REVIEW

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

  • Robert CUNNINGHAM 1 ,
  • Di MA 2 ,
  • Lingjun LI , 1,2
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  • 1. Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue 1101 University Avenue, Madison, WI 53706, USA
  • 2. School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA

Received date: 28 Jan 2012

Accepted date: 09 Mar 2012

Published date: 01 Aug 2012

Copyright

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg

Abstract

The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large data sets of proteins or peptides involved in various biologic and disease progression processes generating testable hypothesis for complex biologic questions. This review provides an introduction to relevant topics in proteomics and peptidomics including biologic material selection, sample preparation, separation techniques, peptide fragmentation, post-translational modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature, remaining challenges, and emerging technologies for proteomics and peptidomics are presented.

Cite this article

Robert CUNNINGHAM , Di MA , Lingjun LI . Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery[J]. Frontiers in Biology, 2012 , 7(4) : 313 -335 . DOI: 10.1007/s11515-012-1218-y

Acknowledgments

Preparation of this manuscript was supported in part by the University of Wisconsin Graduate School, Wisconsin Alzheimer’s Disease Research Center Pilot Grant, and a Department of Defense Pilot Award. L.L. acknowledges an H. I. Romnes Faculty Fellowship.
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

DOI PMID

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 M A, 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

DOI PMID

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

DOI PMID

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

PMID

5
Al-Tarawneh S K, Border M B, Dibble C F, Bencharit S (2011). Defining salivary biomarkers using mass spectrometry-based proteomics: a systematic review. OMICS, 15(6): 353-361

DOI PMID

6
Albalat A, Mischak H, Mullen W (2011a). Clinical application of urinary proteomics/peptidomics. Expert Rev Proteomics, 8(5): 615-629

DOI PMID

7
Albalat A, Mischak H, Mullen W (2011b). Urine proteomics in clinical applications: technologies, principal considerations and clinical implementation. Prilozi, 32(1): 13-44

PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

11
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

DOI PMID

12
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

DOI PMID

13
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

DOI PMID

14
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

DOI PMID

15
Belov M E, Prasad S, Prior D C, Danielson W F 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

DOI PMID

16
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

DOI PMID

17
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

DOI PMID

18
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

DOI PMID

19
Burke T W, Mant C T, Black J A, Hodges R S (1989). Strong cation-exchange high-performance liquid chromatography of peptides. Effect of non-specific hydrophobic interactions and linearization of peptide retention behaviour. J Chromatogr, 476: 377-389

PMID

20
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

DOI PMID

21
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

DOI PMID

22
Castagnola M, Cabras T, Vitali A, Sanna M T, Messana I (2011). Biotechnological implications of the salivary proteome. Trends Biotechnol, 29(8): 409-418

DOI PMID

23
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

DOI PMID

24
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

DOI PMID

25
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

DOI PMID

26
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

DOI PMID

27
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

DOI PMID

28
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

DOI PMID

29
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

DOI PMID

30
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

DOI PMID

31
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

DOI PMID

32
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

DOI PMID

33
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

DOI PMID

34
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

DOI PMID

35
Cohen P (2000). The regulation of protein function by multisite phosphorylation—a 25 year update. Trends Biochem Sci, 25(12): 596-601

DOI PMID

36
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

DOI PMID

37
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

DOI PMID

38
Craig R, Beavis R C (2004). TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20(9): 1466-1467

DOI PMID

39
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

DOI PMID

40
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

DOI PMID

41
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

DOI PMID

42
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

DOI PMID

43
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

DOI PMID

44
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

DOI PMID

45
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

PMID

46
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

DOI PMID

47
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

DOI PMID

48
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

DOI PMID

49
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

DOI PMID

50
Di Palma S, Boersema P J, Heck A J, Mohammed S (2011a). Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis. Anal Chem, 83(9): 3440-3447

PMID

51
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

DOI PMID

52
Diez R, Herbstreith M, Osorio C, Alzate O (2010). 2-D Fluorescence Difference Gel Electrophoresis (DIGE) in Neuroproteomics

