TDP-43 dysfunction leads to the inclusion of cryptic exons in hundreds of transcripts, which can generate de novo proteins. In TDP-43–depleted human iPSC-derived neurons, mRNA transcripts with cryptic exons produce de novo proteins, and these peptides are found in CSF samples from ALS/FTD patients. Using transcriptomic and proteomic analyses, 65 peptides mapping to 12 cryptic exons were identified. These cryptic exons are predictive of those expressed in postmortem brain tissue from TDP-43 proteinopathy patients. The inclusion of cryptic peptide sequences in proteins alters their interactions with other proteins, potentially affecting their function. 18 de novo peptides across 13 genes were found in CSF samples from ALS/FTD patients. The study demonstrates that cryptic exon translation provides new insights into ALS/FTD pathophysiology and may offer a strategy to assess TDP-43 function in patient CSF. TDP-43 loss causes widespread cryptic splicing events that affect hundreds of transcripts. Cryptic exons can reduce mRNA stability and protein expression, but some may be translated into de novo proteins. The study shows that TDP-43–depleted human iPSC-derived neurons express cryptic exons that generate de novo proteins. These proteins are detected in postmortem brain tissue and CSF samples from ALS/FTD patients. The study validates the presence of de novo proteins in TDP-43–depleted neurons and shows that these proteins can alter the interactomes of their target proteins. The study also identifies cryptic peptides in CSF samples from ALS/FTD patients, suggesting that TDP-43-related de novo peptides are present in these patients. The study demonstrates that cryptic exons can be translated into de novo proteins, which may alter protein interactions and function. The findings suggest that TDP-43 dysfunction leads to the generation of de novo proteins that could contribute to ALS/FTD pathophysiology. The study also shows that these de novo proteins are present in CSF samples from ALS/FTD patients, indicating that they may be used as biomarkers for disease. The study provides a framework for developing clinical-grade tests to measure TDP-43 function in biospecimens. The study highlights the importance of understanding the role of cryptic peptides in diseases involving TDP-43 pathology and provides a basis for further research into the mechanisms underlying ALS/FTD.TDP-43 dysfunction leads to the inclusion of cryptic exons in hundreds of transcripts, which can generate de novo proteins. In TDP-43–depleted human iPSC-derived neurons, mRNA transcripts with cryptic exons produce de novo proteins, and these peptides are found in CSF samples from ALS/FTD patients. Using transcriptomic and proteomic analyses, 65 peptides mapping to 12 cryptic exons were identified. These cryptic exons are predictive of those expressed in postmortem brain tissue from TDP-43 proteinopathy patients. The inclusion of cryptic peptide sequences in proteins alters their interactions with other proteins, potentially affecting their function. 18 de novo peptides across 13 genes were found in CSF samples from ALS/FTD patients. The study demonstrates that cryptic exon translation provides new insights into ALS/FTD pathophysiology and may offer a strategy to assess TDP-43 function in patient CSF. TDP-43 loss causes widespread cryptic splicing events that affect hundreds of transcripts. Cryptic exons can reduce mRNA stability and protein expression, but some may be translated into de novo proteins. The study shows that TDP-43–depleted human iPSC-derived neurons express cryptic exons that generate de novo proteins. These proteins are detected in postmortem brain tissue and CSF samples from ALS/FTD patients. The study validates the presence of de novo proteins in TDP-43–depleted neurons and shows that these proteins can alter the interactomes of their target proteins. The study also identifies cryptic peptides in CSF samples from ALS/FTD patients, suggesting that TDP-43-related de novo peptides are present in these patients. The study demonstrates that cryptic exons can be translated into de novo proteins, which may alter protein interactions and function. The findings suggest that TDP-43 dysfunction leads to the generation of de novo proteins that could contribute to ALS/FTD pathophysiology. The study also shows that these de novo proteins are present in CSF samples from ALS/FTD patients, indicating that they may be used as biomarkers for disease. The study provides a framework for developing clinical-grade tests to measure TDP-43 function in biospecimens. The study highlights the importance of understanding the role of cryptic peptides in diseases involving TDP-43 pathology and provides a basis for further research into the mechanisms underlying ALS/FTD.