoe D L, Lee C S (2003). Capillary isoelectric focusing-based multidimensional concentration/separation platform for proteome analysis. Anal Chem, 75(13): 3145-3152.
31. Chen R, Jiang X, Conaway M C, Mohtashemi I, Hui L, Viner R, Li L (2010). Mass spectral analysis of neuropeptide expression and distribution in the nervous system of the lobster Homarus americanus. J Proteome Res, 9(2): 818-832.
32. Chen R, Ma M, Hui L, Zhang J, Li L (2009). Measurement of neuropeptides in crustacean hemolymph via MALDI mass spectrometry. J Am Soc Mass Spectrom, 20(4): 708-718.
33. Chi A, Huttenhower C, Geer L Y, Coon J J, Syka J E, Bai D L, Shabanowitz J, Burke D J, Troyanskaya O G, Hunt D F (2007). Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA, 104(7): 2193-2198.
34. Chien K Y, Liu H C, Goshe M B (2011). Development and application of a phosphoproteomic method using electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), IMAC, and LC-MS/MS analysis to study Marek's Disease Virus infection. J Proteome Res, 10(9): 4041-4053.
35. Choe L, D'Ascenzo M, Relkin N R, Pappin D, Ross P, Williamson B, Guertin S, Pribil P, Lee K H (2007). 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics, 7(20): 3651-3660.
36. Cohen P (2000). The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem Sci, 25(12): 596-601.
37. Colgrave M L, Xi L, Lehnert S A, Flatscher-Bader T, Wadensten H, Nilsson A, Andren P E, Wijffels G (2011). Neuropeptide profiling of the bovine hypothalamus: thermal stabilization is an effective tool in inhibiting post-mortem degradation. Proteomics, 11(7): 1264-1276.
38. Court M, Selevsek N, Matondo M, Allory Y, Garin J, Masselon C D, Domon B (2011). Toward a standardized urine proteome analysis methodology. Proteomics, 11(6): 1160-1171.
39. Craig R, Beavis R C (2004). TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20(9): 1466-1467.
40. Craig R, Cortens J P, Beavis R C (2004). Open source system for analyzing, validating, and storing protein identification data. J Proteome Res, 3(6): 1234-1242.
41. D'Ascenzo M, Choe L, Lee K H (2008). iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data. Brief Funct Genomics Proteomics, 7(2): 127-135.
42. Dai L, Li C, Shedden K A, Lee C J, Li C, Quoc H, Simeone D M, Lubman D M (2010). Quantitative proteomic profiling studies of pancreatic cancer stem cells. J Proteome Res, 9(7): 3394-3402.
43. Datta A, Park J E, Li X, Zhang H, Ho Z S, Heese K, Lim S K, Tam J P, Sze S K (2010). Phenotyping of an in vitro model of ischemic penumbra by iTRAQ-based shotgun quantitative proteomics. J Proteome Res, 9(1): 472-484.
44. Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser D F, Burkhard P R, Sanchez J C (2008). Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem, 80(8): 2921-2931.
45. Dayon L, Pasquarello C, Hoogland C, Sanchez J C, Scherl A (2010). Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags. J Proteomics, 73(4): 769-777.
46. De La Monte S M, Wands J R (2001). The AD7c-NTP neuronal thread protein biomarker for detecting Alzheimer's disease. J Alzheimers Dis, 3(3): 345-353.
47. Decramer S, Gonzalez de Peredo A, Breuil B, Mischak H, Monsarrat B, Bascands J L, Schanstra J P (2008). Urine in clinical proteomics. Mol Cell Proteomics, 7(10): 1850-1862.
48. Desiderio C, Rossetti D V, Iavarone F, Messana I, Castagnola M (2010). Capillary electrophoresis-mass spectrometry: recent trends in clinical proteomics. J Pharm Biomed Anal, 53(5): 1161-1169.
49. Deutsch E W, Lam H, Aebersold R (2008). PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep, 9(5): 429-434.
50. Devic I, Hwang H, Edgar J S, Izutsu K, Presland R, Pan C, Goodlett D R, Wang Y, Armaly J, Tumas V, Zabetian C P, Leverenz J B, Shi M, Zhang J (2011). Salivary α-synuclein and DJ-1: potential biomarkers for Parkinson's disease. Brain, 134(7): e178.
51. Di Palma S, Boersema P J, Heck A J, Mohammed S (2011a). Zwitterionic hydrophilic interaction liquid chromatography (ZICHILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis. Anal Chem, 83(9): 3440-3447.
52. Di Palma S, Stange D, van de Wetering M, Clevers H, Heck A J, Mohammed S (2011b). Highly sensitive proteome analysis of FACS-sorted adult colon stem cells. J Proteome Res, 10(8): 3814-3819.
53. Diez R, Herbstreith M, Osorio C, Alzate O (2010). 2-D Fluorescence Difference Gel Electrophoresis (DIGE) in Neuroproteomics.
54. Dowell J A, Heyden W V, Li L (2006). Rat neuropeptidomics by LCMS/MS and MALDI-FTMS: Enhanced dissection and extraction techniques coupled with 2D RP-RP HPLC. J Proteome Res, 5(12): 3368-3375.
55. Dowell J A, Johnson J A, Li L (2009). Identification of astrocyte secreted proteins with a combination of shotgun proteomics and bioinformatics. J Proteome Res, 8(8): 4135-4143.
56. Dowling P, Clynes M (2011). Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specific biomarkers. Proteomics, 11(4): 794-804.
57. Edelmann M J (2011). Strong cation exchange chromatography in analysis of posttranslational modifications: innovations and perspectives. J Biomed Biotechnol, 2011: 1.
58. Eliuk S M, Maltby D, Panning B, Burlingame A L (2010). High resolution electron transfer dissociation studies of unfractionated intact histones from murine embryonic stem cells using on-line capillary LC separation: determination of abundant histone isoforms and post-translational modifications. Mol Cell Proteomics, 9(5): 824-837.
