-
1
-
-
84860464109
-
Mass spectrometry-based proteomics: Existing capabilities and future directions
-
Angel, T.E., Aryal, U.K., Hengel, S.M., Baker, E.S., Kelly, R.T., Robinson, E.W., Smith, R.D.: Mass spectrometry-based proteomics: existing capabilities and future directions. Chem. Soc. Rev. 41, 3912-3928 (2012)
-
(2012)
Chem. Soc. Rev.
, vol.41
, pp. 3912-3928
-
-
Angel, T.E.1
Aryal, U.K.2
Hengel, S.M.3
Baker, E.S.4
Kelly, R.T.5
Robinson, E.W.6
Smith, R.D.7
-
2
-
-
84866150007
-
Mass spectrometry based proteomics, background, status, and future needs
-
Roepstorff, P.: Mass spectrometry based proteomics, background, status, and future needs. Protein Cell 3, 641-647 (2012)
-
(2012)
Protein Cell
, vol.3
, pp. 641-647
-
-
Roepstorff, P.1
-
3
-
-
84864805910
-
Mass spectrometry-based proteomics for systems biology
-
Sabido, E., Selevsek, N., Aebersold, R.: Mass spectrometry-based proteomics for systems biology. Curr. Opin. Biotechnol. 23, 591-597 (2012)
-
(2012)
Curr. Opin. Biotechnol.
, vol.23
, pp. 591-597
-
-
Sabido, E.1
Selevsek, N.2
Aebersold, R.3
-
4
-
-
84878646340
-
Status of mass spectrometry-based proteomics and metabolomics in basic and translational research
-
Kelleher, N.L.: Status of mass spectrometry-based proteomics and metabolomics in basic and translational research. Biochemistry 52, 3794-3796 (2013)
-
(2013)
Biochemistry
, vol.52
, pp. 3794-3796
-
-
Kelleher, N.L.1
-
5
-
-
84876148755
-
Protein analysis by shotgun/bottom-up proteomics
-
Zahang, Y., Fonslow, B.R., Shan, B., Baek, M.-C., Yates, J.R.: Protein analysis by shotgun/bottom-up proteomics. Chem. Rev. 113, 2343-2394 (2013)
-
(2013)
Chem. Rev.
, vol.113
, pp. 2343-2394
-
-
Zahang, Y.1
Fonslow, B.R.2
Shan, B.3
Baek, M.-C.4
Yates, J.R.5
-
6
-
-
21844457685
-
Fragmentation pathways of protonated peptides
-
Paizs, B., Suhai, S.: Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 24, 508-548 (2004)
-
(2004)
Mass Spectrom. Rev.
, vol.24
, pp. 508-548
-
-
Paizs, B.1
Suhai, S.2
-
7
-
-
0242653718
-
Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation
-
Kapp, E.A., Schutz, F., Reid, G.E., Eddes, J.S., Moritz, R.L., O'Hair, R.A.J., Speed, T.P., Simpson, R.J.: Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 75, 6251-6264 (2003)
-
(2003)
Anal. Chem.
, vol.75
, pp. 6251-6264
-
-
Kapp, E.A.1
Schutz, F.2
Reid, G.E.3
Eddes, J.S.4
Moritz, R.L.5
O'Hair, R.A.J.6
Speed, T.P.7
Simpson, R.J.8
-
8
-
-
0030000913
-
Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions
-
Cox, K.A., Gaskell, S.J., Morris, M., Whiting, A.: Role of the site of protonation in the low-energy decompositions of gas-phase peptide ions. J. Am. Soc. Mass Spectrom. 7, 522-531 (1996)
-
(1996)
J. Am. Soc. Mass Spectrom.
, vol.7
, pp. 522-531
-
-
Cox, K.A.1
Gaskell, S.J.2
Morris, M.3
Whiting, A.4
-
9
-
-
0029810698
-
Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: Evidence for the mobile proton model
-
Dongre, A.R., Jones, J.L., Somagyi, A., Wysocki, V.H.: Influence of peptide composition, gas-phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model. J. Am. Chem. Soc. 118, 8365-8374 (1996)
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 8365-8374
-
-
Dongre, A.R.1
Jones, J.L.2
Somagyi, A.3
Wysocki, V.H.4
-
10
-
-
0034501099
-
Mobile and localized protons: A framework for understanding peptide dissociation
-
Wysocki, V.H., Tsaprailis, G., Smith, L.L., Breci, L.A.: Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 35, 1399-1406 (2000)
-
(2000)
