1
|
Pérez Compte D, Etourneau L, Hesse AM, Kraut A, Barthelon J, Sturm N, Borges H, Biennier S, Courçon M, de Saint Loup M, Mignot V, Costentin C, Burger T, Couté Y, Bruley C, Decaens T, Jaquinod M, Boursier J, Brun V. Plasma ALS and Gal-3BP differentiate early from advanced liver fibrosis in MASLD patients. Biomark Res 2024; 12:44. [PMID: 38679739 PMCID: PMC11057169 DOI: 10.1186/s40364-024-00583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/19/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND Metabolic dysfunction-associated steatotic liver disease (MASLD) is estimated to affect 30% of the world's population, and its prevalence is increasing in line with obesity. Liver fibrosis is closely related to mortality, making it the most important clinical parameter for MASLD. It is currently assessed by liver biopsy - an invasive procedure that has some limitations. There is thus an urgent need for a reliable non-invasive means to diagnose earlier MASLD stages. METHODS A discovery study was performed on 158 plasma samples from histologically-characterised MASLD patients using mass spectrometry (MS)-based quantitative proteomics. Differentially abundant proteins were selected for verification by ELISA in the same cohort. They were subsequently validated in an independent MASLD cohort (n = 200). RESULTS From the 72 proteins differentially abundant between patients with early (F0-2) and advanced fibrosis (F3-4), we selected Insulin-like growth factor-binding protein complex acid labile subunit (ALS) and Galectin-3-binding protein (Gal-3BP) for further study. In our validation cohort, AUROCs with 95% CIs of 0.744 [0.673 - 0.816] and 0.735 [0.661 - 0.81] were obtained for ALS and Gal-3BP, respectively. Combining ALS and Gal-3BP improved the assessment of advanced liver fibrosis, giving an AUROC of 0.796 [0.731. 0.862]. The {ALS; Gal-3BP} model surpassed classic fibrosis panels in predicting advanced liver fibrosis. CONCLUSIONS Further investigations with complementary cohorts will be needed to confirm the usefulness of ALS and Gal-3BP individually and in combination with other biomarkers for diagnosis of liver fibrosis. With the availability of ELISA assays, these findings could be rapidly clinically translated, providing direct benefits for patients.
Collapse
Affiliation(s)
- David Pérez Compte
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Lucas Etourneau
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
- Université Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Anne-Marie Hesse
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Alexandra Kraut
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Justine Barthelon
- Université Grenoble Alpes, Clinique Universitaire d'Hépato-Gastroentérologie, CHU Grenoble Alpes, 38000, Grenoble, France
| | - Nathalie Sturm
- Université Grenoble Alpes, Clinique Universitaire d'Hépato-Gastroentérologie, CHU Grenoble Alpes, 38000, Grenoble, France
| | - Hélène Borges
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Salomé Biennier
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Marie Courçon
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Marc de Saint Loup
- Hepato-Gastroenterology Department, University Hospital, Angers, France
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Victoria Mignot
- Université Grenoble Alpes, Clinique Universitaire d'Hépato-Gastroentérologie, CHU Grenoble Alpes, 38000, Grenoble, France
- Univ. Grenoble Alpes, Institute for Advanced Biosciences-INSERM U1209/ CNRS UMR 5309, Grenoble, France
| | - Charlotte Costentin
- Université Grenoble Alpes, Clinique Universitaire d'Hépato-Gastroentérologie, CHU Grenoble Alpes, 38000, Grenoble, France
- Univ. Grenoble Alpes, Institute for Advanced Biosciences-INSERM U1209/ CNRS UMR 5309, Grenoble, France
| | - Thomas Burger
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France
| | - Thomas Decaens
- Université Grenoble Alpes, Clinique Universitaire d'Hépato-Gastroentérologie, CHU Grenoble Alpes, 38000, Grenoble, France
- Univ. Grenoble Alpes, Institute for Advanced Biosciences-INSERM U1209/ CNRS UMR 5309, Grenoble, France
| | - Michel Jaquinod
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France.
| | - Jérôme Boursier
- Hepato-Gastroenterology Department, University Hospital, Angers, France
- HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France
| | - Virginie Brun
- Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, FR2048 ProFI, EDyP team, 17 Avenue des Martyrs, 38000, Grenoble, France.
- Univ. Grenoble Alpes, CEA, Leti, 38000, Grenoble, France.
| |
Collapse
|
2
|
Antunes AV, Shahinas M, Swale C, Farhat DC, Ramakrishnan C, Bruley C, Cannella D, Robert MG, Corrao C, Couté Y, Hehl AB, Bougdour A, Coppens I, Hakimi MA. In vitro production of cat-restricted Toxoplasma pre-sexual stages. Nature 2024; 625:366-376. [PMID: 38093015 PMCID: PMC10781626 DOI: 10.1038/s41586-023-06821-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/01/2023] [Indexed: 12/26/2023]
Abstract
Sexual reproduction of Toxoplasma gondii, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described1,2. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. 1), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on Toxoplasma sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.
