-
1
-
-
84867057236
-
Analysing signalling networks by mass spectrometry
-
JØrgensen C, Locard-Paulet M. Analysing signalling networks by mass spectrometry. Amino. Acids 43(3), 1061-1074 (2012)
-
(2012)
Amino. Acids
, vol.43
, Issue.3
, pp. 1061-1074
-
-
JØrgensen, C.1
Locard-Paulet, M.2
-
2
-
-
79955831978
-
Improved peptide identification by targeted fragmentation using CID HCD and ETD on an LTQ-Orbitrap Velos
-
Frese CK, Altelaar AFM, Hennrich ML et al. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J. Proteome Res. 10(5), 2377-2388 (2011)
-
(2011)
J. Proteome Res.
, vol.10
, Issue.5
, pp. 2377-2388
-
-
Frese, C.K.1
Altelaar, A.F.M.2
Hennrich, M.L.3
-
3
-
-
0035298820
-
Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode
-
Steen H, Küster B, Fernandez M, Pandey A, Mann M. Detection of tyrosine phosphorylated peptides by precursor ion scanning quadrupole TOF mass spectrometry in positive ion mode. Anal. Chem. 73(7), 1440-1448 (2001)
-
(2001)
Anal. Chem.
, vol.73
, Issue.7
, pp. 1440-1448
-
-
Steen, H.1
Küster, B.2
Fernandez, M.3
Pandey, A.4
Mann, M.5
-
4
-
-
0035478709
-
Analysis of phosphorylated proteins and peptides by mass spectrometry
-
McLachlin DT, Chait BT. Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 5(5), 591-602 (2001)
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, Issue.5
, pp. 591-602
-
-
McLachlin, D.T.1
Chait, B.T.2
-
5
-
-
0032810855
-
Preliminary comparison of precursor scans and liquid chromatography- tandem mass spectrometry on a hybrid quadrupole time-of-flight mass spectrometer
-
Borchers C, Parker CE, Deterding LJ, Tomer KB. Preliminary comparison of precursor scans and liquid chromatography- tandem mass spectrometry on a hybrid quadrupole time-of-flight mass spectrometer. J. Chromatogr. A 854(1-2), 119-130 (1999)
-
(1999)
J. Chromatogr. A
, vol.854
, Issue.1-2
, pp. 119-130
-
-
Borchers, C.1
Parker, C.E.2
Deterding, L.J.3
Tomer, K.B.4
-
6
-
-
84879593559
-
Review of software tools for design and analysis of large scale MRM proteomic datasets
-
Colangelo CM, Chung L, Bruce C, Cheung K-H. Review of software tools for design and analysis of large scale MRM proteomic datasets. Methods 61(3), 287-298 (2013)
-
(2013)
Methods
, vol.61
, Issue.3
, pp. 287-298
-
-
Colangelo, C.M.1
Chung, L.2
Bruce, C.3
Cheung, K.-H.4
-
7
-
-
33645715370
-
Multiple reaction monitoring as a method for identifying protein posttranslational modifications
-
Cox DM, Zhong F, Du M, Duchoslav E, Sakuma T, McDermott JC. Multiple reaction monitoring as a method for identifying protein posttranslational modifications. J. Biomol. Tech. 16(2), 83-90 (2005)
-
(2005)
J. Biomol. Tech.
, vol.16
, Issue.2
, pp. 83-90
-
-
Cox, D.M.1
Zhong, F.2
Du, M.3
Duchoslav, E.4
Sakuma, T.5
McDermott, J.C.6
-
8
-
-
24044553566
-
Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity
-
Unwin RD, Griffiths JR, Leverentz MK, Grallert A, Hagan IM, Whetton AD. Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol. Cell Proteomics 4(8), 1134-1144 (2005)
-
(2005)
Mol. Cell Proteomics
, vol.4
, Issue.8
, pp. 1134-1144
-
-
Unwin, R.D.1
Griffiths, J.R.2
Leverentz, M.K.3
Grallert, A.4
Hagan, I.M.5
Whetton, A.D.6
-
9
-
-
0842288891
-
Factors that affect ion trap data-dependent MS/MS in proteomics
-
Wenner BR, Lynn BC. Factors that affect ion trap data-dependent MS/MS in proteomics. J. Am. Soc. Mass Spectrom. 15(2), 150-157 (2004)
-
(2004)
J. Am. Soc. Mass Spectrom.
, vol.15
, Issue.2
, pp. 150-157
-
-
Wenner, B.R.1
Lynn, B.C.2
-
10
-
-
34250722602
-
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
-
Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl Acad. Sci. USA. 104(14), 5860-5865 (2007)
-
(2007)
Proc. Natl Acad. Sci. USA.
