Biomedical Engineering Reference
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sem, W., and Buhmann, J. M. (2005)
NovoHMM: a hidden Markov model for de
novo peptide sequencing. Anal. Chem. 77 ,
7265-7273.
118. Grossmann, J., Roos, F. F., Cieliebak, M.,
Liptak, Z., Mathis, L. K., Muller, M.,
Gruissem, W., and Baginsky, S. (2005)
AUDENS: a tool for automated peptide
de novo sequencing. J. Proteome Res. 4 ,
1768-1774.
119. Alves, G., and Yu, Y. K. (2005) Robust
accurate identification of peptides (RAId):
deciphering MS2 data using a structured
library search with de novo based statis-
tics. Bioinformatics (Oxford, England) 21 ,
3726-3732.
120. Dancik, V., Addona, T. A., Clauser, K. R.,
Vath, J. E., and Pevzner, P. A. (1999) De
novo peptide sequencing via tandem mass
spectrometry. J. Comput. Biol. 6 , 327-342.
121. Frank, A., and Pevzner, P. (2005) PepNovo:
de novo peptide sequencing via probabilis-
tic network modeling. Anal. Chem. 77 ,
964-973.
122. Shevchenko, A. (2001) Evaluation of the
efficiency of in-gel digestion of proteins
by peptide isotopic labeling and MALDI
mass spectrometry. Anal. Biochem. 296 ,
279-283.
123. Mackey, A. J., Haystead, T. A., and Pearson,
W. R. (2002) Getting more from less: algo-
rithms for rapid protein identification with
multiple short peptide sequences. Mol. Cell.
Proteomics 1 , 139-147.
124. Zhang, N., Li, X. J., Ye, M., Pan,
S., Schwikowski, B., and Aebersold, R.
(2005) ProbIDtree: an automated soft-
ware program capable of identifying mul-
tiple peptides from a single collision-
induced dissociation spectrum collected by
a tandem mass spectrometer. Proteomics 5 ,
4096-4106.
125. Hoopmann, M. R., Finney, G. L., and
MacCoss, M. J. (2007) High-speed data
reduction, feature detection, and MS/MS
spectrum quality assessment of shotgun
proteomics data sets using high-resolution
mass spectrometry. Anal. Chem. 79 ,
5620-5632.
126. Olsen, J. V., Blagoev, B., Gnad, F.,
Macek, B., Kumar, C., Mortensen, P.,
and Mann, M. (2006) Global, in vivo,
and site-specific phosphorylation dynam-
ics in signaling networks. Cell 127 ,
635-648.
127. Kersey, P., Bower, L., Morris, L., Horne,
A., Petryszak, R., Kanz, C., Kanapin, A.,
Das, U., Michoud, K., Phan, I., Gattiker,
A., Kulikova, T., Faruque, N., Duggan,
K., McLaren, P., Reimholz, B., Duret,
L., Penel, S., Reuter, I., and Apweiler,
R. (2005) Integr8 and Genome Reviews:
integrated views of complete genomes
and proteomes. Nucleic Acids Res. 33 ,
D297-D302.
128. Hao, P., He, W. Z., Huang, Y., Ma, L. X.,
Xu, Y., Xi, H., Wang, C., Liu, B. S., Wang,
J. M., Li, Y. X., and Zhong, Y. (2005)
MPSS: an integrated database system for
surveying a set of proteins. Bioinformatics
(Oxford, England) 21 , 2142-2143.
129. Carvalho, P. C., Fischer, J. S., Chen, E. I.,
Domont, G. B., Carvalho, M. G., Degrave,
W. M., Yates, J. R., 3rd, and Barbosa, V. C.
(2009) GO Explorer: a gene-ontology tool
to aid in the interpretation of shotgun pro-
teomics data. Proteome Sci. 7 ,6.
130. Barrell, D., Dimmer, E., Huntley, R.
P., Binns, D., O'Donovan, C., and
Apweiler, R. (2009) The GOA database in
2009an integrated Gene Ontology Anno-
tation resource. Nucleic Acids Res. 37 ,
D396-D403.
131. Prince, J. T., Carlson, M. W., Wang, R.,
Lu, P., and Marcotte, E. M. (2004) The
need for a public proteomics repository.
Nat. Biotechnol. 22 , 471-472.
132. Mathivanan, S., Ahmed, M., Ahn, N. G.,
Alexandre, H., Amanchy, R., Andrews, P.
C., Bader, J. S., Balgley, B. M., Bantscheff,
M., Bennett, K. L., Bjorling, E., Bla-
goev, B., Bose, R., Brahmachari, S. K.,
Burlingame, A. S., Bustelo, X. R., Cagney,
G., Cantin, G. T., Cardasis, H. L., Celis,
J. E., Chaerkady, R., Chu, F., Cole, P.
A., Costello, C. E., Cotter, R. J., Crock-
ett, D., DeLany, J. P., De Marzo, A. M.,
DeSouza, L. V., Deutsch, E. W., Drans-
field, E., Drewes, G., Droit, A., Dunn, M.
J., Elenitoba-Johnson, K., Ewing, R. M.,
Van Eyk, J., Faca, V., Falkner, J., Fang,
X., Fenselau, C., Figeys, D., Gagne, P.,
Gelfi, C., Gevaert, K., Gimble, J. M., Gnad,
F., Goel, R., Gromov, P., Hanash, S. M.,
Hancock, W. S., Harsha, H. C., Hart,
G., Hays, F., He, F., Hebbar, P., Helsens,
K., Hermeking, H., Hide, W., Hjerno, K.,
Hochstrasser, D. F., Hofmann, O., Horn,
D. M., Hruban, R. H., Ibarrola, N., James,
P., Jensen, O. N., Jensen, P. H., Jung,
P., Kandasamy, K., Kheterpal, I., Kikuno,
R. F., Korf, U., Korner, R., Kuster, B.,
Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre,
M., Lehvaslaiho, M., Lescuyer, P., Levan-
der, F., Lim, M. S., Lobke, C., Loo, J. A.,
Mann, M., Martens, L., Martinez-Heredia,
J., McComb, M., McRedmond, J., Mehrle,
A., Menon, R., Miller, C. A., Mischak, H.,
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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