J. Mass Spectrom.
, vol.35
, pp. 1399-1406
-
-
Wysocki, V.H.1
Tsaprailis, G.2
Smith, L.L.3
Breci, L.A.4
-
11
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.K., McCarmack, A.L., Yates III, J.R.: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994)
-
(1994)
J. Am. Soc. Mass Spectrom.
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCarmack, A.L.2
Yates, J.R.3
-
12
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins, D.N., Pappin, D.J.C., Creasy, D.M., Cottrell, J.S.: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999)
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.C.2
Creasy, D.M.3
Cottrell, J.S.4
-
13
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig, R., Beavis, R.C.: TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467 (2004)
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
14
-
-
0742305695
-
Intensity-based protein identification by machine learning from a library of tandem mass spectra
-
Elias, J.E., Gibbons, F.D., King, O.D., Roth, F.P., Gygi, S.P.: Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22, 214-219 (2004)
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 214-219
-
-
Elias, J.E.1
Gibbons, F.D.2
King, O.D.3
Roth, F.P.4
Gygi, S.P.5
-
15
-
-
79953676624
-
SQID: An intensity-incorporated protein identification algorithm for tandem mass spectrometr
-
Li, W., Ji, L., Goya, J., Tan, G., Wysocki, V.H.: SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometr. J. Proteome Res. 10, 1593-1602 (2011)
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1593-1602
-
-
Li, W.1
Ji, L.2
Goya, J.3
Tan, G.4
Wysocki, V.H.5
-
16
-
-
0026816653
-
Some proline substituent effects in the tandem mass spectrum of protonated pentaalanine
-
Schwartz, B.L., Bursey, M.M.: Some proline substituent effects in the tandem mass spectrum of protonated pentaalanine. Biol. Mass Spectrom. 21, 92-96 (1992)
-
(1992)
Biol. Mass Spectrom.
, vol.21
, pp. 92-96
-
-
Schwartz, B.L.1
Bursey, M.M.2
-
17
-
-
0027461675
-
Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization
-
Loo, J.A., Edmonds, C.A., Smith, R.D.: Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization. Anal. Chem. 65, 425-438 (1993)
-
(1993)
Anal. Chem.
, vol.65
, pp. 425-438
-
-
Loo, J.A.1
Edmonds, C.A.2
Smith, R.D.3
-
18
-
-
0027692925
-
Identification of the facile gas-phase cleavage of the Asp-Pro and Asp-Xxx peptide bonds in matrix-assisted laser desorption time of flight mass spectrometry
-
Yu, W., Vath, J.E., Huberty, M.C., Martin, S.A.: Identification of the facile gas-phase cleavage of the Asp-Pro and Asp-Xxx peptide bonds in matrix-assisted laser desorption time of flight mass spectrometry. Anal. Chem. 65, 3015-3023 (1993)
-
(1993)
Anal. Chem.
, vol.65
, pp. 3015-3023
-
-
Yu, W.1
Vath, J.E.2
Huberty, M.C.3
Martin, S.A.4
-
19
-
-
0029823591
-
Probing the proline effect in CID of protonated peptides
-
Vaisar, T., Urban, J.: Probing the proline effect in CID of protonated peptides. J. Mass Spectrom. 31, 1185-1187 (1996)
-
(1996)
J. Mass Spectrom.
, vol.31
, pp. 1185-1187
-
-
Vaisar, T.1
Urban, J.2
-
20
-
-
0034162454
-
Ion trap activation of the (M + 2H)2+ and (M + 17H)17+ ions of human hemoglobin b-chain
-
Schaaff, T.G., Cargile, B.J., Stephanson Jr., J.L., McLuckey, S.A.: Ion trap activation of the (M + 2H)2+ and (M + 17H)17+ ions of human hemoglobin b-chain. Anal. Chem. 72, 899-907 (2000)
-
(2000)
Anal. Chem.
