-
2
-
-
0036589851
-
Integrating top-down and bottom-up mass spectrometric approaches for proteomic analysis of Shewanella oneidensis
-
DOI 10.1021/pr025508a
-
NC Verberkmoes JL Bundy JL Hause KG Asano J Razumovskaya F Larimer RL Hettich JL Stephenson 2002 Integrating top-down and bottom-up mass spectrometric approaches for proteomic analysis of Shewanella onneidensis J Proteome Res. 1 239 252 12645901 10.1021/pr025508a 1:CAS:528:DC%2BD38XjtFahtbo%3D (Pubitemid 36050254)
-
(2002)
Journal of Proteome Research
, vol.1
, Issue.3
, pp. 239-252
-
-
VerBerkmoes, N.C.1
Bundy, J.L.2
Hauser, L.3
Asano, K.G.4
Razumovskaya, J.5
Larimer, F.6
Hettich, R.L.7
Stephenson Jr., J.L.8
-
3
-
-
0036399228
-
Shotgun proteomics and biomarker discovery
-
12364816 1:CAS:528:DC%2BD38Xns1Cltbc%3D
-
WH McDonald JR Yates 2002 Shotgun proteomics and biomarker discovery Dis Markers. 18 99 105 12364816 1:CAS:528:DC%2BD38Xns1Cltbc%3D
-
(2002)
Dis Markers.
, vol.18
, pp. 99-105
-
-
McDonald, W.H.1
Yates, J.R.2
-
4
-
-
27644555055
-
Interpretation of shotgun proteomic data: The protein inference problem
-
DOI 10.1074/mcp.R500012-MCP200
-
AI Vesvizhskii A Aebersold 2005 Interpretation of shotgun proteomic data: the protein interference problem Mol Cell Proteomics. 4 1419 1440 10.1074/mcp.R500012-MCP200 (Pubitemid 41555469)
-
(2005)
Molecular and Cellular Proteomics
, vol.4
, Issue.10
, pp. 1419-1440
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
5
-
-
0141989734
-
PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry
-
14558135 10.1002/rcm.1196 1:CAS:528:DC%2BD3sXotlGnurs%3D
-
B Ma K Zhang C Hendrie C Liang M Li A Doherty-Kirby G Lajoie 2003 PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry Rapid Commun Mass Spectrom. 17 2337 2342 14558135 10.1002/rcm.1196 1:CAS:528:DC%2BD3sXotlGnurs%3D
-
(2003)
Rapid Commun Mass Spectrom.
, vol.17
, pp. 2337-2342
-
-
Ma, B.1
Zhang, K.2
Hendrie, C.3
Liang, C.4
Li, M.5
Doherty-Kirby, A.6
Lajoie, G.7
-
6
-
-
0000857494
-
An approach to correlate tandem mass spectral database of peptides with amino acid sequences in a protein database
-
10.1016/1044-0305(94)80016-2 1:CAS:528:DyaK2MXhvF2htLw%3D
-
JK Eng AL McCormack JR Yates III 1994 An approach to correlate tandem mass spectral database of peptides with amino acid sequences in a protein database J Am Soc Mass Spectrom. 5 976 989 10.1016/1044-0305(94)80016-2 1:CAS:528:DyaK2MXhvF2htLw%3D
-
(1994)
J Am Soc Mass Spectrom.
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates Iii, J.R.3
-
7
-
-
46249114017
-
Rapid and accurate peptide identifications from tandem mass spectra
-
18505281 10.1021/pr800127y 1:CAS:528:DC%2BD1cXmtlCqtbo%3D
-
CY Park AA Klammer L Käll MJ MacCoss WS Noble 2008 Rapid and accurate peptide identifications from tandem mass spectra J Proteome Res. 7 3022 2027 18505281 10.1021/pr800127y 1:CAS:528:DC%2BD1cXmtlCqtbo%3D
-
(2008)
J Proteome Res.
