Cancer type abbreviations
TumorDetail
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
Announcements
1. normalized expression

MaxQuant software (version 2.0.2.0) 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. Violin plot

The pathological stage analysis of proteins or phosphorylation sites is shown by violin plot.

X-axis represents the different pathological stage specified by users.

Y-axis represents normalized abundance of proteins or phosphorylation sites.