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.

Figure legend
1. scatter plot

The correlation analysis of pairwise proteins or phosphorylation sites is shown by scatter plot.

X-axis and y-axis represent the normalized abundance of pairwise protein or phosphorylation site specified by users.