, vol.7
, pp. 3022-2027
-
-
Park, C.Y.1
Klammer, A.A.2
Käll, L.3
MacCoss, M.J.4
Noble, W.S.5
-
8
-
-
55949085148
-
A fast SEQUEST cross correlation algorithm
-
18774840 10.1021/pr800420s 1:CAS:528:DC%2BD1cXhtVymtL7M
-
JK Eng B Fischer J Grossmann MJ MacCoss 2008 A fast SEQUEST cross correlation algorithm J Proteome Res 7 4598 4602 18774840 10.1021/pr800420s 1:CAS:528:DC%2BD1cXhtVymtL7M
-
(2008)
J Proteome Res
, vol.7
, pp. 4598-4602
-
-
Eng, J.K.1
Fischer, B.2
Grossmann, J.3
MacCoss, M.J.4
-
9
-
-
0033434080
-
Probability-based on protein identification by searching database using mass spectrometry data
-
10612281 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID- ELPS3551>3.0.CO;2-2 1:CAS:528:DC%2BD3cXhtF2ntw%3D%3D
-
DN Perkins JC Pappin DM Creasy JS Cottrell 1999 Probability-based on protein identification by searching database using mass spectrometry data Electrophoresis 20 3551 3567 10612281 10.1002/(SICI)1522-2683(19991201)20: 18<3551::AID-ELPS3551>3.0.CO;2-2 1:CAS:528:DC%2BD3cXhtF2ntw%3D%3D
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, J.C.2
Creasy, D.M.3
Cottrell, J.S.4
-
10
-
-
23144462378
-
DeNovoID: A web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
-
DOI 10.1093/nar/gki461
-
BD Halligan V Ruotti SN Twigger AS Greene 2005 DeNovoID: A web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectrometry Nucleic Acids Res 33 376 381 10.1093/nar/gki461 (Pubitemid 44529947)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Halligan, B.D.1
Ruotti, V.2
Twigger, S.N.3
Greene, A.S.4
-
11
-
-
23944455372
-
Peptide sequence tags for fast database search in mass-spectrometry
-
DOI 10.1021/pr050011x
-
A Frank S Tanner V Bafna PA Pevzner 2005 Peptide sequence tags for fast database search in mass spectrometry J Proteome Res 4 1287 1295 16083278 10.1021/pr050011x 1:CAS:528:DC%2BD2MXltVyltrY%3D (Pubitemid 41208683)
-
(2005)
Journal of Proteome Research
, vol.4
, Issue.4
, pp. 1287-1295
-
-
Frank, A.1
Tanner, S.2
Bafna, V.3
Pevzner, P.4
-
12
-
-
3242660851
-
Prediction of low-energy collision-induced dissociation spectra of peptides
-
DOI 10.1021/ac049951b
-
Z Zhang 2004 Prediction of low-energy collision induced dissociation spectra of peptides Anal Chem 76 3908 3922 15253624 10.1021/ac049951b 1:CAS:528:DC%2BD2cXktlWmtLs%3D (Pubitemid 38943659)
-
(2004)
Analytical Chemistry
, vol.76
, Issue.14
, pp. 3908-3922
-
-
Zhang, Z.1
-
13
-
-
0037953090
-
Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
-
DOI 10.1021/ac026424o
-
DL Tabb MJ MacCoss CC Wu SD Anderson JR Yates 2003 Similarity among tandem mass spectra from proteomic experiments: detection, significance and utility Anal Chem. 75 2470 2477 12918992 10.1021/ac026424o 1:CAS:528: DC%2BD3sXivVaqu7c%3D (Pubitemid 36582834)
-
(2003)
Analytical Chemistry
, vol.75
, Issue.10
, pp. 2470-2477
-
-
Tabb, D.L.1
MacCoss, M.J.2
Wu, C.C.3
Anderson, S.D.4
Yates III, J.R.5
-
15
-
-
1842580753
-
Improving large-scale proteomics by clustering of mass spectrometry data
-
DOI 10.1002/pmic.200300652
-
