annotation.pd: Example of annotation file for raw.pd, which is the PSM...
In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
annotation.pd R Documentation
Example of annotation file for raw.pd,
which is the PSM output of Proteome Discoverer
Description
Annotation of example data, raw.pd, in this package.
It should be prepared by users.
The variables are as follows:
Usage
annotation.pd
Format
A data frame with 150 rows and 7 variables.
Details
Run : MS run ID. It should be the same as Spectrum.File info
in raw.pd.
Channel : Labeling information (126, ... 131). It should be
consistent with the channel columns in raw.pd.
Condition : Condition (ex. Healthy, Cancer, Time0)
Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in
a single mass spectrometry experiment. If the channal doesn't have sample, please add ‘Empty’ under Condition.
TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates.
For example, if ‘TechRepMixture’ = 1, 2 are the two technical replicates of one mixture, then they should match
with same ‘Mixture’ value.
Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth.
Then one technical replicate of one mixture should correspond to multuple fractions.
For example, if ‘Fraction’ = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects,
then they should have same ‘TechRepMixture’ and ‘Mixture’ value.
BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add ‘Empty’ under BioReplicate.
Examples
head(annotation.pd)
Vitek-Lab/MSstatsTMT documentation built on Nov. 18, 2024, 11:30 a.m.
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| annotation.pd | R Documentation |
Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer
Description
Annotation of example data, raw.pd, in this package. It should be prepared by users. The variables are as follows:
Usage
annotation.pd
Format
A data frame with 150 rows and 7 variables.
Details
Run : MS run ID. It should be the same as Spectrum.File info in raw.pd.
Channel : Labeling information (126, ... 131). It should be consistent with the channel columns in raw.pd.
Condition : Condition (ex. Healthy, Cancer, Time0)
Mixture : Mixture of samples labeled with different TMT reagents, which can be analyzed in a single mass spectrometry experiment. If the channal doesn't have sample, please add ‘Empty’ under Condition.
TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates. For example, if ‘TechRepMixture’ = 1, 2 are the two technical replicates of one mixture, then they should match with same ‘Mixture’ value.
Fraction : Fraction ID. One technical replicate of one mixture may be fractionated into multiple fractions to increase the analytical depth. Then one technical replicate of one mixture should correspond to multuple fractions. For example, if ‘Fraction’ = 1, 2, 3 are three fractions of the first technical replicate of one TMT mixture of biological subjects, then they should have same ‘TechRepMixture’ and ‘Mixture’ value.
BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add ‘Empty’ under BioReplicate.
Examples
head(annotation.pd)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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