53
Dowell J A, Heyden W V, Li L (2006). Rat neuropeptidomics by LC-MS/MS and MALDI-FTMS: Enhanced dissection and extraction techniques coupled with 2D RP-RP HPLC. J Proteome Res, 5(12): 3368-3375

DOI PMID

54
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

DOI PMID

55
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

DOI PMID

56
Edelmann M J (2011). Strong cation exchange chromatography in analysis of posttranslational modifications: innovations and perspectives. J Biomed Biotechnol, 2011: 1

DOI PMID

57
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

DOI PMID

58
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

DOI

59
Filiou M D, Martins-de-Souza D, Guest P C, Bahn S, Turck C W (2012). To label or not to label: Applications of quantitative proteomics in neuroscience research. Proteomics,

DOI

60
Fonslow B R, Yates J R 3rd (2009). Capillary electrophoresis applied to proteomic analysis. J Sep Sci, 32(8): 1175-1188

DOI PMID

61
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

DOI PMID

62
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

DOI PMID

63
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

DOI PMID

64
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

DOI PMID

65
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

DOI PMID

66
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

DOI PMID

67
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

DOI PMID

68
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

DOI PMID

69
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

DOI PMID

70
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

DOI PMID

71
Gilmore J M, Washburn M P (2010). Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics, 73(11): 2078-2091

DOI PMID

72
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

DOI PMID

73
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

74
Groen A J, Lilley K S (2010). Proteomics of total membranes and subcellular membranes. Expert Rev Proteomics, 7(6): 867-878

DOI PMID

75
Guiochon G, Marchetti N, Mriziq K, Shalliker R A (2008). Implementations of two-dimensional liquid chromatography. J Chromatogr A, 1189(1-2): 109-168

DOI PMID

76
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

DOI PMID

77
Gygi S P, Rist B, Gerber S A, Turecek F, Gelb M H, Aebersold R (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 17(10): 994-999

DOI PMID

78
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

DOI PMID

79
Hanash S (2004). Building a foundation for the human proteome: the role of the Human Proteome Organization. J Proteome Res, 3(2): 197-199

DOI PMID

80
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

DOI PMID

81
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

DOI PMID

82
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

DOI PMID

83
Helbig A O, Heck A J, Slijper M (2010). Exploring the membrane proteome—challenges and analytical strategies. J Proteomics, 73(5): 868-878

DOI PMID

84
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

DOI PMID

85
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

DOI PMID

86
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

DOI PMID

87
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

PMID

88
Hood L, Friend S H (2011). Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol, 8(3): 184-187

DOI PMID

89
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

DOI PMID

90
Huck C W, 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

DOI PMID

91
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

DOI PMID

92
Hummon A B, Amare A, Sweedler J V (2006). Discovering new invertebrate neuropeptides using mass spectrometry. Mass Spectrom Rev, 25(1): 77-98

DOI PMID

93
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

DOI PMID

94
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

95
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

DOI PMID

96
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

97
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

DOI PMID

98
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 Database issue): D878-D883

DOI PMID

99
Jorge I, Navarro P, Martínez-Acedo P, Núñez E, Serrano H, Alfranca A, Redondo J M, Vázquez J (2009). Statistical model to analyze quantitative proteomics data obtained by 18O/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

DOI PMID

100
Kalume D E, Molina H, Pandey A (2003). Tackling the phosphoproteome: tools and strategies. Curr Opin Chem Biol, 7(1): 64-69

DOI PMID

101
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

DOI PMID

102
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-mass-based fractionation and top-down mass spectrometry. Anal Chem, 84(1): 209-215

DOI PMID

103
Klampfl C W (2009). CE with MS detection: a rapidly developing hyphenated technique. Electrophoresis, 30(S1 Suppl 1): S83-S91

DOI PMID

104
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

DOI PMID

105
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

DOI PMID

106
Kumar C, Mann M (2009). Bioinformatics analysis of mass spectrometry-based proteomics data sets. FEBS Lett, 583(11): 1703-1712