I Beer E Barnea T Ziv A Admon 2004 Improving large-scale proteomics by clustering of mass spectrometry data Proteomics 4 950 960 15048977 10.1002/pmic.200300652 1:CAS:528:DC%2BD2cXjt1Smt78%3D (Pubitemid 38445955)
-
(2004)
Proteomics
, vol.4
, Issue.4
, pp. 950-960
-
-
Beer, I.1
Barnea, E.2
Ziv, T.3
Admon, A.4
-
17
-
-
33747170146
-
Using annotated peptide mass spectrum libraries for protein identification
-
DOI 10.1021/pr0602085
-
R Craig JC Corteins RC Beavis 2006 Using annotated peptide mass spectrum libraries for peptide identification J Proteome Res 5 1843 1849 16889405 10.1021/pr0602085 1:CAS:528:DC%2BD28XmvVeitrs%3D (Pubitemid 44232697)
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.8
, pp. 1843-1849
-
-
Craig, R.1
Cortens, J.C.2
Fenyo, D.3
Beavis, R.C.4
-
18
-
-
33747626954
-
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
-
DOI 10.1021/ac060279n
-
BE Frewen GE Merrihew CC Wu WS Noble MJ MacCoss 2006 Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries Anal Chem 78 5678 5684 16906711 10.1021/ac060279n 1:CAS:528:DC%2BD28XmvVGhsLk%3D (Pubitemid 44265027)
-
(2006)
Analytical Chemistry
, vol.78
, Issue.16
, pp. 5678-5684
-
-
Frewen, B.E.1
Merrihew, G.E.2
Wu, C.C.3
Noble, W.S.4
MacCoss, M.J.5
-
19
-
-
33646903914
-
ModifiComb, a new proteomic tool for mapping substoichiometric post translational modifications, finding novel types of modifications, and fingerprint complex protein mixtures
-
MM Savitski M Nielse RA Zubarev 2006 ModifiComb, a new proteomic tool for mapping substoichiometric post translational modifications, finding novel types of modifications, and fingerprint complex protein mixtures Mol Cell Proteomics 5 934 948
-
(2006)
Mol Cell Proteomics
, vol.5
, pp. 934-948
-
-
Savitski, M.M.1
Nielse, M.2
Zubarev, R.A.3
-
21
-
-
33645715370
-
Sakuma T, McDermott JC. Multiple reaction monitoring as a method for identifying protein posttranslational modifications
-
16030315
-
DM Cox F Zhong M Du E Duchoslav 2005 Sakuma T, McDermott JC. Multiple reaction monitoring as a method for identifying protein posttranslational modifications J Biomol Tech. 16 83 90 16030315
-
(2005)
J Biomol Tech.
, vol.16
, pp. 83-90
-
-
Cox, D.M.1
Zhong, F.2
Du, M.3
Duchoslav, E.4
-
22
-
-
70349576516
-
High-resolution biomarker discovery: Targeted tandem mass spectrometry methods for quantitative validation of transcription factor candidates
-
Denver, CO
-
Hewel JA, Liu J, Onishi K, Fong V, Sandhu C, Talukder S, et al. High-resolution biomarker discovery: Targeted tandem mass spectrometry methods for quantitative validation of transcription factor candidates. Proceedings of the 56th ASMS Conference, Denver, CO, 2008.
-
(2008)
Proceedings of the 56th ASMS Conference
-
-
Hewel, J.A.1
Liu, J.2
Onishi, K.3
Fong, V.4
Sandhu, C.5
Talukder, S.6
-
23
-
-
70349568667
-
Targeted proteomics of transcription factors in breast cancer and embryonic stem cells
-
7th World Congress, Amsterdam, Netherlands
-
Hewel JA, Liu J, Onish K, Fong V, Yue M, Sandhu C, et al. Targeted proteomics of transcription factors in breast cancer and embryonic stem cells. Proceedings of the HUPO 2008, 7th World Congress, Amsterdam, Netherlands, 2008.