Collapse
Affiliation(s)
- Ana Vera Antunes
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Martina Shahinas
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Christopher Swale
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Dayana C Farhat
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | | | - Christophe Bruley
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, Grenoble, France
| | - Dominique Cannella
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Marie G Robert
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Charlotte Corrao
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, UA13 BGE, CNRS, CEA, Grenoble, France
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health and Malaria Research Institute, Baltimore, MD, USA
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France.
| |
Collapse
|
3
|
Antunes AV, Shahinas M, Swale C, Farhat DC, Ramakrishnan C, Bruley C, Cannella D, Corrao C, Cout Y, Hehl AB, Bougdour A, Coppens I, Hakimi MA. In vitro production of cat-restricted Toxoplasma pre-sexual stages by epigenetic reprogramming. bioRxiv 2023:2023.01.16.524187. [PMID: 36711883 PMCID: PMC9882236 DOI: 10.1101/2023.01.16.524187] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sexual reproduction of Toxoplasma gondii , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described 1 . In this study, we found that transcription factors AP2XII-1 and AP2XI-2, expressed in tachyzoite stage that causes acute toxoplasmosis, can silence genes necessary for merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced in vitro under these conditions are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3 1 , which in turn restrict the accessibility of chromatin to the transcriptional machinery. Thus, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. This effective in vitro culture of merozoites paves the way to explore Toxoplasma sexual reproduction without the need to infect kittens and has potential for the development of therapeutics to block parasite transmission.
Collapse
|
4
|
Dupierris V, Hesse AM, Menetrey JP, Bouyssié D, Burger T, Couté Y, Bruley C. Validation of MS/MS Identifications and Label-Free Quantification Using Proline. Methods Mol Biol 2023; 2426:67-89. [PMID: 36308685 DOI: 10.1007/978-1-0716-1967-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the proteomics field, the production and publication of reliable mass spectrometry (MS)-based label-free quantitative results is a major concern. Due to the intrinsic complexity of bottom-up proteomics experiments (requiring aggregation of data relating to both precursor and fragment peptide ions into protein information, and matching this data across samples), inaccuracies and errors can occur throughout the data-processing pipeline. In a classical label-free quantification workflow, the validation of identification results is critical since errors made at this first stage of the workflow may have an impact on the following steps and therefore on the final result. Although false discovery rate (FDR) of the identification is usually controlled by using the popular target-decoy method, it has been demonstrated that this method can sometimes lead to inaccurate FDR estimates. This protocol shows how Proline can be used to validate identification results by using the method based on the Benjamini-Hochberg procedure and then quantify the identified ions and proteins in a single software environment providing data curation capabilities and computational efficiency.
Collapse
Affiliation(s)
- Véronique Dupierris
- Université Grenoble Alpes, CEA, INSERM, BioSanté U1292, CNRS, ProFI FR2048, Grenoble, France
| | - Anne-Marie Hesse
- Université Grenoble Alpes, CEA, INSERM, BioSanté U1292, CNRS, ProFI FR2048, Grenoble, France
| | | | - David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thomas Burger
- Université Grenoble Alpes, CNRS, CEA, INSERM, ProFI FR 2048, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, BioSanté U1292, CNRS, ProFI FR2048, Grenoble, France
| | - Christophe Bruley
- Université Grenoble Alpes, CEA, INSERM, BioSanté U1292, CNRS, ProFI FR2048, Grenoble, France.
| |
Collapse
|
5
|
Pailleux F, Maes P, Jaquinod M, Barthelon J, Darnaud M, Lacoste C, Vandenbrouck Y, Gilquin B, Louwagie M, Hesse AM, Kraut A, Garin J, Leroy V, Zarski JP, Bruley C, Couté Y, Samuel D, Ichai P, Faivre J, Brun V. Mass Spectrometry-Based Proteomics Reveal Alcohol Dehydrogenase 1B as a Blood Biomarker Candidate to Monitor Acetaminophen-Induced Liver Injury. Int J Mol Sci 2021; 22:ijms222011071. [PMID: 34681731 PMCID: PMC8540689 DOI: 10.3390/ijms222011071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022] Open
Abstract
Acute liver injury (ALI) is a severe disorder resulting from excessive hepatocyte cell death, and frequently caused by acetaminophen intoxication. Clinical management of ALI progression is hampered by the dearth of blood biomarkers available. In this study, a bioinformatics workflow was developed to screen omics databases and identify potential biomarkers for hepatocyte cell death. Then, discovery proteomics was harnessed to select from among these candidates those that were specifically detected in the blood of acetaminophen-induced ALI patients. Among these candidates, the isoenzyme alcohol dehydrogenase 1B (ADH1B) was massively leaked into the blood. To evaluate ADH1B, we developed a targeted proteomics assay and quantified ADH1B in serum samples collected at different times from 17 patients admitted for acetaminophen-induced ALI. Serum ADH1B concentrations increased markedly during the acute phase of the disease, and dropped to undetectable levels during recovery. In contrast to alanine aminotransferase activity, the rapid drop in circulating ADH1B concentrations was followed by an improvement in the international normalized ratio (INR) within 10–48 h, and was associated with favorable outcomes. In conclusion, the combination of omics data exploration and proteomics revealed ADH1B as a new blood biomarker candidate that could be useful for the monitoring of acetaminophen-induced ALI.