59. Eng J K, McCormack A L, Yates III J R (1994). An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom, 5(11): 976-989.
60. Filiou MD, Martins-de-Souza D, Guest P C, Bahn S, Turck CW (2012). To label or not to label: Applications of quantitative proteomics in neuroscience research. Proteomics.
61. Fonslow B R, Yates J R 3rd (2009). Capillary electrophoresis applied to proteomic analysis. J Sep Sci, 32(8): 1175-1188.
62. François I, Sandra K, Sandra P (2009). Comprehensive liquid chromatography: fundamental aspects and practical considerations-a review. Anal Chim Acta, 641(1-2): 14-31.
63. Frese C K, Altelaar A F, Hennrich M L, Nolting D, Zeller M, Griep-Raming J, Heck A J, Mohammed S (2011). Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res, 10(5): 2377-2388.
64. Fricker L D (2010). Analysis of mouse brain peptides using mass spectrometry-based peptidomics: implications for novel functions ranging from non-classical neuropeptides to microproteins. Mol Biosyst, 6(8): 1355-1365.
65. Fu Q, Li L (2005). De novo sequencing of neuropeptides using reductive isotopic methylation and investigation of ESI QTOF MS/MS fragmentation pattern of neuropeptides with N-terminal dimethylation. Anal Chem, 77(23): 7783-7795.
66. Geer L Y, Markey S P, Kowalak J A, Wagner L, Xu M, Maynard D M, Yang X, Shi W, Bryant S H (2004). Open mass spectrometry search algorithm. J Proteome Res, 3(5): 958-964.
67. Gelman J S, Fricker L D (2010). Hemopressin and other bioactive peptides from cytosolic proteins: are these non-classical neuropeptides? AAPS J, 12(3): 279-289.
68. Gelman J S, Sironi J, Castro L M, Ferro E S, Fricker L D (2010). Hemopressins and other hemoglobin-derived peptides in mouse brain: comparison between brain, blood, and heart peptidome and regulation in Cpefat/fat mice. J Neurochem, 113(4): 871-880.
69. Gelman J S, Sironi J, Castro L M, Ferro E S, Fricker L D (2011). Peptidomic analysis of human cell lines. J Proteome Res, 10(4): 1583-1592.
70. Geromanos S J, Vissers J P, Silva J C, Dorschel C A, Li G Z, Gorenstein M V, Bateman R H, Langridge J I (2009). The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics, 9(6): 1683-1695.
71. Gilar M, Olivova P, Daly A E, Gebler J C (2005). Orthogonality of separation in two-dimensional liquid chromatography. Anal Chem, 77(19): 6426-6434.
72. Gilmore J M, Washburn M P (2010). Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics, 73(11): 2078-2091.
73. Giron P, Dayon L, Turck N, Hoogland C, Sanchez J C (2011). Quantitative analysis of human cerebrospinal fluid proteins using a combination of cysteine tagging and amine-reactive isobaric labeling. J Proteome Res, 10(1): 249-258.
74. Griffin N M, Schnitzer J E (2011). Overcoming key technological challenges in using mass spectrometry for mapping cell surfaces in tissues. Mol Cell Proteomics 10, R110 000935.
75. Groen A J, Lilley K S (2010). Proteomics of total membranes and subcellular membranes. Expert Rev Proteomics, 7(6): 867-878.
76. Guiochon G, Marchetti N, Mriziq K, Shalliker R A (2008). Implementations of two-dimensional liquid chromatography. J Chromatogr A, 1189(1-2): 109-168.
77. Guo T, Lee C S, Wang W, DeVoe D L, Balgley B M (2006). Capillary separations enabling tissue proteomics-based biomarker discovery. Electrophoresis, 27(18): 3523-3532.
78. Gygi S P, Rist B, Gerber S A, Turecek F, Gelb MH, Aebersold R (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 17(10): 994-999.
79. Han Y, Ma B, Zhang K (2005). SPIDER: software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol, 3(3): 697-716.
80. Hanash S (2004). Building a foundation for the human proteome: the role of the Human Proteome Organization. J Proteome Res, 3(2): 197-199.
81. Haqqani A S, Kelly J F, Stanimirovic D B (2008). Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags. Methods Mol Biol, 439: 225-240.
82. Haselberg R, de Jong G J, Somsen G W (2007). Capillary electrophoresis-mass spectrometry for the analysis of intact proteins. J Chromatogr A, 1159(1-2): 81-109.
83. Haselberg R, de Jong G J, Somsen G W (2011). Capillary electrophoresis-mass spectrometry for the analysis of intact proteins 2007-2010. Electrophoresis, 32(1): 66-82.
84. Helbig A O, Heck A J, Slijper M (2010). Exploring the membrane proteome-challenges and analytical strategies. J Proteomics, 73(5): 868-878.
85. Herberth M, Koethe D, Cheng T M, Krzyszton N D, Schoeffmann S, Guest P C, Rahmoune H, Harris L W, Kranaster L, Leweke F M, Bahn S (2011). Impaired glycolytic response in peripheral blood mononuclear cells of first-onset antipsychotic-naive schizophrenia patients. Mol Psychiatry, 16(8): 848-859.
86. Herbst A, McIlwain S, Schmidt J J, Aiken J M, Page C D, Li L (2009). Prion disease diagnosis by proteomic profiling. J Proteome Res, 8(2): 1030-1036.
87. Holten-Andersen M N, Murphy G, Nielsen H J, Pedersen A N, Christensen I J, Høyer-Hansen G, Brünner N, Stephens R W (1999). Quantitation of TIMP-1 in plasma of healthy blood donors and patients with advanced cancer. Br J Cancer, 80(3-4): 495-503.