, vol.104
, Issue.14
, pp. 5860-5865
-
-
Wolf-Yadlin, A.1
Hautaniemi, S.2
Lauffenburger, D.A.3
White, F.M.4
-
11
-
-
33845902530
-
Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics
-
Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev. Proteomics 3(6), 611-619 (2006)
-
(2006)
Expert Rev. Proteomics
, vol.3
, Issue.6
, pp. 611-619
-
-
Wu, L.1
Han, D.K.2
-
12
-
-
77955455399
-
Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies
-
Houel S, Abernathy R, Renganathan K, Meyer-Arendt K, Ahn NG, Old WM. Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J. Proteome Res. 9(8), 4152-4160 (2010)
-
(2010)
J. Proteome Res.
, vol.9
, Issue.8
, pp. 4152-4160
-
-
Houel, S.1
Abernathy, R.2
Renganathan, K.3
Meyer-Arendt, K.4
Ahn, N.G.5
Old, W.M.6
-
13
-
-
55249111329
-
Precursor-ion mass re-estimation improves peptide identification on hybrid instruments
-
Luethy R, Kessner DE, Katz JE et al. Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J. Proteome Res. 7(9), 4031-4039 (2008)
-
(2008)
J. Proteome Res.
, vol.7
, Issue.9
, pp. 4031-4039
-
-
Luethy, R.1
Kessner, D.E.2
Katz, J.E.3
-
14
-
-
79953719716
-
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS
-
Michalski A, Cox J, Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 10(4), 1785-1793 (2011)
-
(2011)
J. Proteome Res.
, vol.10
, Issue.4
, pp. 1785-1793
-
-
Michalski, A.1
Cox, J.2
Mann, M.3
-
15
-
-
0037795741
-
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
-
Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA. 100(12), 6940-6945 (2003)
-
(2003)
Proc. Natl Acad. Sci. USA.
, vol.100
, Issue.12
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
16
-
-
78650151240
-
Stable-isotope dilution LC-MS for quantitative biomarker analysis
-
Ciccimaro E, Blair IA. Stable-isotope dilution LC-MS for quantitative biomarker analysis. Bioanalysis 2(2), 311-341 (2010)
-
(2010)
Bioanalysis
, vol.2
, Issue.2
, pp. 311-341
-
-
Ciccimaro, E.1
Blair, I.A.2
-
17
-
-
79953227740
-
Increased selectivity, analytical precision, and throughput in targeted proteomics
-
Kiyonami R, Schoen A, Prakash A et al. Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol. Cell Proteomics 10(2), M110.002931 (2011)
-
(2011)
Mol. Cell Proteomics
, vol.10
, Issue.2
-
-
Kiyonami, R.1
Schoen, A.2
Prakash, A.3
-
18
-
-
84874053586
-
Screening method using selected reaction monitoring for targeted proteomics studies of nasal lavage fluid
-
Mörtstedt H, Kåredal MH, Jönsson BAG, Lindh CH. Screening method using selected reaction monitoring for targeted proteomics studies of nasal lavage fluid. J. Proteome Res. 12(1), 234-247 (2012)
-
(2012)
J. Proteome Res.
, vol.12
, Issue.1
, pp. 234-247
-
-
Mörtstedt, H.1
Kåredal, M.H.2
Jönsson, B.A.G.3
Lindh, C.H.4
-
19
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
-
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotech. 17(10), 994-999 (1999)
-
(1999)
Nat. Biotech.
, vol.17
, Issue.10
, pp. 994-999
-
-
Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
-
21
-
-
19944432197
-
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3(12), 1154-1169 (2004)
-
(2004)
Mol. Cell Proteomics
, vol.3
, Issue.12
, pp. 1154-1169
-
-
Ross, P.L.1
Huang, Y.N.2
Marchese, J.N.3
-
22
-
-
33646269941
-
A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies
-
Zieske LR. A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J. Exp. Bot. 57(7), 1501-1508 (2006)
-
(2006)
J. Exp. Bot.
, vol.57
, Issue.7
, pp. 1501-1508
-
-
Zieske, L.R.1
-
23
-
-
77957595022
-
A proteomic approach for plasma biomarker discovery with 8-plex iTRAQ labeling and SCX-LC-MS/MS
-
Ye H, Sun L, Huang X, Zhang P, Zhao X. A proteomic approach for plasma biomarker discovery with 8-plex iTRAQ labeling and SCX-LC-MS/MS. Mol. Cell Biochem. 343(1-2), 91-99 (2010)
-
(2010)
Mol. Cell Biochem.
, vol.343
, Issue.1-2
, pp. 91-99
-
-
Ye, H.1
Sun, L.2
Huang, X.3
Zhang, P.4
Zhao, X.5
-
24
-
-
12444345515
-
Tandem Mass Tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
-
Thompson A, Schäfer J, Kuhn K et al. Tandem Mass Tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75(18), 4942-4942 (2003)
-
(2003)
Anal. Chem.
