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This article is to share with you about the format of meta files when proteusTMT analyzes proteome data. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

When analyzing proteome data by proteusTMT, the format of meta file is very important.

Proteome data, after protein identification and quantification by Maxquant, R package "proteusTMT" can be used for differential expression analysis and statistical analysis.

The key is how to set the sample tag information and grouping information in the meta file.

Meta file in the following format (split by tab):

Measure experiment sample condition replicateReporter intensity 0 1 A 1Reporter intensity 0 2 A 1Reporter intensity 0 2 A 2Reporter intensity 0 3 A 2Reporter intensity 0 3 A 3Reporter intensity 1 1 B 1Reporter intensity 1 2 B 2Reporter intensity 1 3 B 3Reporter intensity 2 1C -1 C 1Reporter intensity 2 2 C 2Reporter intensity 2 3 C 2Reporter intensity 2 3 C 3Reporter intensity 3 1 D 1Reporter intensity 3 2 D 1Reporter intensity 3 2 D 2Reporter intensity 3 3 D 3Reporter intensity 4 1 Q 1Reporter intensity 4 2 Q 2Reporter intensity 4 3 Q Murray 3 Q 3

Measure: specifies the order of labeled ions for the sample

Experiment: set which batch of data is generated

Sample: specify the sample number

Condition: specify sample grouping

Replicate: specifies the number of the biological duplicate sample

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