88. Holten-Andersen M N, Schrohl A S, Brünner N, Nielsen H J, Høgdall C K, Høgdall E V (2003). Evaluation of sample handling in relation to levels of tissue inhibitor of metalloproteinases-1 measured in blood by immunoassay. Int J Biol Markers, 18(3): 170-176.
89. Hood L, Friend S H (2011). Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol, 8(3): 184-187.
90. Hsu J L, Huang S Y, Chow N H, Chen S H (2003). Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem, 75(24): 6843-6852.
91. Huck CW, Bakry R, Huber L A, Bonn G K (2006). Progress in capillary electrophoresis coupled to matrix-assisted laser desorption/ionization - time of flight mass spectrometry. Electrophoresis, 27(11): 2063-2074.
92. Hui L, Cunningham R, Zhang Z, Cao W, Jia C, Li L (2011). Discovery and characterization of the Crustacean hyperglycemic hormone precursor related peptides (CPRP) and orcokinin neuropeptides in the sinus glands of the blue crab Callinectes sapidus using multiple tandem mass spectrometry techniques. J Proteome Res, 10(9): 4219-4229.
93. Hummon A B, Amare A, Sweedler J V (2006). Discovering new invertebrate neuropeptides using mass spectrometry. Mass Spectrom Rev, 25(1): 77-98.
94. Hwang S I, Thumar J, Lundgren D H, Rezaul K, Mayya V, Wu L, Eng J, Wright M E, Han D K (2007). Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene, 26(1): 65-76.
95. Inutan E D, Richards A L, Wager-Miller J, Mackie K, McEwen C N, Trimpin S (2010). Laserspray ionization, a new method for protein analysis directly from tissue at atmospheric pressure with ultrahigh mass resolution and electron transfer dissociation. Mol Cell Proteomics, 10.
96. Jahn H, Wittke S, Zürbig P, Raedler T J, Arlt S, Kellmann M, Mullen W, Eichenlaub M, Mischak H, Wiedemann K (2011). Peptide fingerprinting of Alzheimer's disease in cerebrospinal fluid: identification and prospective evaluation of new synaptic biomarkers. PLoS ONE, 6(10): e26540.
97. Jedrychowski M P, Huttlin E L, Haas W, Sowa M E, Rad R, Gygi S P (2011). Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics, 10.
98. Johannesson N, Olsson L, Bäckström D, Wetterhall M, Danielsson R, Bergquist J (2007). Screening for biomarkers in plasma from patients with gangrenous and phlegmonous appendicitis using CE and CEC in combination with MS. Electrophoresis, 28(9): 1435-1443.
99. Jones P, Côté R G, Cho S Y, Klie S, Martens L, Quinn A F, Thorneycroft D, Hermjakob H (2007). PRIDE: new developments and new datasets. Nucleic Acids Res, 36(Database issue): D878-D883.
100. 16O labeling and linear ion trap mass spectrometry: application to the study of vascular endothelial growth factor-induced angiogenesis in endothelial cells. Mol Cell Proteomics, 8(5): 1130-1149.
101. Kalume D E, Molina H, Pandey A (2003). Tackling the phosphoproteome: tools and strategies. Curr Opin Chem Biol, 7(1): 64-69.
102. Keene S D, Greco T M, Parastatidis I, Lee S H, Hughes E G, Balice-Gordon R J, Speicher D W, Ischiropoulos H (2009). Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome. Proteomics, 9(3): 768-782.
103. Kellie J F, Catherman A D, Durbin K R, Tran J C, Tipton J D, Norris J L, Witkowski C E 2nd, Thomas P M, Kelleher N L (2012). Robust analysis of the yeast proteome under 50 kDa by molecular-massbased fractionation and top-down mass spectrometry. Anal Chem, 84(1): 209-215.
104. Klampfl C W (2009). CE with MS detection: a rapidly developing hyphenated technique. Electrophoresis, 30(Suppl 1): S83-S91.
105. Koutroukides T A, Guest P C, Leweke F M, Bailey D M, Rahmoune H, Bahn S, Martins-de-Souza D (2011). Characterization of the human serum depletome by label-free shotgun proteomics. J Sep Sci, 34(13): 1621-1626.
106. Krishnamurthy D, Levin Y, Harris L W, Umrania Y, Bahn S, Guest P C (2011). Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry. Proteomics, 11(3): 495-500.
107. Kumar C, Mann M (2009). Bioinformatics analysis of mass spectrometry-based proteomics data sets. FEBS Lett, 583(11): 1703-1712.
108. Kuwabara Y, Mine K, Katayama A, Inagawa T, Akira S, Takeshita T (2009). Proteomic analyses of recombinant human follicle-stimulating hormone and urinary-derived gonadotropin preparations. J Reprod Med, 54(8): 459-466.
109. Li L, Garden RW, Sweedler J V (2000). Single-cell MALDI: a new tool for direct peptide profiling. Trends Biotechnol, 18(4): 151-160.
110. Li L, Sweedler J V (2008). Peptides in the brain: mass spectrometrybased measurement approaches and challenges. Annu Rev Anal Chem (Palo Alto Calif), 1(1): 451-483.
111. Li Y, Champion M M, Sun L, Champion P A, Wojcik R, Dovichi N J (2012). Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry as an alternative proteomics platform to ultraperformance liquid chromatography-electrospray ionizationtandem mass spectrometry for samples of intermediate complexity. Anal Chem, 84(3): 1617-1622.
112. Lilley K S, Razzaq A, Dupree P (2002). Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation. Curr Opin Chem Biol, 6(1): 46-50.
113. Lippi G, Guidi G C, Mattiuzzi C, Plebani M (2006). Preanalytical variability: the dark side of the moon in laboratory testing. Clin Chem Lab Med, 44(4): 358-365.
114. Liu H, Håkansson K (2006). Electron capture dissociation of tyrosine Osulfated peptides complexed with divalent metal cations. Anal Chem, 78(21): 7570-7576.