, vol.75
, Issue.18
, pp. 4942-4942
-
-
Thompson, A.1
Schäfer, J.2
Kuhn, K.3
-
25
-
-
77955159809
-
Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap
-
Pichler P, Koöcher T, Holzmann J et al. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap. Anal. Chem. 82(15), 6549-6558 (2010)
-
(2010)
Anal. Chem.
, vol.82
, Issue.15
, pp. 6549-6558
-
-
Pichler, P.1
Koöcher, T.2
Holzmann, J.3
-
26
-
-
13244260803
-
A novel strategy for quantitative proteomics using isotope-coded protein labels
-
Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5(1), 4-15 (2005)
-
(2005)
Proteomics
, vol.5
, Issue.1
, pp. 4-15
-
-
Schmidt, A.1
Kellermann, J.2
Lottspeich, F.3
-
27
-
-
80052377476
-
ICPL Labeling strategies for proteome research
-
Gevaert, K, Vandekerckhove, J (Eds) Humana Press, NY, USA
-
Lottspeich F, Kellermann J. ICPL Labeling strategies for proteome research. In: Gel-Free Proteomics. Gevaert, K, Vandekerckhove, J (Eds) Humana Press, NY, USA 55-64 (2011)
-
(2011)
Gel-Free Proteomics
, pp. 55-64
-
-
Lottspeich, F.1
Kellermann, J.2
-
28
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong S-E, Blagoev B, Kratchmarova I et al. 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 (2002)
-
(2002)
Mol. Cell Proteomics
, vol.1
, Issue.5
, pp. 376-386
-
-
Ong, S.-E.1
Blagoev, B.2
Kratchmarova, I.3
-
29
-
-
34247396011
-
A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC) Nat
-
Ong S-E, Mann M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC) Nat. Protocols 1(6), 2650-2660 (2007)
-
(2007)
Protocols
, vol.1
, Issue.6
, pp. 2650-2660
-
-
Ong, S.-E.1
Mann, M.2
-
30
-
-
84887923189
-
-
The 18th IMSC. Bremen, Germany
-
Hewel J, Schutkowski M, Liu J, White C, Emili A. FAIMS/MS/MS: development of high-throughput targeted peptide monitoring for the detection of low abundant protein markers. In: The 18th IMSC. Bremen, Germany (2009)
-
(2009)
FAIMS/MS/MS: Development of High-throughput Targeted Peptide Monitoring for the Detection of Low Abundant Protein Markers
-
-
Hewel, J.1
Schutkowski, M.2
Liu, J.3
White, C.4
Emili, A.5
-
31
-
-
70649087115
-
Multiple reaction monitoring cubed for protein quantification at the low nanogram/ milliliter level in nondepleted human serum
-
Fortin T, Salvador A, Charrier JP et al. Multiple reaction monitoring cubed for protein quantification at the low nanogram/ milliliter level in nondepleted human serum. Anal. Chem. 81(22), 9343-9352 (2009)
-
(2009)
Anal. Chem.
, vol.81
, Issue.22
, pp. 9343-9352
-
-
Fortin, T.1
Salvador, A.2
Charrier, J.P.3
-
32
-
-
84860854049
-
Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics
-
Shi T, Su D, Liu T et al. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics 12(8), 1074-1092 (2012)
-
(2012)
Proteomics
, vol.12
, Issue.8
, pp. 1074-1092
-
-
Shi, T.1
Su, D.2
Liu, T.3
-
33
-
-
84861990380
-
Selected reaction monitoring-based proteomics: Workflows, potential, pitfalls and future directions
-
Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Meth. 9(6), 555-566 (2012)
-
(2012)
Nat. Meth.
, vol.9
, Issue.6
, pp. 555-566
-
-
Picotti, P.1
Aebersold, R.2
-
34
-
-
42649091860
-
Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics
-
Mirzaei H, McBee JK, Watts J, Aebersold R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol. Cell Proteomics 7(4), 813-823 (2008)
-
(2008)
Mol. Cell Proteomics
, vol.7
, Issue.4
, pp. 813-823
-
-
Mirzaei, H.1
McBee, J.K.2
Watts, J.3
Aebersold, R.4
-
35
-
-
74049131716
-
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
-
Picotti P, Rinner O, Stallmach R et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Meth. 7(1), 43-46 (2010)
-
(2010)
Nat. Meth.
, vol.7
, Issue.1
, pp. 43-46
-
-
Picotti, P.1
Rinner, O.2
Stallmach, R.3
-
36
-
-
59149084542
-
Targeted proteomic strategy for clinical biomarker discovery
-
Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol. 3(1), 33-44 (2009)
-
(2009)
Mol. Oncol.
, vol.3
, Issue.1
, pp. 33-44
-
-
Schiess, R.1
Wollscheid, B.2
Aebersold, R.3
-
37
-
-
79960214321
-
A targeted proteomics-based pipeline for verification of biomarkers in plasma
-
Whiteaker JR, Lin C, Kennedy J et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 29(7), 625-634 (2011)
-
(2011)
Nat. Biotechnol.
