Biology Reference
In-Depth Information
Novel statistical tools implemented in COVAIN allow the exploration
of new relationships within the data. The complete software
including step-by-step-tutorials is available at
http://www.univie.
ac.at/mosys/software.html
.
The platform allows the rapid and
convenient analysis of proteomics data and provides many more
features which were not be discussed here due to space limitations
but can be explored by the user himself. We encourage our col-
leagues to explore the toolbox and also give feedback for improve-
ments which can be implemented in future.
References
1. Weckwerth W (2011) Unpredictability of
metabolism: the key role of metabolomics
science in combination with next-generation
genome sequencing. Anal Bioanal Chem
400:1967-1978
2. Weckwerth W (2003) Metabolomics in systems
biology. Annu Rev Plant Biol 54:669-689
3. Hoehenwarter W, van Dongen JT, Wienkoop S
et al (2008) A rapid approach for phenotype-
screening and database independent detection of
cSNP/protein polymorphism using mass accuracy
precursor alignment. Proteomics 8:4214-4425
4. Lehmann U, Wienkoop S, Tschoep H et al
(2008) If the antibody fails: a mass western
approach. Plant J 55:1039-1046
5. Sun X, Weckwerth W (2012) COVAIN: a
toolbox for uni- and multivariate statistics,
time-series and correlation network analysis
and inverse estimation of the differential
Jacobian from metabolomics covariance data.
Metabolomics 8:81-93
6. Doerfl er H, Lyon D, Nägele T et al (2013)
Granger causality in integrated GC-MS and
LC-MS metabolomics data reveals the inter-
face of primary and secondary metabolism.
Metabolomics 9(3):564-574
7. Mari A, Lyon D, Fragner L et al (2013)
Phytochemical composition of Potentilla anse-
rina L. analyzed by an integrative GC-MS and
LC-MS metabolomics platform. Metabolomics
9:599-607
8. Hummel J, Niemann M, Wienkoop S et al
(2007) ProMEX: a mass spectral reference
database for proteins and protein phosphoryla-
tion sites. BMC Bioinformatics 8:216
9. Wienkoop S, Staudinger C, Hoehenwarter W
et al (2012) ProMEX: a mass spectral refer-
ence database for plant proteomics. Front
Plant Sci 3:125
10. Hoehenwarter W, Larhlimi A, Hummel J et al
(2011) MAPA distinguishes genotype-specifi c
variability of highly similar regulatory protein
isoforms in potato tuber. J Proteome Res
10:2979-2991
11. Egelhofer V, Hoehenwarter W, Lyon D,
Weckwerth W, Wienkoop S (2013) Using
ProtMAX to create high mass accuracy precursor
alignments from label-free quantitative mass
spectrometry data generated in large shotgun
proteomics experiments. Nat Protoc 8:595-601
12. Chen Y, Hoehenwarter W, Weckwerth W
(2010) Comparative analysis of phytohor-
mone
‐
responsive phosphoproteins in
Arabidopsis thaliana using TiO2
‐
phosphopep-
tide enrichment and mass accuracy precursor
alignment. Plant J 63:1-17
13. Chen Y, Liu P, Hoehenwarter W et al (2012)
Proteomic and phosphoproteomic analysis of
picea wilsonii pollen development under nutri-
ent limitation. J Proteome Res 11:4180-4190
14. Hoehenwarter W, Thomas M, Nukarinen E
et al (2013) Identifi cation of Novel in vivo
MAP Kinase Substrates in Arabidopsis thaliana
Through Use of Tandem Metal Oxide Affi nity
Chromatography. Mol Cell Proteomics 12(2):
369-380
15. Desiderio DM, Kai M (1983) Preparation of
stable isotope-incorporated peptide internal
standards for fi eld desorption mass- spectrometry
quantifi cation of peptides in biologic tissue.
Biomed Mass Spectrom 10:471-479
16. Wienkoop S, May P, Kempa S et al (2010)
Targeted proteomics for Chlamydomonas
reinhardtii combined with rapid subcellular
protein fractionation, metabolomics and meta-
bolic fl ux analyses. Mol Biosyst 6:1018-1031
17. Wolschin F, Weckwerth W (2005) Combining
metal oxide affi nity chromatography (MOAC)
and selective mass spectrometry for robust
identifi cation of in vivo protein phosphoryla-
tion sites. Plant Methods 1:9
18. Wolschin F, Wienkoop S, Weckwerth W
(2005) Enrichment of phosphorylated pro-
teins and peptides from complex mixtures
using metal oxide/hydroxide affi nity chroma-
tography (MOAC). Proteomics 5:4389-4397
19. Larsen MR, Thingholm TE, Jensen ON et al
(2005) Highly selective enrichment of phos-