115. Liu H, Lam L, Dasgupta P K (2011a). Expanding the linear dynamic range for multiple reaction monitoring in quantitative liquid chromatography-tandem mass spectrometry utilizing natural isotopologue transitions. Talanta, 87: 307-310.
116. Liu H, Sadygov R G, Yates J R 3rd (2004a). A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem, 76(14): 4193-4201.
117. Liu J, Erassov A, Halina P, Canete M, Nguyen D V, Chung C, Cagney G, Ignatchenko A, Fong V, Emili A (2008). Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications. Anal Chem, 80(20): 7846-7854.
118. Liu J, Wang H, Cooks R G, Ouyang Z (2011b). Leaf spray: direct chemical analysis of plant material and living plants by mass spectrometry. Anal Chem, 83(20): 7608-7613.
119. Liu J, Wang H, Manicke N E, Lin J M, Cooks R G, Ouyang Z (2010). Development, characterization, and application of paper spray ionization. Anal Chem, 82(6): 2463-2471.
120. Liu T, Qian W J, Gritsenko M A, Xiao W, Moldawer L L, Kaushal A, Monroe M E, Varnum S M, Moore R J, Purvine S O, Maier R V, Davis R W, Tompkins R G, Camp D G 2nd, Smith R D, and the Inflammation and the Host Response to Injury Large Scale Collaborative Research Programm (2006a). High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics, 5(10): 1899-1913.
121. Liu T, Qian WJ, Mottaz HM, Gritsenko MA, Norbeck A D, Moore R J, Purvine S O, Camp D G 2nd, Smith R D (2006b). Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol Cell Proteomics, 5(11): 2167-2174.
122. Liu X, Plasencia M, Ragg S, Valentine S J, Clemmer D E (2004b). Development of high throughput dispersive LC-ion mobility-TOFMS techniques for analysing the human plasma proteome. Brief Funct Genomics Proteomics, 3(2): 177-186.
123. Lopez M F, Kuppusamy R, Sarracino D A, Prakash A, Athanas M, Krastins B, Rezai T, Sutton J N, Peterman S, Nicolaides K (2011). Mass spectrometric discovery and selective reaction monitoring (SRM) of putative protein biomarker candidates in first trimester Trisomy 21 maternal serum. J Proteome Res, 10(1): 133-142.
124. Ma M, Chen R, Ge Y, He H, Marshall A G, Li L (2009). Combining bottom-up and top-down mass spectrometric strategies for de novo sequencing of the crustacean hyperglycemic hormone from Cancer borealis. Anal Chem, 81(1): 240-247.
125. Maccarrone G, Milfay D, Birg I, Rosenhagen M, Holsboer F, Grimm R, Bailey J, Zolotarjova N, Turck C W (2004). Mining the human cerebrospinal fluid proteome by immunodepletion and shotgun mass spectrometry. Electrophoresis, 25(14): 2402-2412.
126. Makridakis M, Vlahou A (2010). Secretome proteomics for discovery of cancer biomarkers. J Proteomics, 73(12): 2291-2305.
127. Marimuthu A, O'Meally R N, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar D S, Pinto S M, Sharma R, Renuse S, Goel R, Christopher R, Delanghe B, Cole R N, Harsha H C, Pandey A (2011). A comprehensive map of the human urinary proteome. J Proteome Res, 10(6): 2734-2743.
128. Marouga R, David S, Hawkins E (2005). The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal Bioanal Chem, 382(3): 669-678.
129. Martins-de-Souza D, Guest P C, Guest F L, Bauder C, Rahmoune H, Pietsch S, Roeber S, Kretzschmar H, Mann D, Baborie A, Bahn S (2012). Characterization of the human primary visual cortex and cerebellum proteomes using shotgun mass spectrometry-data-independent analyses. Proteomics, 12(3): 500-504.
130. Matsubara J, Honda K, Ono M, Sekine S, Tanaka Y, Kobayashi M, Jung G, Sakuma T, Nakamori S, Sata N, Nagai H, Ioka T, Okusaka T, Kosuge T, Tsuchida A, Shimahara M, Yasunami Y, Chiba T, Yamada T (2011). Identification of adipophilin as a potential plasma biomarker for colorectal cancer using label-free quantitative mass spectrometry and protein microarray. Cancer Epidemiol Biomarkers Prev, 20(10): 2195-2203.
131. McAlister G C, Phanstiel D, Wenger C D, Lee M V, Coon J J (2010). Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal Chem, 82(1): 316-322.
132. McEwen C N, Larsen B S, Trimpin S (2010). Laserspray ionization on a commercial atmospheric pressure-MALDI mass spectrometer ion source: selecting singly or multiply charged ions. Anal Chem, 82(12): 4998-5001.
133. Menschaert G, Vandekerckhove T T, Baggerman G, Schoofs L, Luyten W, van Criekinge W (2010). Peptidomics coming of age: a review of contributions from a bioinformatics angle. J Proteome Res, 9(5): 2051-2061.
134. Michalski A, Damoc E, Hauschild J P, Lange O, Wieghaus A, Makarov A, Nagaraj N, Cox J, Mann M, Horning S (2011). Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics, 10: M111 011015.
135. Miliotis T, Ali L, Palm J E, Lundqvist A J, Ahnoff M, Andersson T B, Hilgendorf C (2011). Development of a highly sensitive method using liquid chromatography-multiple reaction monitoring to quantify membrane P-glycoprotein in biological matrices and relationship to transport function. Drug Metab Dispos, 39(12): 2440-2449.
136. Mischak H, Delles C, Klein J, Schanstra J P (2010). Urinary proteomics based on capillary electrophoresis-coupled mass spectrometry in kidney disease: discovery and validation of biomarkers, and clinical application. Adv Chronic Kidney Dis, 17(6): 493-506.