, vol.72
, pp. 899-907
-
-
Schaaff, T.G.1
Cargile, B.J.2
Stephanson, Jr.J.L.3
McLuckey, S.A.4
-
21
-
-
0034695361
-
Refining the model for selective cleavage at acid residues in arginine-containing protonated peptides
-
Tsaprailis, G., Somogyi, A., Nikolaev, E.N., Wysocki, V.H.: Refining the model for selective cleavage at acid residues in arginine-containing protonated peptides. Int. J. Mass Spectrom. 195/196, 467-479 (2000)
-
(2000)
Int. J. Mass Spectrom.
, vol.195-196
, pp. 467-479
-
-
Tsaprailis, G.1
Somogyi, A.2
Nikolaev, E.N.3
Wysocki, V.H.4
-
22
-
-
0035860202
-
The exploitation of selective cleavage of singly protonated peptide ions adjacent to aspartic acid residues using a quadrupole orthogonal time-of-flight mass spectrometer equipped with a matrix-assisted laser desorption/ionization source
-
Sullivan, A.G., Brancia, F.L., Tyldesley, R., Bateman, R., Sidhu, K., Hubbard, S.J., Oliver, S.G., Gaskell, S.J.: The exploitation of selective cleavage of singly protonated peptide ions adjacent to aspartic acid residues using a quadrupole orthogonal time-of-flight mass spectrometer equipped with a matrix-assisted laser desorption/ionization source. Int. J. Mass Spectrom. 210/211, 665-676 (2001)
-
(2001)
Int. J. Mass Spectrom.
, vol.210-211
, pp. 665-676
-
-
Sullivan, A.G.1
Brancia, F.L.2
Tyldesley, R.3
Bateman, R.4
Sidhu, K.5
Hubbard, S.J.6
Oliver, S.G.7
Gaskell, S.J.8
-
23
-
-
0036684103
-
The influence of histidine on cleavage c-terminal to acidic residues in doubly protonated tryptic peptides
-
Huang, Y., Wysocki, V.H., Tabb, D.L., Yates, J.R.I.: The influence of histidine on cleavage c-terminal to acidic residues in doubly protonated tryptic peptides. Int. J. Mass Spectrom. 291, 233-244 (2002)
-
(2002)
Int. J. Mass Spectrom.
, vol.291
, pp. 233-244
-
-
Huang, Y.1
Wysocki, V.H.2
Tabb, D.L.3
Yates, J.R.I.4
-
24
-
-
0038034116
-
Cleavage N-terminal to proline: Analsis of a database of peptide tandem mass spectra
-
Breci, L.A., Tabb, D.L., Yates, J.R.I., Wysocki, V.H.: Cleavage N-terminal to proline: analsis of a database of peptide tandem mass spectra. Anal. Chem. 75, 1963-1971 (2003)
-
(2003)
Anal. Chem.
, vol.75
, pp. 1963-1971
-
-
Breci, L.A.1
Tabb, D.L.2
Yates, J.R.I.3
Wysocki, V.H.4
-
25
-
-
2342517539
-
Fragmentation of protonated tripeptides: The proline effect revisited
-
Grewal, R.N., El Aribi, E.H., Harrison, A.G., Siu, K.W.M., Hopkinson, A.C.: Fragmentation of protonated tripeptides: the proline effect revisited. J. Phys. Chem. B 108, 4899-4908 (2004)
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 4899-4908
-
-
Grewal, R.N.1
El Aribi, E.H.2
Harrison, A.G.3
Siu, K.W.M.4
Hopkinson, A.C.5
-
26
-
-
20444459841
-
Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns
-
Huang, Y., Triscari, J.M., Tseng, G.C., Pasa-Tolic, L., Lipton, M.S., Smith, R.D., Wysocki, V.H.: Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem. 77, 5800-5813 (2005)
-
(2005)
Anal. Chem.
, vol.77
, pp. 5800-5813
-
-
Huang, Y.1
Triscari, J.M.2
Tseng, G.C.3
Pasa-Tolic, L.4
Lipton, M.S.5
Smith, R.D.6
Wysocki, V.H.7
-
27
-
-
25144454028
-
Fragmentation reactions of deprotonated peptides containing proline. The proline effect
-
Harrison, A.G., Young, A.B.: Fragmentation reactions of deprotonated peptides containing proline. The proline effect. J. Mass Spectrom. 40, 1173-1186 (2005)
-
(2005)