, vol.29
, Issue.7
, pp. 625-634
-
-
Whiteaker, J.R.1
Lin, C.2
Kennedy, J.3
-
38
-
-
0036636552
-
A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation
-
Bateman RH, Carruthers R, Hoyes JB et al. A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 13(7), 792-803 (2002)
-
(2002)
J. Am. Soc. Mass Spectrom
, vol.13
, Issue.7
, pp. 792-803
-
-
Bateman, R.H.1
Carruthers, R.2
Hoyes, J.B.3
-
39
-
-
31644446949
-
Absolute quantification of proteins by LCMSE : A virtue of parallel ms acquisition
-
Silva JC, Gorenstein MV, Li G-Z, Vissers JPC, Geromanos SJ. Absolute quantification of proteins by LCMSE : A virtue of parallel ms acquisition. Mol. Cell Proteomics 5(1), 144-156 (2006)
-
(2006)
Mol. Cell Proteomics
, vol.5
, Issue.1
, pp. 144-156
-
-
Silva, J.C.1
Gorenstein, M.V.2
Li, G.-Z.3
Vissers, J.P.C.4
Geromanos, S.J.5
-
40
-
-
33645725976
-
Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: A sweet tale
-
Silva JC, Denny R, Dorschel C et al. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: A sweet tale. Mol. Cell Proteomics 5(4), 589-607 (2006)
-
(2006)
Mol. Cell Proteomics
, vol.5
, Issue.4
, pp. 589-607
-
-
Silva, J.C.1
Denny, R.2
Dorschel, C.3
-
41
-
-
0038047154
-
Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer
-
Purvine S, Eppel J-T, Yi EC, Goodlett DR. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 3(6), 847-850 (2003)
-
(2003)
Proteomics
, vol.3
, Issue.6
, pp. 847-850
-
-
Purvine, S.1
Eppel, J.-T.2
Yi, E.C.3
Goodlett, D.R.4
-
42
-
-
31344449923
-
A general precursor ion-like scanning mode on quadrupole-TOF instruments compatible with chromatographic separation
-
Niggeweg R, Köcher T, Gentzel M et al. A general precursor ion-like scanning mode on quadrupole-TOF instruments compatible with chromatographic separation. Proteomics 6(1), 41-53 (2006)
-
(2006)
Proteomics
, vol.6
, Issue.1
, pp. 41-53
-
-
Niggeweg, R.1
Köcher, T.2
Gentzel, M.3
-
43
-
-
63049084861
-
The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS
-
Geromanos SJ, Vissers JPC, Silva JC et al. 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 (2009)
-
(2009)
Proteomics
, vol.9
, Issue.6
, pp. 1683-1695
-
-
Geromanos, S.J.1
Vissers, J.P.C.2
Silva, J.C.3
-
44
-
-
63049138916
-
Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures
-
Li G-Z, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 9(6), 1696-1719 (2009)
-
(2009)
Proteomics
, vol.9
, Issue.6
, pp. 1696-1719
-
-
Li, G.-Z.1
Vissers, J.P.C.2
Silva, J.C.3
Golick, D.4
Gorenstein, M.V.5
Geromanos, S.J.6
-
45
-
-
77954365852
-
Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation
-
Blackburn K, Mbeunkui F, Mitra SK, Mentzel T, Goshe MB. Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation. J. Proteome Res. 9(7), 3621-3637 (2010)
-
(2010)
J. Proteome Res.
, vol.9
, Issue.7
, pp. 3621-3637
-
-
Blackburn, K.1
Mbeunkui, F.2
Mitra, S.K.3
Mentzel, T.4
Goshe, M.B.5
-
46
-
-
79960763879
-
Quantification of proteins using data-independent analysis (MSE) in simple and complex samples: A systematic evaluation
-
Levin Y, Hradetzky E, Bahn S. Quantification of proteins using data-independent analysis (MSE) in simple and complex samples: A systematic evaluation. Proteomics 11(16), 3273-3287 (2011)
-
(2011)
Proteomics
, vol.11
, Issue.16
, pp. 3273-3287
-
-
Levin, Y.1
Hradetzky, E.2
Bahn, S.3
-
47
-
-
67650351489
-
A comparison of labeling and label-free mass spectrometry-based proteomics approaches
-
Patel VJ, Thalassinos K, Slade SE et al. A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J. Proteome Res. 8(7), 3752-3759 (2009)
-
(2009)
J. Proteome Res.
, vol.8
, Issue.7
, pp. 3752-3759
-
-
Patel, V.J.1
Thalassinos, K.2
Slade, S.E.3
-
48
-
-
84857367827
-
Analysis of membrane proteome by data-dependent LC-MS/MS combined with data-independent LC-MSE technique
-
Kwon J, Park S, Park C, Kwon S-O, Choi J-S. Analysis of membrane proteome by data-dependent LC-MS/MS combined with data-independent LC-MSE technique. J. Anal. Sci. Technol. 1(1), 78-85 (2010)
-
(2010)
