The choice between NIT and SILAC labeling largely depends on the specific
requirements of a project.
Both SILAC and NIT labeling can label virtually every peptides from digestion
of a complex protein mixture. Both methods can be used to detect changes
in protein abundance as well as changes in posttranslational
modifications.
The major advantage of SILAC labeling is that the samples are metabolically
labeled, so separations at protein level will not introduce error. So it
is possible to fractionate samples at both protein level and peptide
level, e.g. 2-D fractionation at protein level followed by 2-D
fractionation at peptide level, although such a 4-dimentional
fractionation will result a very large number of samples for MS
analysis. The main disadvantage of SILAC method is that tissue or blood
samples cannot be labeled by SILAC technique. Some cell lines are also
difficult to grow in SILAC. The high cost of SILAC media is sometimes a
concern too.
The major advantage of NIT method is its ability
to label virtually any type of protein samples, including cells, tissue
and blood samples. The cost of labeling reagents is very low compared to
SILAC media. The main disadvantage is that labeling is performed after
proteolytic digestion, so fractionation is carried out at peptide level.
Normally it is limited to two-dimensional separations (SCX and RP-LC)
before MS analysis.
The Choice Between NIT and SILAC labeling Techniques