137. Molina H, Matthiesen R, Kandasamy K, Pandey A (2008). Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal Chem, 80(13): 4825-4835.
138. Moore N H, Costa L G, Shaffer S A, Goodlett D R, Guizzetti M (2009). Shotgun proteomics implicates extracellular matrix proteins and protease systems in neuronal development induced by astrocyte cholinergic stimulation. J Neurochem, 108(4): 891-908.
139. Murakoshi Y, Honda K, Sasazuki S, Ono M, Negishi A, Matsubara J, Sakuma T, Kuwabara H, Nakamori S, Sata N, Nagai H, Ioka T, Okusaka T, Kosuge T, Shimahara M, Yasunami Y, Ino Y, Tsuchida A, Aoki T, Tsugane S, Yamada T (2011). Plasma biomarker discovery and validation for colorectal cancer by quantitative shotgun mass spectrometry and protein microarray. Cancer Sci, 102(3): 630-638.
140. Nagaraj N, D'souza R C, Cox J, Olsen J V, Mann M (2010). Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res, 9(12): 6786-6794.
141. Neilson K A, Ali N A, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, van Sluyter S C, Haynes P A (2011). Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics, 11(4): 535-553.
142. Neue K, Mormann M, Peter-Katalinić J, Pohlentz G (2011). Elucidation of glycoprotein structures by unspecific proteolysis and direct nanoESI mass spectrometric analysis of ZIC-HILIC-enriched glycopeptides. J Proteome Res, 10(5): 2248-2260.
143. Oh-Ishi M, Maeda T (2002). Separation techniques for high-molecularmass proteins. J Chromatogr B Analyt Technol Biomed Life Sci, 771(1-2): 49-66.
144. Olsen J V, Macek B, Lange O, Makarov A, Horning S, Mann M (2007). Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods, 4(9): 709-712.
145. Olsen J V, Vermeulen M, Santamaria A, Kumar C, Miller M L, Jensen L J, Gnad F, Cox J, Jensen T S, Nigg E A, Brunak S, Mann M (2010). Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal, 3(104): ra3.
146. Omenn G S, States D J, Adamski M, Blackwell T W, Menon R, Hermjakob H, Apweiler R, Haab B B, Simpson R J, Eddes J S, Kapp E A, Moritz R L, Chan DW, Rai A J, Admon A, Aebersold R, Eng J, Hancock W S, Hefta S A, Meyer H, Paik Y K, Yoo J S, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu C Y, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher D W, Hanash S M (2005). Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publiclyavailable database. Proteomics, 5(13): 3226-3245.
147. Ong S E, Blagoev B, Kratchmarova I, Kristensen D B, Steen H, Pandey A, Mann M (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics, 1(5): 376-386.
148. Ong S E, Kratchmarova I, Mann M (2003). Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res, 2(2): 173-181.
149. Ossola R, Schiess R, Picotti P, Rinner O, Reiter L, Aebersold R (2011). Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites. Methods Mol Biol, 728: 179-194.
150. Ottervald J, Franzén B, Nilsson K, Andersson L I, Khademi M, Eriksson B, Kjellström S, Marko-Varga G, Végvári A, Harris R A, Laurell T, Miliotis T, Matusevicius D, Salter H, Ferm M, Olsson T (2010). Multiple sclerosis: Identification and clinical evaluation of novel CSF biomarkers. J Proteomics, 73(6): 1117-1132.
151. Ow S Y, Salim M, Noirel J, Evans C, Wright P C (2011). Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation. Proteomics, 11(11): 2341-2346.
152. Perkins D N, Pappin D J, Creasy D M, Cottrell J S (1999). Probabilitybased protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20(18): 3551-3567.
153. Pimienta G, Chaerkady R, Pandey A (2009). SILAC for global phosphoproteomic analysis. Methods Mol Biol, 527: 107-116, x.
154. Prentice R L, Paczesny S, Aragaki A, Amon L M, Chen L, Pitteri S J, McIntosh M, Wang P, Buson Busald T, Hsia J (2010). Novel proteins associated with risk for coronary heart disease or stroke among postmenopausal women identified by in-depth plasma proteome profiling. Genome, Med 2: 48.
155. Rai A J, Gelfand C A, Haywood B C, Warunek D J, Yi J, Schuchard M D, Mehigh R J, Cockrill S L, Scott G B, Tammen H, Schulz-Knappe P, Speicher D W, Vitzthum F, Haab B B, Siest G, Chan D W (2005). HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics, 5(13): 3262-3277.
156. Rajagopal M U, Hathout Y, MacDonald T J, Kieran M W, Gururangan S, Blaney SM, Phillips P, Packer R, Gordish-Dressman H, Rood B R (2011). Proteomic profiling of cerebrospinal fluid identifies prostaglandin D2 synthase as a putative biomarker for pediatric medulloblastoma: A pediatric brain tumor consortium study. Proteomics, 11(5): 935-943.
157. Ramos A A, Yang H, Rosen L E, Yao X (2006). Tandem parallel fragmentation of peptides for mass spectrometry. Anal Chem, 78(18): 6391-6397.
158. Ray S, Britschgi M, Herbert C, Takeda-Uchimura Y, Boxer A, Blennow K, Friedman L F, Galasko D R, Jutel M, Karydas A, Kaye J A, Leszek J, Miller B L, Minthon L, Quinn J F, Rabinovici G D, Robinson W H, Sabbagh M N, So Y T, Sparks D L, Tabaton M, Tinklenberg J, Yesavage J A, Tibshirani R, Wyss-Coray T (2007). Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med, 13(11): 1359-1362.
159. Righetti P G, Fasoli E, Boschetti E (2011). Combinatorial peptide ligand libraries: the conquest of the' hidden proteome' advances at great strides. Electrophoresis, 32(9): 960-966.