J. Anal. Sci. Technol.
, vol.1
, Issue.1
, pp. 78-85
-
-
Kwon, J.1
Park, S.2
Park, C.3
Kwon, S.-O.4
Choi, J.-S.5
-
49
-
-
84879367507
-
Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies
-
Shliaha PV, Bond NJ, Gatto L, Lilley KS. Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. J. Proteome Res. 12(6), 2323-2339 (2013)
-
(2013)
J. Proteome Res.
, vol.12
, Issue.6
, pp. 2323-2339
-
-
Shliaha, P.V.1
Bond, N.J.2
Gatto, L.3
Lilley, K.S.4
-
50
-
-
84879391561
-
Improving qualitative and quantitative performance for MSE-based label-free proteomics
-
Bond NJ, Shliaha PV, Lilley KS, Gatto L. Improving qualitative and quantitative performance for MSE-based label-free proteomics. J. Proteome Res. 12(6), 2340-2353 (2013)
-
(2013)
J. Proteome Res.
, vol.12
, Issue.6
, pp. 2340-2353
-
-
Bond, N.J.1
Shliaha, P.V.2
Lilley, K.S.3
Gatto, L.4
-
51
-
-
34249657456
-
Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease
-
Vissers JPC, Langridge JI, Aerts JMFG. Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol. Cell Proteomics 6(5), 755-766 (2007)
-
(2007)
Mol. Cell Proteomics
, vol.6
, Issue.5
, pp. 755-766
-
-
Vissers, J.P.C.1
Langridge, J.I.2
Aerts, J.M.F.G.3
-
52
-
-
67650354396
-
Antipsychotic treatment alters protein expression associated with presynaptic function and nervous system development in rat frontal cortex
-
Ma D, Chan MK, Lockstone HE et al. Antipsychotic treatment alters protein expression associated with presynaptic function and nervous system development in rat frontal cortex. J. Proteome Res. 8(7), 3284-3297 (2009)
-
(2009)
J. Proteome Res.
, vol.8
, Issue.7
, pp. 3284-3297
-
-
Ma, D.1
Chan, M.K.2
Lockstone, H.E.3
-
53
-
-
73649097245
-
Expression profiling of fibroblasts identifies cell cycle abnormalities in Schizophrenia
-
Wang L, Lockstone HE, Guest PC et al. Expression profiling of fibroblasts identifies cell cycle abnormalities in Schizophrenia. J. Proteome Res. 9(1), 521-527 (2009)
-
(2009)
J. Proteome Res.
, vol.9
, Issue.1
, pp. 521-527
-
-
Wang, L.1
Lockstone, H.E.2
Guest, P.C.3
-
54
-
-
77958496632
-
Global proteomic profiling reveals altered proteomic signature in schizophrenia serum
-
Levin Y, Wang L, Schwarz E, Koethe D, Leweke FM, Bahn S. Global proteomic profiling reveals altered proteomic signature in schizophrenia serum. Mol. Psychiatry 15(11), 1088-1100 (2010)
-
(2010)
Mol. Psychiatry
, vol.15
, Issue.11
, pp. 1088-1100
-
-
Levin, Y.1
Wang, L.2
Schwarz, E.3
Koethe, D.4
Leweke, F.M.5
Bahn, S.6
-
55
-
-
79251509589
-
Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry
-
Krishnamurthy D, Levin Y, Harris LW, Umrania Y, Bahn S, Guest PC. Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry. Proteomics 11(3), 495-500 (2011)
-
(2011)
Proteomics
, vol.11
, Issue.3
, pp. 495-500
-
-
Krishnamurthy, D.1
Levin, Y.2
Harris, L.W.3
Umrania, Y.4
Bahn, S.5
Guest, P.C.6
-
56
-
-
60849086516
-
Absolute protein quantification by LC/MSE for global analysis of salicylic acid-induced plant protein secretion responses
-
Cheng F-y, Blackburn K, Lin Y-m, Goshe MB, Williamson JD. Absolute protein quantification by LC/MSE for global analysis of salicylic acid-induced plant protein secretion responses. J. Proteome Res. 8(1), 82-93 (2008)
-
(2008)
J. Proteome Res.
, vol.8
, Issue.1
, pp. 82-93
-
-
Cheng, F.-Y.1
Blackburn, K.2
Lin, Y.-M.3
Goshe, M.B.4
Williamson, J.D.5
-
57
-
-
77949599395
-
Data-independent liquid chromatography/mass spectrometry (LC/ MSE) detection and quantification of the secreted Apium graveolens pathogen defense protein mannitol dehydrogenase
-
Blackburn K, Cheng F-y, Williamson JD, Goshe MB. Data-independent liquid chromatography/mass spectrometry (LC/ MSE) detection and quantification of the secreted Apium graveolens pathogen defense protein mannitol dehydrogenase. Rapid Comm. Mass Spectro. 24(7), 1009-1016 (2010)
-
(2010)
Rapid Comm. Mass Spectro.
