Biology Reference
In-Depth Information
intact proteins using 'top down' mass spectrometry. Anal Chem
2003;75:4081
[67] Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P,
et al. Global, in vivo, and site-specific phosphorylation dynamics
in signaling networks. Cell 2006;127:635
6.
[50] Zamdborg L, LeDuc RD, Glowacz KJ, Kim YB, Viswanathan V,
Spaulding IT, et al. ProSight PTM 2.0: improved protein identi-
fication and characterization for top down mass spectrometry.
Nucleic Acids Res 2007;35:W701 e 6.
[51] Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M,
Schmidt A, et al. Identification of cross-linked peptides from large
sequence databases. Nat Methods 2008;5:315 e 8.
[52] Rappsilber J. The beginning of a beautiful friendship: cross-
linking/mass spectrometry and modelling of proteins and multi-
protein complexes. J Struct Biol 2011;173:530 e 40.
[53] Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A,
et al. PEAKS: powerful software for peptide de novo sequencing
by tandem mass spectrometry. Rapid Commun Mass Spectrom
2003;17:2337 e 42.
[54] Ma B, Johnson R. De novo sequencing and homology searching.
Mol Cell Proteomics 2012;11. O111 014902.
[55] Cox J, Michalski A, Mann M. Software lock mass by two-
dimensional minimization of peptide mass errors. Journal of the
American Society for Mass Spectrometry 2011;22:1373 e 80.
[56] Sadygov RG, Cociorva D, Yates 3rd JR. Large-scale database
searching using tandem mass spectra: looking up the answer in
the back of the topic. Nat Methods 2004;1:195 e 202.
[57] Dancik V, Addona TA, Clauser KR, Vath JE, Pevzner PA. De
novo peptide sequencing via tandem mass spectrometry. Journal
of computational biology: a journal of computational molecular
cell biology 1999;6:327
e
48.
[68] Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP. A proba-
bility-based approach for high-throughput protein phosphoryla-
tion analysis and site localization. Nat Biotechnol 2006;24:
1285 e 92.
[69] Bailey CM, Sweet SMM, Cunningham DL, Zeller M, Heath JK,
Cooper HJ. SLoMo: Automated Site Localization of Modifica-
tions from ETD/ECD Mass Spectra. J Proteome Res 2009;8:
1965 e 71.
[70] Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T,
Bantscheff M, et al. Confident phosphorylation site localization
using
e
the Mascot Delta
Score. Mol Cell
Proteomics
2012;11(3):M110.003830.
[71] Taus T, Kocher T, Pichler P, Paschke C, Schmidt A, Henrich C,
et al. Universal and confident phosphorylation site localization
using phosphoRS. J Proteome Res 2011;10:5354 e 62.
[72] Creasy DM, Cottrell JS. Error tolerant searching of uninterpreted
tandem mass spectrometry data. Proteomics 2002;2:1426 e 34.
[73] Savitski MM, Nielsen ML, Zubarev RA. ModifiComb, a new
proteomic tool for mapping substoichiometric post-translational
modifications, finding novel types of modifications, and finger-
printing complex protein mixtures. Mol Cell Proteomics
2006;5:935
48.
[74] Nesvizhskii AI, Aebersold R. Interpretation of shotgun proteomic
data: the protein inference problem. Mol Cell Proteomics
2005;4:1419 e 40.
[75] Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quan-
titative mass spectrometry in proteomics: a critical review. Anal
Bioanal Chem 2007;389:1017 e 31.
[76] Ow SY, Salim M, Noirel J, Evans C, Rehman I, Wright PC.
iTRAQ underestimation in simple and complex mixtures: 'the
good, the bad and the ugly'. Journal of proteome research
2009;8:5347 e 55.
[77] Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE,
et al. iTRAQ labeling is superior to mTRAQ for quantitative
global proteomics and phosphoproteomics. Mol Cell Proteomics
2012;11:M111.014423.
[78] Christoforou A, Lilley KS. Taming the isobaric tagging elephant
in the room in quantitative proteomics. Nat Methods 2011;8:
911 e 3.
[79] Malmstrom J, Lee H, Aebersold R. Advances in proteomic work-
flows for systems biology. Curr Opin Biotechnol 2007;18:378 e 84.
[80] Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A,
Dephoure N, et al. Global analysis of protein expression in yeast.
Nature 2003;425:737 e 41.
[81] Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R.
Full dynamic range proteome analysis of S. cerevisiae by targeted
proteomics. Cell 2009;138:795
e
42.
[58] Mann M, Wilm M. Error-tolerant identification of peptides in
sequence databases by peptide sequence tags. Anal Chem
1994;66:4390 e 9.
[59] Eng JK, McCormack AL, Yates JR. An approach to correlate
tandem mass spectral data of peptides with amino acid sequences
in a protein database. J Am Soc Mass Spectrom 1994;5:976 e 89.
[60] Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-
based protein identification by searching sequence databases
using mass spectrometry data. Electrophoresis 1999;20:3551 e 67.
[61] Cox J, Neuhauser N,Michalski A, ScheltemaRA, Olsen JV,MannM.
Andromeda: a peptide search engine integrated into the MaxQuant
environment. Journal of proteome research 2011;10:1794 e 805.
[62] Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical
statistical model to estimate the accuracy of peptide identifica-
tions made by MS/MS and database search. Analytical chemistry
2002;74:5383 e 92.
[63] Brosch M, Yu L, Hubbard T, Choudhary J. Accurate and sensitive
peptide identification with Mascot Percolator. J Proteome Res
2009;8:3176 e 81.
[64] Elias JE, Gygi SP. Target-decoy search strategy for increased
confidence in large-scale protein identifications by mass spec-
trometry. Nat Methods 2007;4:207
e
14.
[65] Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of
proteomic data generated by tandem mass spectrometry. Nat
Methods 2007;4:787
806.
[82] Thakur SS, Geiger T, Chatterjee B, Bandilla P, Frohlich F, Cox J,
et al. Deep and highly sensitive proteome coverage by LC-MS/
MS without prefractionation. Mol Cell Proteomics 2011;10.
M110.003699.
[83] Nagaraj N, Kulak NA, Cox J, Neuhaus N, Mayr K, Hoerning O,
et al. Systems-wide perturbation analysis with near complete
coverage of the yeast proteome by single-shot UHPLC runs on
e
e
97.
[66] Geiger T, Wehner A, Schaab C, Cox J, Mann M. Comparative
proteomic analysis of eleven common cell lines reveals ubiquitous
but varying expression of most proteins. Mol Cell Proteomics
2012;11(3):M111.014050.
e
Search WWH ::




Custom Search