160. Ringman J M, Schulman H, Becker C, Jones T, Bai Y, Immermann F, Cole G, Sokolow S, Gylys K, Geschwind D H, Cummings J L, Wan H I (2012). Proteomic changes in cerebrospinal fluid of presymptomatic and affected persons carrying familial Alzheimer disease mutations. Arch Neurol, 69(1): 96-104.
161. Roche S, Gabelle A, Lehmann S (2008). Clinical proteomics of the cerebrospinal fluid: Towards the discovery of new biomarkers. Proteomics Clin Appl, 2(3): 428-436.
162. Ross P L, Huang Y N, Marchese J N, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin D J (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics, 3(12): 1154-1169.
163. Rozek W, Ricardo-Dukelow M, Holloway S, Gendelman H E, Wojna V, Melendez L M, Ciborowski P (2007). Cerebrospinal fluid proteomic profiling of HIV-1-infected patients with cognitive impairment. J Proteome Res, 6(11): 4189-4199.
164. Rucevic M, Hixson D, Josic D (2011). Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis, 32(13): 1549-1564.
165. Rudrabhatla P, Jaffe H, Pant H C (2011). Direct evidence of phosphorylated neuronal intermediate filament proteins in neurofi-brillary tangles (NFTs): phosphoproteomics of Alzheimer's NFTs. FASEB J, 25(11): 3896-3905.
166. Sáez-Valero J, Fodero L R, Sjögren M, Andreasen N, Amici S, Gallai V, Vanderstichele H, Vanmechelen E, Parnetti L, Blennow K, Small D H (2003). Glycosylation of acetylcholinesterase and butyrylcholinesterase changes as a function of the duration of Alzheimer's disease. J Neurosci Res, 72(4): 520-526.
167. Scatena R, Bottoni P, Pontoglio A, Giardina B (2010). Revisiting the Warburg effect in cancer cells with proteomics. The emergence of new approaches to diagnosis, prognosis and therapy. Proteomics Clin Appl, 4(2): 143-158.
168. Schiess R, Wollscheid B, Aebersold R (2009). Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol, 3(1): 33-44.
169. Schmidt A, Kellermann J, Lottspeich F (2005). A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics, 5(1): 4-15.
170. Scholz B, Alm H, Mattsson A, Nilsson A, Kultima K, Savitski M M, Fälth M, Sköld K, Brunström B, Andren P E, Dencker L (2010). Neuropeptidomic analysis of the embryonic Japanese quail diencephalon. BMC Dev Biol, 10(1): 30.
171. Schutzer S E, Liu T, Natelson B H, Angel T E, Schepmoes A A, Purvine S O, Hixson K K, Lipton M S, Camp D G, Coyle P K, Smith R D, Bergquist J (2010). Establishing the proteome of normal human cerebrospinal fluid. PLoS ONE, 5(6): e10980.
172. Searle B C (2010). Scaffold: a bioinformatic tool for validating MS/MSbased proteomic studies. Proteomics, 10(6): 1265-1269.
173. Second T P, Blethrow J D, Schwartz J C, Merrihew G E, MacCoss M J, Swaney D L, Russell J D, Coon J J, Zabrouskov V (2009). Dualpressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem, 81(18): 7757-7765.
174. Seeley E H, Caprioli RM (2011). MALDI imaging mass spectrometry of human tissue: method challenges and clinical perspectives. Trends Biotechnol, 29(3): 136-143.
175. Selvaraju S, Rassi Z E (2012). Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-an update covering the period 2008-2011. Electrophoresis, 33(1): 74-88.
176. Shen Y, Tolić N, Xie F, Zhao R, Purvine S O, Schepmoes A A, Moore R J, Anderson G A, Smith R D (2011). Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods. J Proteome Res, 10(9): 3929-3943.
177. Sheta E A, Appel S H, Goldknopf I L (2006). 2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases. Expert Rev Proteomics, 3(1): 45-62.
178. Shteynberg D, Deutsch E W, Lam H, Eng J K, Sun Z, Tasman N, Mendoza L, Moritz R L, Aebersold R, Nesvizhskii A I (2011). iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics, 10: M111 007690.
179. Silva J C, Denny R, Dorschel C A, Gorenstein M, Kass I J, Li G Z, McKenna T, Nold M J, Richardson K, Young P, Geromanos S (2005). Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem, 77(7): 2187-2200.
180. Silveyra M X, Cuadrado-Corrales N, Marcos A, Barquero M S, Rábano A, Calero M, Sáez-Valero J (2006). Altered glycosylation of acetylcholinesterase in Creutzfeldt-Jakob disease. J Neurochem, 96(1): 97-104.
181. Simpson D C, Smith R D (2005). Combining capillary electrophoresis with mass spectrometry for applications in proteomics. Electrophoresis, 26(7-8): 1291-1305.
182. Singh S, Springer M, Steen J, Kirschner M W, Steen H (2009). FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J Proteome Res, 8(5): 2201-2210.
183. Sjödin M O, Bergquist J, Wetterhall M (2010). Mining ventricular cerebrospinal fluid from patients with traumatic brain injury using hexapeptide ligand libraries to search for trauma biomarkers. J Chromatogr B Analyt Technol Biomed Life Sci, 878(22): 2003-2012.
184. Snovida S I, Bodnar E D, Viner R, Saba J, Perreault H (2010). A simple cellulose column procedure for selective enrichment of glycopeptides and characterization by nano LC coupled with electron-transfer and high-energy collisional-dissociation tandem mass spectrometry. Carbohydr Res, 345(6): 792-801.
185. Sobott F, Watt S J, Smith J, Edelmann M J, Kramer H B, Kessler B M (2009). Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination. J Am Soc Mass Spectrom, 20(9): 1652-1659.
186. Song C, Ye M, Han G, Jiang X, Wang F, Yu Z, Chen R, Zou H (2010). Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides. Anal Chem, 82(1): 53-56.
