Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 87

Gevaert, K., Vandekerckhove, J., and
Apweiler, R. (2005) PRIDE: the pro-
teomics identifications database. Proteomics
5 , 3537-3545.
77. Keller, A., Eng, J., Zhang, N., Li, X. J.,
and Aebersold, R. (2005) A uniform pro-
teomics MS/MS analysis platform utilizing
open XML file formats. Mol. Syst. Biol. 1 ,
2005.0017.
78. Kessner, D., Chambers, M., Burke, R.,
Agus, D., and Mallick, P. (2008) Prote-
oWizard: open source software for rapid
proteomics tools development. Bioinfor-
matics (Oxford, England) 24 , 2534-2536.
79. Zhang, N., Aebersold, R., and
Schwikowski, B. (2002) ProbID: a prob-
abilistic algorithm to identify peptides
through sequence database searching using
tandem mass spectral data. Proteomics 2 ,
1406-1412.
80. Geer, L. Y., Markey, S. P., Kowalak, J. A.,
Wagner, L., Xu, M., Maynard, D. M., Yang,
X., Shi, W., and Bryant, S. H. (2004) Open
mass spectrometry search algorithm. J. Pro-
teome Res. 3 , 958-964.
81. Heller, M., Ye, M., Michel, P. E., Morier,
P., Stalder, D., Junger, M. A., Aebersold,
R., Reymond, F., and Rossier, J. S. (2005)
Added value for tandem mass spectrometry
shotgun proteomics data validation through
isoelectric focusing of peptides. J. Proteome
Res. 4 , 2273-2282.
82. Craig, R., and Beavis, R. C. (2004) TAN-
DEM: matching proteins with tandem mass
spectra. Bioinformatics (Oxford, England)
20 , 1466-1467.
83. Shilov, I. V., Seymour, S. L., Patel, A. A.,
Loboda, A., Tang, W. H., Keating, S. P.,
Hunter, C. L., Nuwaysir, L. M., and Scha-
effer, D. A. (2007) The Paragon Algorithm,
a next generation search engine that uses
sequence temperature values and feature
probabilities to identify peptides from tan-
dem mass spectra. Mol. Cell. Proteomics 6 ,
1638-1655.
84. Tabb, D. L., Fernando, C. G., and Cham-
bers, M. C. (2007) MyriMatch: highly
accurate tandem mass spectral peptide iden-
tification by multivariate hypergeometric
analysis. J. Proteome Res. 6 , 654-661.
85. Tabb, D. L., Saraf, A., and Yates, J. R.,
3rd (2003) GutenTag: high-throughput
sequence tagging via an empirically derived
fragmentation model. Anal. Chem. 75 ,
6415-6421.
86. Tanner, S., Shu, H., Frank, A., Wang, L.
C., Zandi, E., Mumby, M., Pevzner, P. A.,
and Bafna, V. (2005) InsPecT: identifica-
tion of posttranslationally modified peptides

from tandem mass spectra. Anal. Chem. 77 ,
4626-4639.
87. Wilkins, M. R., Gasteiger, E., Wheeler,
C. H., Lindskog, I., Sanchez, J. C.,
Bairoch, A., Appel, R. D., Dunn, M. J.,
and Hochstrasser, D. F. (1998) Multi-
ple parameter cross-species protein iden-
tification using MultiIdenta world-wide
web accessible tool. Electrophoresis 19 ,
3199-3206.
88. Han, Y., Ma, B., and Zhang, K. (2004)
SPIDER: software for protein identification
from sequence tags with de novo sequenc-
ing error. Proc./IEEE Comput. Syst. Bioin-
formatics Conf. CSB , 206-215.
89. Qin, J., Fenyo, D., Zhao, Y., Hall, W.
W., Chao, D. M., Wilson, C. J., Young,
R. A., and Chait, B. T. (1997) A strategy
for rapid, high-confidence protein identifi-
cation. Anal. Chem. 69 , 3995-4001.
90. May, D., Fitzgibbon, M., Liu, Y., Holz-
man, T., Eng, J., Kemp, C. J., Whiteaker,
J., Paulovich, A., and McIntosh, M. (2007)
A platform for accurate mass and time anal-
yses of mass spectrometry data. J. Proteome
Res. 6 , 2685-2694.
91. Lam, H., Deutsch, E. W., Eddes, J. S., Eng,
J. K., King, N., Stein, S. E., and Aebersold,
R. (2007) Development and validation of a
spectral library searching method for pep-
tide identification from MS/MS. Proteomics
7 , 655-667.
92. Frewen, B., and MacCoss, M. J. (2007)
Using BiblioSpec for creating and search-
ing tandem MS peptide libraries. Current
protocols in bioinformatics/editorial board,
Andreas D. Baxevanis ... [ et al Chapter 13 ,
Unit 13.7].
93. Frank, A. M., Bandeira, N., Shen, Z., Tan-
ner, S., Briggs, S. P., Smith, R. D., and
Pevzner, P. A. (2008) Clustering millions
of tandem mass spectra. J. Proteome Res. 7 ,
113-122.
94. Palagi, P. M., Walther, D., Quadroni, M.,
Catherinet, S., Burgess, J., Zimmermann-
Ivol, C. G., Sanchez, J. C., Binz, P. A.,
Hochstrasser, D. F., and Appel, R. D.
(2005) MSight: an image analysis software
for liquid chromatography-mass spectrom-
etry. Proteomics 5 , 2381-2384.
95. Li, X. J., Pedrioli, P. G., Eng, J., Mar-
tin, D., Yi, E. C., Lee, H., and Aebersold,
R. (2004) A tool to visualize and evaluate
data obtained by liquid chromatography-
electrospray ionization-mass spectrometry.
Anal. Chem. 76 , 3856-3860.
96. Gehlenborg, N., Yan, W., Lee, I. Y., Yoo,
H., Nieselt, K., Hwang, D., Aebersold, R.,
and Hood, L. (2009) Prequipsan extensible