DOI PMID

107
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

PMID

108
Li L, Garden R W, Sweedler J V (2000). Single-cell MALDI: a new tool for direct peptide profiling. Trends Biotechnol, 18(4): 151-160

DOI PMID

109
Li L, Sweedler J V (2008). Peptides in the brain: mass spectrometry-based measurement approaches and challenges. Annu Rev Anal Chem (Palo Alto Calif), 1(1): 451-483

DOI PMID

110
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 ionization-tandem mass spectrometry for samples of intermediate complexity. Anal Chem, 84(3): 1617-1622

DOI PMID

111
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

DOI PMID

112
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

DOI PMID

113
Liu H, Håkansson K (2006). Electron capture dissociation of tyrosine O-sulfated peptides complexed with divalent metal cations. Anal Chem, 78(21): 7570-7576

DOI PMID

114
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

DOI PMID

115
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

DOI PMID

116
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

DOI PMID

117
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

DOI PMID

118
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

DOI PMID

119
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

DOI PMID

120
Liu T, Qian W J, Mottaz H M, Gritsenko M A, 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

DOI PMID

121
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

DOI PMID

122
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

DOI PMID

123
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

DOI PMID

124
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

DOI PMID

125
Makridakis M, Vlahou A (2010). Secretome proteomics for discovery of cancer biomarkers. J Proteomics, 73(12): 2291-2305

DOI PMID

126
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

DOI PMID

127
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

DOI PMID

128
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

DOI PMID

129
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

DOI PMID

130
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

DOI PMID

131
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

DOI PMID

132
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

DOI PMID

133
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

134
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

DOI PMID

135
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

DOI PMID

136
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

DOI PMID

137
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

DOI PMID

138
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

DOI PMID

139
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

DOI PMID

140
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

DOI PMID

141
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

DOI PMID

142
Oh-Ishi M, Maeda T (2002). Separation techniques for high-molecular-mass proteins. J Chromatogr B Analyt Technol Biomed Life Sci, 771(1-2): 49-66

DOI PMID

143
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

DOI PMID

144
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

DOI PMID

145
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 D W, 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 publicly-available database. Proteomics, 5(13): 3226-3245

DOI PMID

146
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

DOI PMID

147
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

DOI PMID

148
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

DOI PMID

149
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

DOI PMID

150
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

DOI PMID

151
Perkins D N, Pappin D J, Creasy D M, Cottrell J S (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20(18): 3551-3567

DOI PMID

152
Pimienta G, Chaerkady R, Pandey A (2009). SILAC for global phosphoproteomic analysis. Methods Mol Biol, 527: 107-116, x (x.)

DOI PMID

153
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

154
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

DOI PMID

155
Rajagopal M U, Hathout Y, MacDonald T J, Kieran M W, Gururangan S, Blaney S M, 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

DOI PMID

156
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

DOI PMID

157
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

DOI PMID

158
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

DOI PMID

159
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

DOI PMID

160
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

DOI PMID

161
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

DOI PMID

162
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

DOI PMID

163
Rucevic M, Hixson D, Josic D (2011). Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis, 32(13): 1549-1564

DOI PMID

164
Rudrabhatla P, Jaffe H, Pant H C (2011). Direct evidence of phosphorylated neuronal intermediate filament proteins in neurofibrillary tangles (NFTs): phosphoproteomics of Alzheimer’s NFTs. FASEB J, 25(11): 3896-3905

DOI PMID

165
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

DOI PMID

166
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

DOI PMID

167
Schiess R, Wollscheid B, Aebersold R (2009). Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol, 3(1): 33-44

DOI PMID

168
Schmidt A, Kellermann J, Lottspeich F (2005). A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics, 5(1): 4-15

DOI PMID

169
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

DOI PMID

170
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

DOI PMID

171
Searle B C (2010). Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics, 10(6): 1265-1269

DOI PMID

172
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). Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem, 81(18): 7757-7765

DOI PMID

173
Seeley E H, Caprioli R M (2011). MALDI imaging mass spectrometry of human tissue: method challenges and clinical perspectives. Trends Biotechnol, 29(3): 136-143

