deepPedAllMeltome

Deep thermal proteome profiling of pediatric acute lymphoblastic leukemia cell lines

R

The R directory holds R analysis code.

Data

Data is stored in the data directory and shared separately.

• target_psmtable.txt: PSM-centric
• peptides_table.txt: peptide-centric
• symbols_table.txt: gene-symbol centric
• proteins_table.txt: protein-centric (ENSPs, comprise isoforms)
• genes_table.txt: gene-centric (ENSGs)

Proteomics data was analyzed using this pipeline.

• Search: msgfPlus, Percolator
• Quantitation: IsobaricAnalyzer (OpenMS)

Meta data

Meta data is stored in the meta directory.

• sample_meta.txt: the sample (cell line) information
• channel_meta.txt: the TMT channels (and relating temperatures)
• meltome_sample_meta.txt: the meltome sample information (e.g. which channels correspond to which temperatures)