J. Mass Spectrom.
, vol.40
, pp. 1173-1186
-
-
Harrison, A.G.1
Young, A.B.2
-
28
-
-
36348942817
-
MS/MS of protonated polyproline peptides; The influence of N-terminal protonation on dissociation
-
Unnithan, A.G., Myer, M.J., Veale, C.J., Dannell, A.S.: MS/MS of protonated polyproline peptides; the influence of N-terminal protonation on dissociation. J. Am. Soc. Mass Spectrom. 18, 2198-2205 (2007)
-
(2007)
J. Am. Soc. Mass Spectrom.
, vol.18
, pp. 2198-2205
-
-
Unnithan, A.G.1
Myer, M.J.2
Vealec, J.3
Dannell, A.S.4
-
29
-
-
38649129381
-
A data mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns
-
Huang, Y., Tseng, G.C., Yuan, S., Pasa-Tolic, L., Lipton, M.S., Smith, R.D., Wysocki, V.H.: A data mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns. J. Proteome Res. 7, 70-79 (2008)
-
(2008)
J. Proteome Res.
, vol.7
, pp. 70-79
-
-
Huang, Y.1
Tseng, G.C.2
Yuan, S.3
Pasa-Tolic, L.4
Lipton, M.S.5
Smith, R.D.6
Wysocki, V.H.7
-
30
-
-
79955869424
-
Towards understanding the tandem mass spectra of protonated oligopeptides. 2. The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp)
-
Bleiholder, C., Suhai, S., Harrison, A.G., Paizs, B.: Towards understanding the tandem mass spectra of protonated oligopeptides. 2. The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). J. Am. Soc. Mass Spectrom. 21, 1032-1039 (2011)
-
(2011)
J. Am. Soc. Mass Spectrom.
, vol.21
, pp. 1032-1039
-
-
Bleiholder, C.1
Suhai, S.2
Harrison, A.G.3
Paizs, B.4
-
31
-
-
79952762453
-
The role of proton bridges in selective cleavage of Ser-, Thr-, Cys-, Met-, Asp-, and Asn-containing peptides
-
Zhang, Q., Perkins, B., Tan, G., Wysocki, V.H.: The role of proton bridges in selective cleavage of Ser-, Thr-, Cys-, Met-, Asp-, and Asn-containing peptides. Int. J. Mass Spectrom. 300, 108-117 (2011)
-
(2011)
Int. J. Mass Spectrom.
, vol.300
, pp. 108-117
-
-
Zhang, Q.1
Perkins, B.2
Tan, G.3
Wysocki, V.H.4
-
32
-
-
84879906810
-
The ornithine effect in peptide cation dissociation
-
McGee, W.M., McLuckey, S.A.: The ornithine effect in peptide cation dissociation. J. Mass Spectrom. 48, 856-861 (2013)
-
(2013)
J. Mass Spectrom.
, vol.48
, pp. 856-861
-
-
McGee, W.M.1
McLuckey, S.A.2
-
33
-
-
84987419408
-
Proposal for a common nomenclature for sequence ions in mass spectra of peptides
-
1:CAS:528:DyaL2MXlvVOgtg%3D%3D
-
Roepstorff, P.: Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11, 601 (1984)
-
(1984)
Biomed. Mass Spectrom.
, vol.11
, pp. 601
-
-
Roepstorff, P.1
-
34
-
-
84873884847
-
Influence of N-terminal residue composition on the structure of proline-containing b2 + ions
-
Gucinski, A.C., Chamot-Rooke, J., Steinmetz, V., Somogyi, A., Wysocki, V.H.: Influence of N-terminal residue composition on the structure of proline-containing b2 + ions. J Phys. Chem. A 117, 1291-1298 (2013)
-
(2013)
J Phys. Chem. A
, vol.117
, pp. 1291-1298
-
-
Gucinski, A.C.1
Chamot-Rooke, J.2
Steinmetz, V.3
Somogyi, A.4
Wysocki, V.H.5
-
35
-
-
0036107048
-
Proton affinities of proline analogs using the kinetic method with full entropy analysis
-
Kuntz, A.F., Boynton, A.W., David, G.A., Colyer, K.E., Poutsma, J.C.: Proton affinities of proline analogs using the kinetic method with full entropy analysis. J. Am. Soc. Mass Spectrom. 13, 72-81 (2002)
-
(2002)