DOI PMID

174
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

DOI PMID

175
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

DOI PMID

176
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

DOI PMID

177
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

178
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

DOI PMID

179
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

DOI PMID

180
Simpson D C, Smith R D (2005). Combining capillary electrophoresis with mass spectrometry for applications in proteomics. Electrophoresis, 26(7-8): 1291-1305

DOI PMID

181
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

DOI PMID

182
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

DOI PMID

183
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

DOI PMID

184
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

DOI PMID

185
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

DOI PMID

186
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

DOI PMID

187
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

DOI PMID

188
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

DOI PMID

189
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

DOI PMID

190
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

DOI PMID

191
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

DOI PMID

192
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

DOI PMID

193
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

DOI PMID

194
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

DOI PMID

195
Tian Y, Zhang H (2010). Glycoproteomics and clinical applications. Proteomics Clin Appl, 4(2): 124-132

DOI PMID

196
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

DOI PMID

197
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

DOI PMID

198
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

DOI PMID

199
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

DOI PMID

200
Valentine S J, Plasencia M D, 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

DOI PMID

201
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

DOI PMID

202
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

DOI PMID

203
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

DOI PMID

204
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

DOI PMID

205
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

PMID

206
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

DOI PMID

207
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

DOI PMID

208
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

DOI PMID

209
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

DOI PMID

210
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

PMID

211
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 off-line to MALDI-TOF and MALDI-TOF/TOF-MS. Anal Chem, 78(13): 4342-4351

DOI PMID

212
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

DOI

213
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

DOI PMID

214
Wei X, Li L (2009). Comparative glycoproteomics: approaches and applications. Brief Funct Genomics Proteomics, 8(2): 104-113

DOI PMID

215
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

DOI PMID

216
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.

217
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

DOI PMID

218
Wiśniewski J R (2011). Tools for phospho- and glycoproteomics of plasma membranes. Amino Acids, 41(2): 223-233

DOI PMID

219
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

PMID

220
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

DOI PMID

221
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

DOI PMID

222
Xiang Y, Koomen J M (2012). Evaluation of direct Infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Anal Chem

223
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

DOI PMID

224
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

DOI PMID

225
Yoo H J, Wang N, Zhuang S, Song H, Håkansson K (2011). Negative-ion electron capture dissociation: radical-driven fragmentation of charge-increased gaseous peptide anions. J Am Chem Soc, 133(42): 16790-16793

DOI PMID

226
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

DOI PMID

227
Ytting H, Christensen I J, Thiel S, Jensenius J C, Svendsen M N, Nielsen L, Lottenburger T, Nielsen H J (2007). Biological variation in circulating levels of mannan-binding lectin (MBL) and MBL-associated serine protease-2 and the influence of age, gender and physical exercise. Scand J Immunol, 66(4): 458-464

DOI PMID

228
Yuan X, Desiderio D M (2005a). Human cerebrospinal fluid peptidomics. J Mass Spectrom, 40(2): 176-181

DOI PMID

229
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

DOI PMID

230
Yuan X, Desiderio D M (2005c). Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics, 5(2): 541-550

DOI PMID

231
Yuki D, Sugiura Y, Zaima N, Akatsu H, Hashizume Y, Yamamoto T, Fujiwara M, Sugiyama K, Setou M (2011). Hydroxylated and non-hydroxylated sulfatide are distinctly distributed in the human cerebral cortex. Neuroscience, 193: 44-53

DOI PMID

232
Zarei M, Sprenger A, Metzger F, Gretzmeier C, Dengjel J (2011). Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches. J Proteome Res, 10(8): 3474-3483

DOI PMID

233
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 (xi.)

DOI PMID

234
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

DOI PMID

235
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

PMID

236
Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie 000, G A 000, Ma B (2011b). PEAKS DB: De Novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics

237
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

DOI PMID

238
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

DOI PMID

239
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

DOI PMID

240
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

DOI PMID

241
Zhu W, Smith J W, Huang C M (2010). Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol, 2010: 1

DOI PMID

242
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

DOI PMID

243
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

DOI

244
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

DOI PMID

245
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

DOI PMID

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