Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells
The identification of small proteins and proteins produced from unannotated open reading frames (called alternative proteins or AltProts) has changed our vision of the proteome and has attracted more and more attention from the scientific community. Despite several studies investigating particular A...
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2024-11-01
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| author | Clémence Guillon Carole Pichereaux Ikrame Lazar Karima Chaoui Emmanuelle Mouton-Barbosa Mehdi Liauzun Edith Gourbeyre Pinar Altiner David Bouyssié Alexandre Stella Odile Burlet-Schiltz Serge Plaza Yvan Martineau Bertrand Fabre |
| author_facet | Clémence Guillon Carole Pichereaux Ikrame Lazar Karima Chaoui Emmanuelle Mouton-Barbosa Mehdi Liauzun Edith Gourbeyre Pinar Altiner David Bouyssié Alexandre Stella Odile Burlet-Schiltz Serge Plaza Yvan Martineau Bertrand Fabre |
| author_sort | Clémence Guillon |
| collection | DOAJ |
| description | The identification of small proteins and proteins produced from unannotated open reading frames (called alternative proteins or AltProts) has changed our vision of the proteome and has attracted more and more attention from the scientific community. Despite several studies investigating particular AltProts in diseases and demonstrating their importance in such context, we are still missing data on their expression and functions in many pathologies. Among these, pancreatic ductal adenocarcinoma (PDAC) is a particularly relevant case to study alternative proteins. Indeed, late detection of this disease, notably due to the lack of reliable biomarkers of early-stage PDAC, and the fact that tumors rapidly develop resistance to most of the treatments used in the clinics warrant the exploration of new repertoires of molecules. In the present article, we aim to investigate the alternative proteome of pancreatic cancer cell lines as a first attempt to decipher the expression of AltProts in PDAC. Thanks to a combined data-dependent and data-independent acquisition mass spectrometry workflow, we were able to identify tryptic peptides matching 113 AltProts in a panel of 6 cell lines. In addition, we identified AltProts differentially expressed between pancreatic cancer cell lines and other cells (HeLa and HEK293T). Finally, mining the TCGA and Gtex databases showed that the corresponding transcripts encoding several AltProts we identified are differentially expressed between PDAC tumors and normal tissues and are correlated with the patient’s survival. |
| format | Article |
| id | doaj-art-e6b0dd9b8b7d47b6a03124e57c0cdb72 |
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| issn | 2073-4409 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj-art-e6b0dd9b8b7d47b6a03124e57c0cdb722025-08-20T02:38:41ZengMDPI AGCells2073-44092024-11-011323196610.3390/cells13231966Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer CellsClémence Guillon0Carole Pichereaux1Ikrame Lazar2Karima Chaoui3Emmanuelle Mouton-Barbosa4Mehdi Liauzun5Edith Gourbeyre6Pinar Altiner7David Bouyssié8Alexandre Stella9Odile Burlet-Schiltz10Serge Plaza11Yvan Martineau12Bertrand Fabre13Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceMCD, Centre de Biologie Intégrative (CBI), CNRS, UT3, Université de Toulouse, 31400 Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceCentre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III-Paul Sabatier, ERL5294 CNRS, 31432 Toulouse, FranceMCD, Centre de Biologie Intégrative (CBI), CNRS, UT3, Université de Toulouse, 31400 Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, FranceLaboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, FranceCentre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III-Paul Sabatier, ERL5294 CNRS, 31432 Toulouse, FranceLaboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, FranceThe identification of small proteins and proteins produced from unannotated open reading frames (called alternative proteins or AltProts) has changed our vision of the proteome and has attracted more and more attention from the scientific community. Despite several studies investigating particular AltProts in diseases and demonstrating their importance in such context, we are still missing data on their expression and functions in many pathologies. Among these, pancreatic ductal adenocarcinoma (PDAC) is a particularly relevant case to study alternative proteins. Indeed, late detection of this disease, notably due to the lack of reliable biomarkers of early-stage PDAC, and the fact that tumors rapidly develop resistance to most of the treatments used in the clinics warrant the exploration of new repertoires of molecules. In the present article, we aim to investigate the alternative proteome of pancreatic cancer cell lines as a first attempt to decipher the expression of AltProts in PDAC. Thanks to a combined data-dependent and data-independent acquisition mass spectrometry workflow, we were able to identify tryptic peptides matching 113 AltProts in a panel of 6 cell lines. In addition, we identified AltProts differentially expressed between pancreatic cancer cell lines and other cells (HeLa and HEK293T). Finally, mining the TCGA and Gtex databases showed that the corresponding transcripts encoding several AltProts we identified are differentially expressed between PDAC tumors and normal tissues and are correlated with the patient’s survival.https://www.mdpi.com/2073-4409/13/23/1966alternative proteinsmicroproteinsproteomicsshort open reading frame-encoded peptidespancreatic ductal adenocarcinomadata independent acquisition |
| spellingShingle | Clémence Guillon Carole Pichereaux Ikrame Lazar Karima Chaoui Emmanuelle Mouton-Barbosa Mehdi Liauzun Edith Gourbeyre Pinar Altiner David Bouyssié Alexandre Stella Odile Burlet-Schiltz Serge Plaza Yvan Martineau Bertrand Fabre Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells Cells alternative proteins microproteins proteomics short open reading frame-encoded peptides pancreatic ductal adenocarcinoma data independent acquisition |
| title | Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells |
| title_full | Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells |
| title_fullStr | Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells |
| title_full_unstemmed | Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells |
| title_short | Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells |
| title_sort | mass spectrometry based workflow for the identification and quantification of alternative and canonical proteins in pancreatic cancer cells |
| topic | alternative proteins microproteins proteomics short open reading frame-encoded peptides pancreatic ductal adenocarcinoma data independent acquisition |
| url | https://www.mdpi.com/2073-4409/13/23/1966 |
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