Table 1. Summary of selected proteoforms of important genes.

Those genes are related to WNT/β-catenin signaling, mTOR signaling, and PI3K/AKT signaling pathways. “×” suggests that the proteoform is identified in the sample. “ND” indicates that the proteoform is not identified in the sample.

Gene	Pathway	Proteoform	SW480	SW620	Proteoform intensities (SW480/SW620)*
MARK2	WNT/β-catenin signaling	M.(S)[acetyl]SARTPLPTLNERDTEQPTLGHLDSK(PSSKSNMIRGRNSAT) (mass shift: 96 Da, phospho and oxidation)SADEQPHIGNY.R	×	ND	4.8 × 105/2.8 × 104
SOX9	WNT/β-catenin signaling	R.SQYDYTDHQNSSSYYSHAAGQGTGLYSTFTYMNPAQRPMYTPIADTSGV(PSIPQTHS) (mass shift: 78 Da, phospho)PQHWEQPVYTQLTRP.	×	ND	3.0 × 105/4.6 × 104
EIF4B	mTOR signaling	M.AASAKKKNK(KGKTISLTDFL) (mass shift: 122 Da, phospho and acetylation/trimethylation)AEDGGTGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTAPR.A	ND	×	7.5 × 104/4.4 × 105
EIF4B	mTOR signaling	M.(A)[acetyl]ASAKKKNKKGKTISLTDFLAEDGG(T) (mass shift: 80 Da, phospho)GGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDR.S	ND	×	5.0 × 104/3.1 × 105
EIF4EBP1	PI3K/AKT signaling	.MSGGSS(C)[carbamidomethylation]SQTPSRAIPAT(RRVVLGDGVQLPPGDYSTT) (mass shift: 81 Da, phospho) PGGTLFSTTPGGTRIIYDRKFLME(C) (carbamidomethylation) RNSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKRAGGEESQFEMDI	ND	×	6.0 × 104/3.5 × 106
EIF4EBP1	PI3K/AKT signaling	K.TPPRDLPTIPGVTS(PSSDEPPMEASQSHLRNS) (mass shift: 81 Da, phospho) PEDKRAGGEESQFEMDI	×	ND	1.5 × 105/5.0 × 104

*The proteoform intensities were observed by manually checking the raw data based on the migration time, charge, and m/z of proteoforms in the database search results. The average intensity of the identified charge state of each proteoform across the proteoform peak is shown in the table.