Long　noncoding　RNAs　(lncRNAs)　are　closely　associated　with　tumor　development,　and　increasing　evidence　suggests　that　small　open　reading　frame　(smORF)　within　lncRNAs　also　have　the　capability　to　encode　smORF-encoded　peptides　(SEPs).　Here,　we　thoroughly　uncovered　the　SEP　expression　profile　of　hepatocellular　carcinoma　(HCC)　from　tumor　and　adjacent　nontumor　tissues　of　154　HCC　patients　using　high-throughput　mass　spectrometry　(MS).　A　total　of　208　SEPs　were　identified,　with　no　significant　difference　in　abundance　and　stability　compared　with　coding　region　proteins.　Notably,　the　peptide　encoded　by　LINC01007　(LINC01007-33AA)　was　significantly　upregulated　in　HCC　tissues　(p　＜　0.05)　and　could　serve　as　an　independent　risk　factor　affecting　prognosis　(HR　[95%　CI]:　1.31[1.01-1.7]).　This　endogenous　peptide　was　further　confirmed　at　both　the　mRNA　and　protein　levels,　and　its　overexpression　significantly　enhances　the　invasion　and　migration　of　HCC　cells.　These　findings　highlight　the　potential　of　MS-based　methods　to　identify　novel　noncoding　sequence　encoded　functional　peptides　associated　with　tumor　progression.