CPPA is a developed interactive web server for analyzing both protein and protein phosphorylation abundance in 13 different types of tumor tissues and corresponding normal tissues from public datasets, such as CPTAC, using unified analysis pipeline. CPPA provides customizable functions such as differential expression analysis, pathological stages analysis, correlation analysis, survival analysis, and similarity analysis. analysis platform is developed by Hugs from Liu Lab in the School of Pharmaceutical Sciences, Xiamen University.

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The MS raw data CPPA used is acquired from CPTAC project ( https://pdc.cancer.gov/pdc/browse ), followed by a unified search of the protein sequence library by MaxQuant.

Cancer type abbreviations
ESCCEsophageal squamous cell Carcinoma
LUSCLung squamous cell carcinoma
GBMGlioblastoma multiforme
HNSCHead and Neck squamous cell carcinoma
PAADPancreatic adenocarcinoma
LUADLung adenocarcinoma
UCECUterine Corpus Endometrial Carcinoma
KIRCKidney renal clear cell carcinoma
LIHCLiver hepatocellular carcinoma
OVOvarian serous cystadenocarcinoma
STADStomach adenocarcinoma
BRCABreast invasive carcinoma
COADColon adenocarcinoma
1. normalized expression

MaxQuant software (version was used to analyze MS raw files. If the “internal reference”, such as a mixed sample, exists, the reference channel will be set according to the corresponding plex, and the normalization method will be set as ‘Weighted ratio to reference channel’. The expression ratios output by MaxQuant were log2-transformed and normalized using the median centering method across proteins and phosphorylation sites.

2. log2(median)

the meaning of ‘log2 (median)’ represented the log2 transformed median value of normalized expression of proteins or phosphorylation. log2 (median) (N) represented the log2 transformed median value in normal samples. log2 (median) (T) represented the log2 transformed median value in tumor samples.