187. Spirin V, Shpunt A, Seebacher J, Gentzel M, Shevchenko A, Gygi S, Sunyaev S (2011). Assigning spectrum-specific P-values to protein identifications by mass spectrometry. Bioinformatics, 27(8): 1128-1134.
188. Staes A, Demol H, van Damme J, Martens L, Vandekerckhove J, Gevaert K (2004). Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J Proteome Res, 3(4): 786-791.
189. Stauber J, Lemaire R, Franck J, Bonnel D, Croix D, Day R, Wisztorski M, Fournier I, Salzet M (2008). MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting. J Proteome Res, 7(3): 969-978.
190. Stoeckli M, Chaurand P, Hallahan D E, Caprioli R M (2001). Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat Med, 7(4): 493-496.
191. Swaney D L, McAlister G C, Coon J J (2008). Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods, 5(11): 959-964.
192. Syka J E, Coon J J, Schroeder M J, Shabanowitz J, Hunt D F (2004). Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA, 101(26): 9528-9533.
193. Tammen H, Schulte I, Hess R, Menzel C, Kellmann M, Mohring T, Schulz-Knappe P (2005). Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics, 5(13): 3414-3422.
194. Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed A K, Hamon C (2003). Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem, 75(8): 1895-1904.
195. Tian Q, Price N D, Hood L (2012). Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J Intern Med, 271(2): 111-121.
196. Tian Y, Zhang H (2010). Glycoproteomics and clinical applications. Proteomics Clin Appl, 4(2): 124-132.
197. Ting L, Rad R, Gygi S P, Haas W (2011). MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods, 8(11): 937-940.
198. Trimpin S, Inutan E D, Herath T N, McEwen C N (2010). Laserspray ionization, a new atmospheric pressure MALDI method for producing highly charged gas-phase ions of peptides and proteins directly from solid solutions. Mol Cell Proteomics, 9(2): 362-367.
199. Valentine S J, Ewing M A, Dilger J M, Glover M S, Geromanos S, Hughes C, Clemmer D E (2011). Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters. J Proteome Res, 10(5): 2318-2329.
200. Valentine S J, Liu X, Plasencia M D, Hilderbrand A E, Kurulugama R T, Koeniger S L, Clemmer D E (2005). Developing liquid chromatography ion mobility mass spectometry techniques. Expert Rev Proteomics, 2(4): 553-565.
201. Valentine S J, Plasencia MD, Liu X, Krishnan M, Naylor S, Udseth H R, Smith R D, Clemmer D E (2006). Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res, 5(11): 2977-2984.
202. van Dorsselaer A, Carapito C, Delalande F, Schaeffer-Reiss C, Thierse D, Diemer H, McNair D S, Krewski D, Cashman N R (2011). Detection of prion protein in urine-derived injectable fertility products by a targeted proteomic approach. PLoS ONE, 6(3): e17815.
203. Vilim F S, Sasaki K, Rybak J, Alexeeva V, Cropper E C, Jing J, Orekhova I V, Brezina V, Price D, Romanova E V, Rubakhin S S, Hatcher N, Sweedler J V, Weiss K R (2010). Distinct mechanisms produce functionally complementary actions of neuropeptides that are structurally related but derived from different precursors. J Neurosci, 30(1): 131-147.
204. Wagner P D, Vu N D (2000). Histidine to aspartate phosphotransferase activity of nm23 proteins: phosphorylation of aldolase C on Asp-319. Biochem J, 346(3): 623-630.
205. Wang B, Lietz C B, Inutan E D, Leach S M, Trimpin S (2011a). Producing highly charged ions without solvent using laserspray ionization: a total solvent-free analysis approach at atmospheric pressure. Anal Chem, 83(11): 4076-4084.
206. Wang H, Liu J, Cooks R G, Ouyang Z (2010). Paper spray for direct analysis of complex mixtures using mass spectrometry. Angew Chem Int Ed Engl, 49(5): 877-880.
207. Wang H, Manicke N E, Yang Q, Zheng L, Shi R, Cooks R G, Ouyang Z (2011b). Direct analysis of biological tissue by paper spray mass spectrometry. Anal Chem, 83(4): 1197-1201.
208. Wang W, Zhou H, Lin H, Roy S, Shaler T A, Hill L R, Norton S, Kumar P, Anderle M, Becker C H (2003). Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem, 75(18): 4818-4826.
209. Wang Y K, Ma Z, Quinn D F, Fu E W (2002). Inverse 15N-metabolic labeling/mass spectrometry for comparative proteomics and rapid identification of protein markers/targets. Rapid Commun Mass Spectrom, 16(14): 1389-1397.
210. Washburn M P, Wolters D, Yates J R 3rd (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol, 19(3): 242-247.
211. Weekes M P, Antrobus R, Lill J R, Duncan L M, Hör S, Lehner P J (2010). Comparative analysis of techniques to purify plasma membrane proteins. J Biomol Tech, 21(3): 108-115.
212. Wei H, Nolkrantz K, Parkin M C, Chisolm C N, O'Callaghan J P, Kennedy R T (2006). Identification and quantification of neuropeptides in brain tissue by capillary liquid chromatography coupled offline to MALDI-TOF and MALDI-TOF/TOF-MS. Anal Chem, 78(13): 4342-4351.
213. Wei X, Dulberger C, Li L (2010a). Characterization of murine brain membrane glycoproteins by detergent assisted lectin affinity chromatography. Anal Chem, 82(15): 6329-6333.
214. Wei X, Herbst A, Ma D, Aiken J, Li L (2010b). A quantitative proteomic approach to prion disease biomarker research: delving into the glycoproteome. J Proteome Res, 10(6): 2687-2702.
215. Wei X, Li L (2009). Comparative glycoproteomics: approaches and applications. Brief Funct Genomics Proteomics, 8(2): 104-113.