-
(2008)
Proceedings of the HUPO 2008
-
-
Hewel, J.A.1
Liu, J.2
Onish, K.3
Fong, V.4
Yue, M.5
Sandhu, C.6
-
25
-
-
43049090085
-
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring
-
18408245 10.1074/mcp.M800032-MCP200 1:CAS:528:DC%2BD1cXhtVSrs7vO
-
V Lange JA Malmstrom J Didion NL King BP Johansson J Schafer J Rameseder C-H Wong EW Deutsch M-Y Brusniak P Buhlmann L Bjorck B Domon R Aebersold 2008 Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring Mol Cell Proteomics. 7 1489 1500 18408245 10.1074/mcp.M800032-MCP200 1:CAS:528:DC%2BD1cXhtVSrs7vO
-
(2008)
Mol Cell Proteomics.
, vol.7
, pp. 1489-1500
-
-
Lange, V.1
Malmstrom, J.A.2
Didion, J.3
King, N.L.4
Johansson, B.P.5
Schafer, J.6
Rameseder, J.7
Wong, C.-H.8
Deutsch, E.W.9
Brusniak, M.-Y.10
Buhlmann, P.11
Bjorck, L.12
Domon, B.13
Aebersold, R.14
-
26
-
-
51649096674
-
Validation of endogenous peptide identifications using a database of tandem mass spectra
-
18549260 10.1021/pr800036d
-
M Fälth M Svensson A Nilsson K Sköld D Fenyö PE Andren 2008 Validation of endogenous peptide identifications using a database of tandem mass spectra J Proteome Res 7 3049 3053 18549260 10.1021/pr800036d
-
(2008)
J Proteome Res
, vol.7
, pp. 3049-3053
-
-
Fälth, M.1
Svensson, M.2
Nilsson, A.3
Sköld, K.4
Fenyö, D.5
Andren, P.E.6
-
27
-
-
0141955057
-
A method for reducing the time required to match protein sequences with tandem mass spectra
-
14558131 10.1002/rcm.1198 1:CAS:528:DC%2BD3sXotlGnur8%3D
-
R Craig RC Beavis 2003 A method for reducing the time required to match protein sequences with tandem mass spectra Rapid Commun Mass Spectrom. 17 2310 2316 14558131 10.1002/rcm.1198 1:CAS:528:DC%2BD3sXotlGnur8%3D
-
(2003)
Rapid Commun Mass Spectrom.
, vol.17
, pp. 2310-2316
-
-
Craig, R.1
Beavis, R.C.2
-
28
-
-
51649094314
-
Monte Carlo simulation-based algorithms for analysis of shotgun proteomic data
-
10.1021/pr800002u
-
H Xu MA Freitas 2007 Monte Carlo simulation-based algorithms for analysis of shotgun proteomic data J Proteome Res 7 2605 2615 10.1021/pr800002u
-
(2007)
J Proteome Res
, vol.7
, pp. 2605-2615
-
-
Xu, H.1
Freitas, M.A.2
-
30
-
-
30744444934
-
PepHMM: A hidden Markov model based scoring function for mass spectrometry database search
-
DOI 10.1021/ac051319a
-
Y Wan A Yang T Chen 2006 PepHMM: a hidden Markov model based scoring function for mass spectrometry database search Anal Chem 78 432 437 16408924 10.1021/ac051319a 1:CAS:528:DC%2BD2MXht12rtb7E (Pubitemid 43100374)
-
(2006)
Analytical Chemistry
, vol.78
, Issue.2
, pp. 432-437
-
-
Wan, Y.1
Yang, A.2
Chen, T.3
-
31
-
-
42649095977
-
PeakSelect: Preprocessing tandem mass spectra for better peptide identification
-
DOI 10.1002/rcm.3488
-
J Zhang S He CX Ling X Cao R Zeng W Gao 2008 PeakSelect: preprocessing tandem mass spectra for better peptide identification Rapid Commun Mass Spectrom 22 1203 1212 18350561 10.1002/rcm.3488 1:CAS:528:DC%2BD1cXltlCjt7g%3D (Pubitemid 351600770)