, vol.24
, Issue.7
, pp. 1009-1016
-
-
Blackburn, K.1
Cheng, F.-Y.2
Williamson, J.D.3
Goshe, M.B.4
-
58
-
-
84873359716
-
Prefractionation of intact proteins by reversed-phase and anion-exchange chromatography for the differential proteomic analysis of Saccharomyces cerevisiae
-
Stobaugh JT, Fague KM, Jorgenson JW. Prefractionation of intact proteins by reversed-phase and anion-exchange chromatography for the differential proteomic analysis of Saccharomyces cerevisiae. J. Proteome Res. 12(2), 626-636 (2012)
-
(2012)
J. Proteome Res.
, vol.12
, Issue.2
, pp. 626-636
-
-
Stobaugh, J.T.1
Fague, K.M.2
Jorgenson, J.W.3
-
59
-
-
84879388182
-
Application of label-free shotgun nUPLC-MSE and 2-DE approaches in the study of Botrytis cinerea Mycelium
-
Gonzalez-Fernandez R, Aloria K, Arizmendi JM, Jorrin-Novo JV. Application of label-free shotgun nUPLC-MSE and 2-DE approaches in the study of Botrytis cinerea Mycelium. J. Proteome Res. 12(6), 3042-3056 (2013)
-
(2013)
J. Proteome Res.
, vol.12
, Issue.6
, pp. 3042-3056
-
-
Gonzalez-Fernandez, R.1
Aloria, K.2
Arizmendi, J.M.3
Jorrin-Novo, J.V.4
-
60
-
-
77957990113
-
Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
-
Geiger T, Cox J, Mann M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell Proteomics 9(10), 2252-2261 (2010)
-
(2010)
Mol. Cell Proteomics
, vol.9
, Issue.10
, pp. 2252-2261
-
-
Geiger, T.1
Cox, J.2
Mann, M.3
-
61
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
Cox Jr, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: A peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10(4), 1794-1805 (2011)
-
(2011)
J. Proteome Res.
, vol.10
, Issue.4
, pp. 1794-1805
-
-
Jr. Cox1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
Olsen, J.V.5
Mann, M.6
-
62
-
-
84857811076
-
Accurate peptide fragment mass analysis: Multiplexed peptide identification and quantification
-
Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE. Accurate peptide fragment mass analysis: Multiplexed peptide identification and quantification. J. Proteome Res. 11(3), 1621-1632 (2012)
-
(2012)
J. Proteome Res.
, vol.11
, Issue.3
, pp. 1621-1632
-
-
Weisbrod, C.R.1
Eng, J.K.2
Hoopmann, M.R.3
Baker, T.4
Bruce, J.E.5
-
63
-
-
79959958529
-
Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600)
-
Andrews GL, Simons BL, Young JB, Hawkridge AM, Muddiman DC. Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 83(13), 5442-5446 (2011).
-
(2011)
Anal. Chem.
, vol.83
, Issue.13
, pp. 5442-5446
-
-
Andrews, G.L.1
Simons, B.L.2
Young, J.B.3
Hawkridge, A.M.4
Muddiman, D.C.5
-
64
-
-
84876337044
-
Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS
-
Liu Y, Hüttenhain R, Surinova S et al. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13(8), 1247-1256 (2013)
-
(2013)
Proteomics
, vol.13
, Issue.8
, pp. 1247-1256
-
-
Liu, Y.1
Hüttenhain, R.2
Surinova, S.3
-
65
-
-
84887864604
-
Label-free quantitation and mapping of the ErbB2 tumor receptor by multiple protease digestion with data-dependent (MS1) and data-independent (MS2) acquisitions
-
Article ID 791985
-
Held JM, Schilling B, D'Souza AK et al. Label-free quantitation and mapping of the ErbB2 tumor receptor by multiple protease digestion with data-dependent (MS1) and data-independent (MS2) acquisitions. Int. J. Proteomics 2013, Article ID 791985 (2013)
-
(2013)
Int. J. Proteomics 2013
-
-
Held, J.M.1
Schilling, B.2
D'souza, A.K.3
-
66
-
-
84861860481
-
Targeted data extraction of the MS/MS spectra generated by data independent acquisition: A new concept for consistent and accurate proteome analysis
-
Gillet LC, Navarro P, Tate S et al. Targeted data extraction of the MS/MS spectra generated by data independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell Proteomics 11(6), O111.016717 (2012)
-
(2012)
Mol. Cell Proteomics
, vol.11
, Issue.6
-
-
Gillet, L.C.1
Navarro, P.2
Tate, S.3
-
67
-
-
42249108173
-
OpenMS - An open-source software framework for mass spectrometry
-
Sturm M, Bertsch A, Gropl C et al. OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics 9(1), 163 (2008)
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 163
-
-
