3 research outputs found
Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays
Targeted proteomics strategies present a streamlined
hypothesis-driven
approach to analyze specific sets of pathways or disease related proteins.
goDig is a quantitative, targeted tandem mass tag (TMT)-based assay
that can measure the relative abundance differences for hundreds of
proteins directly from unfractionated mixtures. Specific protein groups
or entire pathways of up to 200 proteins can be selected for quantitative
profiling, while leveraging sample multiplexing permits the simultaneous
analysis of up to 18 samples. Despite these benefits, implementing
goDig is not without challenges, as it requires access to an instrument
application programming interface (iAPI), an elution order and spectral
library, a web-based method builder, and dedicated companion software.
In addition, the absence of an example test assay may dissuade researchers
from testing or implementing goDig. Here, we repurpose the TKO11 standardwhich
is commercially available but may also be assembled in-laband
establish it as a de facto test assay for goDig.
We build a proteome-wide goDig yeast library, quantify protein expression
across several gene ontology (GO) categories, and compare these results
to a fully fractionated yeast gold-standard data set. Essentially,
we provide a guide detailing the goDig-based quantification of TKO11,
which can also be used as a template for user-defined assays in other
species
Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays
Targeted proteomics strategies present a streamlined
hypothesis-driven
approach to analyze specific sets of pathways or disease related proteins.
goDig is a quantitative, targeted tandem mass tag (TMT)-based assay
that can measure the relative abundance differences for hundreds of
proteins directly from unfractionated mixtures. Specific protein groups
or entire pathways of up to 200 proteins can be selected for quantitative
profiling, while leveraging sample multiplexing permits the simultaneous
analysis of up to 18 samples. Despite these benefits, implementing
goDig is not without challenges, as it requires access to an instrument
application programming interface (iAPI), an elution order and spectral
library, a web-based method builder, and dedicated companion software.
In addition, the absence of an example test assay may dissuade researchers
from testing or implementing goDig. Here, we repurpose the TKO11 standardwhich
is commercially available but may also be assembled in-laband
establish it as a de facto test assay for goDig.
We build a proteome-wide goDig yeast library, quantify protein expression
across several gene ontology (GO) categories, and compare these results
to a fully fractionated yeast gold-standard data set. Essentially,
we provide a guide detailing the goDig-based quantification of TKO11,
which can also be used as a template for user-defined assays in other
species
Adapting an Isobaric Tag-Labeled Yeast Peptide Standard to Develop Targeted Proteomics Assays
Targeted proteomics strategies present a streamlined
hypothesis-driven
approach to analyze specific sets of pathways or disease related proteins.
goDig is a quantitative, targeted tandem mass tag (TMT)-based assay
that can measure the relative abundance differences for hundreds of
proteins directly from unfractionated mixtures. Specific protein groups
or entire pathways of up to 200 proteins can be selected for quantitative
profiling, while leveraging sample multiplexing permits the simultaneous
analysis of up to 18 samples. Despite these benefits, implementing
goDig is not without challenges, as it requires access to an instrument
application programming interface (iAPI), an elution order and spectral
library, a web-based method builder, and dedicated companion software.
In addition, the absence of an example test assay may dissuade researchers
from testing or implementing goDig. Here, we repurpose the TKO11 standardwhich
is commercially available but may also be assembled in-laband
establish it as a de facto test assay for goDig.
We build a proteome-wide goDig yeast library, quantify protein expression
across several gene ontology (GO) categories, and compare these results
to a fully fractionated yeast gold-standard data set. Essentially,
we provide a guide detailing the goDig-based quantification of TKO11,
which can also be used as a template for user-defined assays in other
species