Biology Reference
In-Depth Information
Table 1.1
(continued)
Platform
MS
References
Profiling
MALDI-
MALDI-TOF
113,114
TOF/MS
SELDI-
SELDI-TOF
115-118
TOF/MS
LC-MS/MS
IT
119
Sample preparation
c
Platform
MS
References
Metabolomics
GC-ESI/MS
TOF-MS
93
ESI (
+
/
−
)-MS
TQ
10,22
ESI-MS/MS
TQ
21
a
Subcellular fractionation was not considered.
b
Cleanup steps (like solid phase extraction) are not listed.
c
Sample preparation for metabolomics includes the following steps: quenching, extraction,
and concentration.
ESI(
), electrospray positive/negative ion mode; LIT, linear ion trap; MS
n
, multiple stages
MS/MS; IP, immunoprecipitation; IT, ion trap; RP, reversed-phase; SAX, strong anion
exchange; SCX, strong cation exchange; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide
gel electrophoresis; TQ, triple quadrupole.
+
/
−
draws upon the complementary nature of ESI and MALDI for efficient
ionization of modified peptides. Moreover, analysis of modified peptides
requires increased information content through better mass accuracy
and resolution of TOF instruments, specific detection of neutral loss
ions by triple quadrupole as well as multiple stages of fragmentation
by triggered neutral losses in LIT. Even so, ion trap is still the leading
instrument whose scanning abilities are often enough to complement
enrichment techniques and LC separation in identifying modified
peptides.
The last two sections of table 1.1 (profiling and metabolomics) under-
score the power of mass measurement as mostly single-stage MS is
performed. Profiling techniques emphasize the utility of solid-phase
support for certain clinical samples.
MASS SPECTROMETRY DATA IN SYSTEMS BIOLOGY
The availability of large data sets such as the global protein expression
data, protein-protein interaction data, and localization data that are
available for
S. cerevisiae
can be used to extend and integrate observa-
tions made from large-scale MS analysis of proteins and metabolites.
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