Sturm, M.1
Bertsch, A.2
Gropl, C.3
-
68
-
-
79952198684
-
OpenMS and TOPP: Open source software for LC-MS data analysis
-
Hamacher, M, Eisenacher, M, Stephan, C (Eds) Humana Press, NY, USA
-
Bertsch A, Gröpl C, Reinert K, Kohlbacher O. OpenMS and TOPP: open source software for LC-MS data analysis. In: Data Mining in Proteomics. Hamacher, M, Eisenacher, M, Stephan, C (Eds) Humana Press, NY, USA 353-367 (2011)
-
(2011)
Data Mining in Proteomics
, pp. 353-367
-
-
Bertsch, A.1
Gröpl, C.2
Reinert, K.3
Kohlbacher, O.4
-
71
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
MacLean B, Tomazela DM, Shulman N et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26(7), 966-968 (2010)
-
(2010)
Bioinformatics
, vol.26
, Issue.7
, pp. 966-968
-
-
Maclean, B.1
Tomazela, D.M.2
Shulman, N.3
-
72
-
-
84860872156
-
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
-
Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics 12(8), 1134-1141 (2012)
-
(2012)
Proteomics
, vol.12
, Issue.8
, pp. 1134-1141
-
-
Bereman, M.S.1
Maclean, B.2
Tomazela, D.M.3
Liebler, D.C.4
Maccoss, M.J.5
-
73
-
-
77954751922
-
Peptide identification from mixture tandem mass spectra
-
Wang J, Perez-Santiago J, Katz JE, Mallick P, Bandeira N. Peptide identification from mixture tandem mass spectra. Mol. Cell Proteomics 9(7), 1476-1485 (2010)
-
(2010)
Mol. Cell Proteomics
, vol.9
, Issue.7
, pp. 1476-1485
-
-
Wang, J.1
Perez-Santiago, J.2
Katz, J.E.3
Mallick, P.4
Bandeira, N.5
-
74
-
-
83055182134
-
Peptide identification by database search of mixture tandem mass spectra
-
Wang J, Bourne PE, Bandeira N. Peptide identification by database search of mixture tandem mass spectra. Mol. Cell Proteomics 10 (2011)
-
Mol. Cell Proteomics
, vol.10
, pp. 2011
-
-
Wang, J.1
Bourne, P.E.2
Bandeira, N.3
-
75
-
-
27744469683
-
ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer
-
Zhang N, Li X-j, Ye M, Pan S, Schwikowski B, Aebersold R. ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics 5(16), 4096-4106 (2005)
-
(2005)
Proteomics
, vol.5
, Issue.16
, pp. 4096-4106
-
-
Zhang, N.1
Li, X.-J.2
Ye, M.3
Pan, S.4
Schwikowski, B.5
Aebersold, R.6
-
76
-
-
84884692206
-
Aldehyde oxidase 1 in human liver cytosols: Quantitative characterization of AOX1 expression level and activity relationship
-
Fu C, Di L, Han X et al. Aldehyde oxidase 1 in human liver cytosols: Quantitative characterization of AOX1 expression level and activity relationship. Drug Metab. Dispos. (2013)
-
(2013)
Drug Metab. Dispos.
-
-
Fu, C.1
Di, L.2
Han, X.3
-
77
-
-
14744293536
-
Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
-
Venable JD, Dong M-Q, Wohlschlegel J, Dillin A, Yates JR. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Meth. 1(1), 39-45 (2004)
-
(2004)
Nat. Meth.
, vol.1
, Issue.1
, pp. 39-45
-
-
Venable, J.D.1
Dong, M.-Q.2
Wohlschlegel, J.3
Dillin, A.4
Yates, J.R.5
-
78
-
-
76149113930
-
Deconvolution of mixture spectra from ion-trap data-independent- acquisition tandem mass spectrometry
-
Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ. Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Anal. Chem. 82(3), 833-841 (2009)
-
(2009)
Anal. Chem.
, vol.82
, Issue.3
, pp. 833-841
-
-
Bern, M.1
Finney, G.2
Hoopmann, M.R.3
Merrihew, G.4
Toth, M.J.5
Maccoss, M.J.6
-
79
-
-
77951947835
-
XDIA: Improving on the label-free data- independent analysis
-
Carvalho PC, Han X, Xu T et al. XDIA: Improving on the label-free data- independent analysis. Bioinformatics 26(6), 847-848 (2010)
-
(2010)
Bioinformatics
, vol.26
, Issue.6
, pp. 847-848
-
-
Carvalho, P.C.1
Han, X.2
Xu, T.3
-
80
-
-
48249100480
-
Detection of co-eluted peptides using database search methods
-
Alves G, Ogurtsov A, Kwok S et al. Detection of co-eluted peptides using database search methods. Biol. Direct 3(1), 1-16 (2008)
-
(2008)
Biol. Direct
, vol.3
, Issue.1
, pp. 1-16
-
-
Alves, G.1
Ogurtsov, A.2
Kwok, S.3
-
81
-
-
84881477986
-
Multiplexed MS/MS for improved data-independent acquisition
-
Egertson JD, Kuehn A, Merrihew GE et al. Multiplexed MS/MS for improved data-independent acquisition. Nat. Meth. 10, 744-746 (2013)
-
(2013)
Nat. Meth.