-
(2008)
Rapid Communications in Mass Spectrometry
, vol.22
, Issue.8
, pp. 1203-1212
-
-
Zhang, J.1
He, S.2
Ling, C.X.3
Cao, X.4
Zeng, R.5
Gao, W.6
-
32
-
-
45549108483
-
Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer
-
18311902 10.1021/pr700836q 1:CAS:528:DC%2BD1cXisVylsb0%3D
-
C Sandhu JA Hewel G Badis S Talukder J Liu TR Hughes A Emili 2008 Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer J Proteome Res 7 1529 1541 18311902 10.1021/pr700836q 1:CAS:528:DC%2BD1cXisVylsb0%3D
-
(2008)
J Proteome Res
, vol.7
, pp. 1529-1541
-
-
Sandhu, C.1
Hewel, J.A.2
Badis, G.3
Talukder, S.4
Liu, J.5
Hughes, T.R.6
Emili, A.7
-
33
-
-
33845436279
-
Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome usina artificial neural networks
-
DOI 10.1021/pr0602038
-
K Shinoda M Sugimoto N Yachie N Sugiyama T Masuda M Robert T Soga M Tomita 2006 Prediction of liquid chromatographic retention time of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks J Proteome Res 5 3312 3317 17137332 10.1021/pr0602038 1:CAS:528:DC%2BD28XhtFCqt7jN (Pubitemid 44904322)
-
(2006)
Journal of Proteome Research
, vol.5
, Issue.12
, pp. 3312-3317
-
-
Shinoda, K.1
Sugimoto, M.2
Yachie, N.3
Sugiyama, N.4
Masuda, T.5
Robert, M.6
Soga, T.7
Tomita, M.8
-
34
-
-
34548041670
-
Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions
-
DOI 10.1021/ac070262k
-
AA Klammer X Yi MJ MacCoss WS Noble 2007 Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions Anal Chem. 79 6111 6118 17622186 10.1021/ac070262k 1:CAS:528:DC%2BD2sXnsVyms7k%3D (Pubitemid 47282320)
-
(2007)
Analytical Chemistry
, vol.79
, Issue.16
, pp. 6111-6118
-
-
Klammer, A.A.1
Yi, X.2
MacCoss, M.J.3
Noble, W.S.4
-
35
-
-
33748515682
-
Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS
-
DOI 10.1021/ac060251b
-
OV Krokhin S Ying JP Cortens D Ghosh V Spicer W Ens KG Standing RC Beavis JA Wilkins 2006 Use of peptide retention time prediction for protein identification by off-line reversed phase HPLC-MALDI MS/MS Anal Chem 78 6265 6259 16944911 10.1021/ac060251b 1:CAS:528:DC%2BD28Xnt12nt7w%3D (Pubitemid 44360142)
-
(2006)
Analytical Chemistry
, vol.78
, Issue.17
, pp. 6265-6269
-
-
Krokhin, O.V.1
Ying, S.2
Cortens, J.P.3
Ghosh, D.4
Spicer, V.5
Ens, W.6
Standing, K.G.7
Beavis, R.C.8
Wilkins, J.A.9
-
36
-
-
60149086356
-
Improving peptide identification using an empirical peptide retention time database
-
19065623 10.1002/rcm.3851 1:CAS:528:DC%2BD1MXptVyksA%3D%3D
-
W Sun L Zhang R Yang C Shao Z Zhang Y Gao 2009 Improving peptide identification using an empirical peptide retention time database Rapid Commun Mass Spectrom. 23 109 118 19065623 10.1002/rcm.3851 1:CAS:528: DC%2BD1MXptVyksA%3D%3D
-
(2009)
Rapid Commun Mass Spectrom.
, vol.23
, pp. 109-118
-
-
Sun, W.1
Zhang, L.2
Yang, R.3
Shao, C.4
Zhang, Z.5
Gao, Y.6
|