J. Am. Soc. Mass Spectrom.
, vol.13
, pp. 72-81
-
-
Kuntz, A.F.1
Boynton, A.W.2
David, G.A.3
Colyer, K.E.4
Poutsma, J.C.5
-
36
-
-
84860517564
-
Proton and potassium affinities of aliphatic and N-methylated aliphatic a amino acids: Effect of alkyl chain length on relative stability of K+-bound Zwitterionic complexes
-
Tsang, Y., Wong, C.C.L., Wong, C.H.S., Cheng, J.M.K., Ma, N.L., Tsang, C.W.: Proton and potassium affinities of aliphatic and N-methylated aliphatic a amino acids: effect of alkyl chain length on relative stability of K+-bound Zwitterionic complexes. Int. J. Mass Spectrom. 316/318, 273-283 (2012)
-
(2012)
Int. J. Mass Spectrom.
, vol.316-318
, pp. 273-283
-
-
Tsang, Y.1
Wong, C.C.L.2
Wong, C.H.S.3
Cheng, J.M.K.4
Ma, N.L.5
Tsang, C.W.6
-
38
-
-
84919914963
-
-
Gaussian, Inc Pittsburgh
-
Millam, J.M., Daniels, A.D., Kudin, K.N., Strain, M.C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G.A., Ayala, P.Y., Cui, Q., Morokuma, K., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Cioslowski, J., Ortiz, J.V., Baboul, A.G., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, N., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Andres, J.L., Gonzalez, C., Head-Gordon, M., Replogle, E.S., Pople, J.A.: Gaussian 98 ver. A.9. Gaussian, Inc, Pittsburgh (1998)
-
(1998)
Gaussian 98 Ver. A.9
-
-
Millam, J.M.1
Daniels, A.D.2
Kudin, K.N.3
Strain, M.C.4
Farkas, O.5
Tomasi, J.6
Barone, V.7
Cossi, M.8
Cammi, R.9
Mennucci, B.10
Pomelli, C.11
Adamo, C.12
Clifford, S.13
Ochterski, J.14
Petersson, G.A.15
Ayala, P.Y.16
Cui, Q.17
Morokuma, K.18
Malick, D.K.19
Rabuck, A.D.20
Raghavachari, K.21
Foresman, J.B.22
Cioslowski, J.23
Ortiz, J.V.24
Baboul, A.G.25
Stefanov, B.B.26
Liu, G.27
Liashenko, A.28
Piskorz, P.29
Komaromi, I.30
Gomperts, R.31
Martin, R.L.32
Fox, D.J.33
Keith, T.34
Al-Laham, M.A.35
Peng, C.Y.36
Nanayakkara, N.37
Challacombe, M.38
Gill, P.M.W.39
Johnson, B.40
Chen, W.41
Wong, M.W.42
Andres, J.L.43
Gonzalez, C.44
Head-Gordon, M.45
Replogle, E.S.46
Pople, J.A.47
more..
-
40
-
-
0000189651
-
Density functional thermochemistry. III. The role of exact exchange
-
Becke, A.D.: Density functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652 (1993)
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
41
-
-
0345491105
-
Development of the Colle-Salvetti correlation energy formula into a functional of the electron density
-
Lee, C., Yang, W., Parr, R.G.: Development of the Colle-Salvetti correlation energy formula into a functional of the electron density. Phys. Rev. B 37, 785-789 (1988)
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
42
-
-
0032366914
-
Evaluated gas phase basicities and proton affinities of molecules: An update
-
Hunter, E.P., Lias, S.G.: Evaluated gas phase basicities and proton affinities of molecules: an update. J. Phys. Chem. Ref. Data 27, 3-656 (1998)
-
(1998)
J. Phys. Chem. Ref. Data
, vol.27
, pp. 3-656
-
-
Hunter, E.P.1
Lias, S.G.2
-
43
-
-
0001469409
-
Low-energy collision-induced dissociation of protonated peptides. Importance of an oxazolone formation for a peptide bond cleavage
-
Vaisar, T., Urban, J.: Low-energy collision-induced dissociation of protonated peptides. Importance of an oxazolone formation for a peptide bond cleavage. Eur. Mass Spectrom. 4, 359-364 (1998)
-
(1998)
Eur. Mass Spectrom.
, vol.4
, pp. 359-364
-
-
Vaisar, T.1
Urban, J.2
|