216. Wenner B R, Lovell M A, Lynn B C (2004). Proteomic analysis of human ventricular cerebrospinal fluid from neurologically normal, elderly subjects using two-dimensional LC-MS/MS. J Proteome Res, 3(1): 97-103.
217. Wilhelm M, Kirchner M, Steen J A, Steen H (2012). mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics 11: O111 011379.
218. Winter D, Steen H (2011). Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MS. Proteomics, 11(24): 4726-4730.
219. Wiśniewski J R (2011). Tools for phospho- and glycoproteomics of plasma membranes. Amino Acids, 41(2): 223-233.
220. Wong M, Schlaggar B L, Buller R S, Storch G A, Landt M (2000). Cerebrospinal fluid protein concentration in pediatric patients: defining clinically relevant reference values. Arch Pediatr Adolesc Med, 154(8): 827-831.
221. Xia Y, Gunawardena H P, Erickson D E, McLuckey S A (2007). Effects of cation charge-site identity and position on electron-transfer dissociation of polypeptide cations. J Am Chem Soc, 129(40): 12232-12243.
222. Xiang F, Ye H, Chen R, Fu Q, Li L (2010). N, N-dimethyl leucines as novel isobaric tandem mass tags for quantitative proteomics and peptidomics. Anal Chem, 82(7): 2817-2825.
223. Xiang Y, Koomen J M (2012). Evaluation of direct Infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Anal Chem.
224. Xie F, Liu T, Qian W J, Petyuk V A, Smith R D (2011). Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem, 286(29): 25443-25449.
225. Ye X, Luke B, Andresson T, Blonder J (2009). 18O stable isotope labeling in MS-based proteomics. Brief Funct Genomics Proteomics, 8(2): 136-144.
226. Yoo H J, Wang N, Zhuang S, Song H, Håkansson K (2011). Negativeion electron capture dissociation: radical-driven fragmentation of charge-increased gaseous peptide anions. J Am Chem Soc, 133(42): 16790-16793.
227. You J S, Gelfanova V, Knierman M D, Witzmann F A, Wang M, Hale J E (2005). The impact of blood contamination on the proteome of cerebrospinal fluid. Proteomics, 5(1): 290-296.
228. Ytting H, Christensen I J, Thiel S, Jensenius J C, Svendsen MN, Nielsen L, Lottenburger T, Nielsen H J (2007). Biological variation in circulating levels of mannan-binding lectin (MBL) and MBLassociated serine protease-2 and the influence of age, gender and physical exercise. Scand J Immunol, 66(4): 458-464.
229. Yuan X, Desiderio D M (2005a). Human cerebrospinal fluid peptidomics. J Mass Spectrom, 40(2): 176-181.
230. Yuan X, Desiderio D M (2005b). Proteomics analysis of human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci, 815(1-2): 179-189.
231. Yuan X, Desiderio D M (2005c). Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics, 5(2): 541-550.
232. Yuki D, Sugiura Y, Zaima N, Akatsu H, Hashizume Y, Yamamoto T, Fujiwara M, Sugiyama K, Setou M (2011). Hydroxylated and nonhydroxylated sulfatide are distinctly distributed in the human cerebral cortex. Neuroscience, 193: 44-53.
233. 2 for global phosphoproteomics approaches. J Proteome Res, 10(8): 3474-3483.
234. Zhang G, Neubert T A (2009). Use of stable isotope labeling by amino acids in cell culture (SILAC) for phosphotyrosine protein identification and quantitation. Methods Mol Biol, 527: 79-92, xi.
235. Zhang H, Guo T, Li X, Datta A, Park J E, Yang J, Lim S K, Tam J P, Sze S K (2011a). Simultaneous characterization of glyco- and phosphoproteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography. Mol Cell Proteomics, 9(4): 635-647.
236. Zhang J, Goodlett D R, Montine T J (2005). Proteomic biomarker discovery in cerebrospinal fluid for neurodegenerative diseases. J Alzheimers Dis, 8(4): 377-386.
237. Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie, G A, Ma B (2011b). PEAKS DB: De Novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics, Online Available December 20, 2011.
238. Zhang Q, Faca V, Hanash S (2011c). Mining the plasma proteome for disease applications across seven logs of protein abundance. J Proteome Res, 10(1): 46-50.
239. Zhang Z, Xu W, Manicke N E, Cooks R G, Ouyang Z (2012). Silica coated paper substrate for paper-spray analysis of therapeutic drugs in dried blood spots. Anal Chem, 84(2): 931-938.
240. Zhou F, Sikorski T W, Ficarro S B, Webber J T, Marto J A (2011). Online nanoflow reversed phase-strong anion exchange-reversed phase liquid chromatography-tandem mass spectrometry platform for efficient and in-depth proteome sequence analysis of complex organisms. Anal Chem, 83(18): 6996-7005.
241. Zhou W, Ross M M, Tessitore A, Ornstein D, Vanmeter A, Liotta L A, Petricoin E F 3rd (2009). An initial characterization of the serum phosphoproteome. J Proteome Res, 8(12): 5523-5531.
242. Zhu W, Smith J W, Huang C M (2010). Mass spectrometry-based labelfree quantitative proteomics. J Biomed Biotechnol, 2010: 1.
243. Zougman A, Pilch B, Podtelejnikov A, Kiehntopf M, Schnabel C, Kumar C, Mann M (2008). Integrated analysis of the cerebrospinal fluid peptidome and proteome. J Proteome Res, 7(1): 386-399.
244. Zubarev R A, Kelleher N L, McLafferty F W (1998). Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process. J Am Chem Soc, 120(13): 3265-3266.
245. Zuberovic A, Hanrieder J, Hellman U, Bergquist J, Wetterhall M (2008). Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples. Eur J Mass Spectrom (Chichester, Eng), 14(2): 249-260.
246. Zybailov B, Coleman M K, Florens L, Washburn M P (2005). Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem, 77(19): 6218-6224.