, vol.10
, pp. 744-746
-
-
Egertson, J.D.1
Kuehn, A.2
Merrihew, G.E.3
-
82
-
-
84861833387
-
Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference Peptides
-
Sherrod SD, Myers MV, Li M et al. Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference Peptides. J. Proteome Res. 11(6), 3467-3479 (2012)
-
(2012)
J. Proteome Res.
, vol.11
, Issue.6
, pp. 3467-3479
-
-
Sherrod, S.D.1
Myers, M.V.2
Li, M.3
-
83
-
-
85033190528
-
Label-free protein quantifcation on tandem mass spectra in an ion trapping device
-
Pak H, Carla Pasquarello, Scherl A. Label-free protein quantifcation on tandem mass spectra in an ion trapping device. J. Integr. OMICS 1(2), 211-215 (2011)
-
(2011)
J. Integr. OMICS
, vol.1
, Issue.2
, pp. 211-215
-
-
Pak, H.1
Carla, P.2
Scherl, A.3
-
84
-
-
84869233177
-
Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics
-
Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell Proteomics 11(11), 1475-1488 (2012)
-
(2012)
Mol. Cell Proteomics
, vol.11
, Issue.11
, pp. 1475-1488
-
-
Peterson, A.C.1
Russell, J.D.2
Bailey, D.J.3
Westphall, M.S.4
Coon, J.J.5
-
85
-
-
84870656540
-
Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer
-
Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell Proteomics 11(12), 1709-1723 (2012)
-
(2012)
Mol. Cell Proteomics
, vol.11
, Issue.12
, pp. 1709-1723
-
-
Gallien, S.1
Duriez, E.2
Crone, C.3
Kellmann, M.4
Moehring, T.5
Domon, B.6
-
86
-
-
57049106891
-
An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures
-
Schmidt A, Gehlenborg N, Bodenmiller B et al. An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol. Cell Proteomics 7(11), 2138-2150 (2008)
-
(2008)
Mol. Cell Proteomics
, vol.7
, Issue.11
, pp. 2138-2150
-
-
Schmidt, A.1
Gehlenborg, N.2
Bodenmiller, B.3
-
87
-
-
84877813399
-
Selectivity of LC-MS/MS analysis: Implication for proteomics experiments
-
Gallien S, Duriez E, Demeure K, Domon B. Selectivity of LC-MS/MS analysis: Implication for proteomics experiments. J. Proteomics 81, 148-158 (2012)
-
(2012)
J. Proteomics
, vol.81
, pp. 148-158
-
-
Gallien, S.1
Duriez, E.2
Demeure, K.3
Domon, B.4
-
88
-
-
67650361220
-
Multiple products monitoring as a robust approach for peptide quantification
-
Baek J-H, Kim H, Shin B, Yu M-H. Multiple products monitoring as a robust approach for peptide quantification. J. Proteome Res. 8(7), 3625-3632 (2009)
-
(2009)
J. Proteome Res.
, vol.8
, Issue.7
, pp. 3625-3632
-
-
Baek, J.-H.1
Kim, H.2
Shin, B.3
Yu, M.-H.4
-
89
-
-
84877803202
-
Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring
-
Hewel JA, Phanse S, Liu J, Bousette N, Gramolini A, Emili A. Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring. J. Proteomics 81(0), 159-172 (2013)
-
(2013)
J. Proteomics
, vol.81
, Issue.0
, pp. 159-172
-
-
Hewel, J.A.1
Phanse, S.2
Liu, J.3
Bousette, N.4
Gramolini, A.5
Emili, A.6
-
90
-
-
84879602122
-
The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification
-
Tsuchiya H, Tanaka K, Saeki Y. The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification. Biochem. Biophys. Res. Commun. 436(2), 223-229 (2013)
-
(2013)
Biochem. Biophys. Res. Commun.
, vol.436
, Issue.2
, pp. 223-229
-
-
Tsuchiya, H.1
Tanaka, K.2
Saeki, Y.3
-
91
-
-
8444223860
-
High-field asymmetric waveform ion mobility spectrometry: A new tool for mass spectrometry
-
Guevremont R. High-field asymmetric waveform ion mobility spectrometry: A new tool for mass spectrometry. J. Chromatogr. A 1058(1-2), 3-19 (2004)
-
(2004)
J. Chromatogr. A
, vol.1058
, Issue.1-2
, pp. 3-19
-
-
Guevremont, R.1
|