Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 83

References

1. Thirkettle, C., and Morris, H. R. (1980)
Computer-assisted sequencing of peptide
mass spectra [proceedings]. Biochem. Soc.
Trans. 8 , 176-177.
2. Johnson, R. S., and Biemann, K. (1989)
Computer program (SEQPEP) to aid in the
interpretation of high-energy collision tan-
dem mass spectra of peptides. Biomed. Env-
iron. Mass Spectrom. 18 , 945-957.
3. Pillay, T. S. (1988) TURBOLYTIK: a pep-
tide cleavage program for personal comput-
ers. Int. I. Bio-med. Comput. 22 , 259-264.
4. Lee, T. D., and Vemuri, S. (1990) MacPro-
Mass: a computer program to correlate mass
spectral data to peptide and protein struc-
tures. Biomed. Environ. Mass Spectrom. 19 ,
639-645.
5. Altschul, S. F., Gish, W., Miller, W., Myers,
E. W., and Lipman, D. J. (1990) Basic local
alignment search tool. J. Mol. Biol. 215 ,
403-410.
6. (2009) GenBank release notes. National
Center for Biotechnology Information.
ftp://ftp.ncbi.nih.gov/genbank/release.
notes/
7. Stults, J. T., Lai, J., McCune, S., and Wet-
zel, R. (1993) Simplification of high-energy
collision spectra of peptides by amino-
terminal derivatization. Anal. Chem. 65 ,
1703-1708.
8. Yates, J. R., 3rd, Eng, J. K., McCormack,
A. L., and Schieltz, D. (1995) Method
to correlate tandem mass spectra of mod-
ified peptides to amino acid sequences in
the protein database. Anal. Chem. 67 ,
1426-1436.
9. Mann, M., and Wilm, M. (1994) Error-
tolerant identification of peptides in
sequence databases by peptide sequence
tags. Anal. Chem. 66 , 4390-4399.
10. Matthiesen, R., (ed.) (2007) Mass spec-
trometry data analysis in proteomics. Vol.
367. Humana Press, Totowa, NJ, USA.
11. Eidhammer, I., Flikka, K., Martens, L.,
and Mikalsen, S. (2007) Computational
methods for mass spectrometry proteomics.
Wiley, Chichester, UK.
12. Pedersen, S. K., Harry, J. L., Sebastian, L.,
Baker, J., Traini, M. D., McCarthy, J. T.,
Manoharan, A., Wilkins, M. R., Gooley, A.
A., Righetti, P. G., Packer, N. H., Williams,
K. L., and Herbert, B. R. (2003) Unseen
proteome: mining below the tip of the ice-
berg to find low abundance and membrane
proteins. J. Proteome Res. 2 , 303-311.
13. Sidhu, K. S., Sangvanich, P., Brancia, F. L.,
Sullivan, A. G., Gaskell, S. J., Wolkenhaue,

O., Oliver, S. G., and Hubbard, S. J. (2001)
Proteomics 1 , 1368-1377.
14. Matthiesen, R., Lundsgaard, M., Welinder,
K. G., and Bauw, G. (2003) Interpreting
peptide mass spectra by VEMS. Bioinfor-
matics (Oxford, England) 19 , 792-793.
15. Cargile, B. J., and Stephenson, J. L., Jr.
(2004) An alternative to tandem mass spec-
trometry: isoelectric point and accurate
mass for the identification of peptides. Anal.
Chem. 76 , 267-275.
16. Cagney, G., Amiri, S., Premawaradena, T.,
Lindo, M., and Emili, A. (2003) In silico
proteome analysis to facilitate proteomics
experiments using mass spectrometry. Pro-
teome Sci. 1 ,5.
17. Matthiesen, R., Trelle, M. B., Hojrup, P.,
Bunkenborg, J., and Jensen, O. N. (2005)
VEMS 3.0: algorithms and computational
tools for tandem mass spectrometry based
identification of post-translational modifi-
cations in proteins. J. Proteome Res. 4 ,
2338-2347.
18. Eng, J. K., McCormack, A. L., and Yates, J.
R. (1994) An approach to correlate tandem
mass spectral data of peptides with amino
acid sequences in a protein database. Am.
Soc. Mass Spectrom. 5 , 976-989.
19. Perkins, D. N., Pappin, D. J., Creasy, D.
M., and Cottrell, J. S. (1999) Probability-
based protein identification by searching
sequence databases using mass spectrome-
try data. Electrophoresis 20 , 3551-3567.
20. Conrads, T. P., Anderson, G. A., Veen-
stra, T. D., Pasa-Tolic, L., and Smith, R.
D. (2000) Utility of accurate mass tags for
proteome-wide protein identification. Anal.
Chem. 72 , 3349-3354.
21. Strittmatter, E. F., Ferguson, P. L., Tang,
K., and Smith, R. D. (2003) Proteome anal-
yses using accurate mass and elution time
peptide tags with capillary LC time-of-flight
mass spectrometry. J.Am.Soc.MassSpec-
trom. 14 , 980-991.
22. Clauser, K. R., Baker, P., and Burlingame,
A. L. (1999) Role of accurate mass mea-
surement (+/-10 ppm) in protein identifi-
cation strategies employing MS or MS/MS
and database searching. Anal. Chem. 71 ,
2871-2882.
23. Mueller, L. N., Brusniak, M. Y., Mani, D.
R., and Aebersold, R. (2008) An assessment
of software solutions for the analysis of mass
spectrometry based quantitative proteomics
data. J. Proteome Res. 7 , 51-61.
24. Monroe, M. E., Tolic, N., Jaitly, N., Shaw,
J. L., Adkins, J. N., and Smith, R. D. (2007)