Collapse
Affiliation(s)
- Floriane Pailleux
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Pauline Maes
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Michel Jaquinod
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Justine Barthelon
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
- Clinique Universitaire d’Hépato-gastroentérologie, Centre Hospitalier Universitaire Grenoble, 38000 Grenoble, France; (V.L.); (J.-P.Z.)
| | - Marion Darnaud
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Claire Lacoste
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Benoît Gilquin
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
- Univ. Grenoble Alpes, CEA, LETI, Clinatec, 38000 Grenoble, France
| | - Mathilde Louwagie
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Anne-Marie Hesse
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Alexandra Kraut
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Jérôme Garin
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Vincent Leroy
- Clinique Universitaire d’Hépato-gastroentérologie, Centre Hospitalier Universitaire Grenoble, 38000 Grenoble, France; (V.L.); (J.-P.Z.)
- Institute for Advanced Biosciences, Université Grenoble Alpes, CNRS, INSERM U1209, 38000 Grenoble, France
| | - Jean-Pierre Zarski
- Clinique Universitaire d’Hépato-gastroentérologie, Centre Hospitalier Universitaire Grenoble, 38000 Grenoble, France; (V.L.); (J.-P.Z.)
- Institute for Advanced Biosciences, Université Grenoble Alpes, CNRS, INSERM U1209, 38000 Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Didier Samuel
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Philippe Ichai
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Jamila Faivre
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Pôle de Biologie Médicale, Paul-Brousse University Hospital, 94800 Villejuif, France
- Correspondence: (J.F.); (V.B.)
| | - Virginie Brun
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
- Univ. Grenoble Alpes, CEA, LETI, Clinatec, 38000 Grenoble, France
- Correspondence: (J.F.); (V.B.)
| |
Collapse
|
6
|
Trauchessec M, Hesse AM, Kraut A, Berard Y, Herment L, Fortin T, Bruley C, Ferro M, Manin C. An innovative standard for LC-MS-based HCP profiling and accurate quantity assessment: Application to batch consistency in viral vaccine samples. Proteomics 2021; 21:e2000152. [PMID: 33459490 DOI: 10.1002/pmic.202000152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/10/2020] [Accepted: 12/18/2020] [Indexed: 11/05/2022]
Abstract
Biotherapeutics, molecules produced from biological systems, require rigorous purification steps to remove impurities including host cell proteins (HCPs). Regulatory guidelines require manufacturers to monitor process-related impurities along the purification workflow. Mass spectrometry (MS) has recently been considered as a complementary method to the well-established ELISA for HCPs quantification, since it has the advantage of unambiguously identifying individual HCP. In this study, we developed an innovative standard dedicated to MS-based HCP profiling analysis in order to monitor the consistency of viral vaccine intermediate purification samples. This standard, termed the HCP-PROFILER standard, is composed of a water-soluble bead (READYBEADS technology) which, after being added into the sample, releases unlabeled peptides in controlled amounts. The standard meets three desired criteria: (1) it is composed of multiple peptides, at different concentration levels, allowing construction of a calibration curve covering the dynamic range of HCPs present in the target sample, ensuring quantification accuracy; (2) it demonstrates high batch-to-batch reproducibility, ensuring quantification robustness and consistency over time; and (3) it is easy to use and avoids user-induced analytical biases. In this study, we present the use of the HCP-PROFILER standard for vaccine batches comparison and downstream process performance studies.
Collapse
Affiliation(s)
- Mathieu Trauchessec
- ANAQUANT, Villeurbanne, France.,CEA, 17 av. des Martyrs, Grenoble, 38000, France
| | | | | | | | | | | | | | - Myriam Ferro
- CEA, 17 av. des Martyrs, Grenoble, 38000, France
| | | |
Collapse
|
7
|
Bouyssié D, Hesse AM, Mouton-Barbosa E, Rompais M, Macron C, Carapito C, Gonzalez de Peredo A, Couté Y, Dupierris V, Burel A, Menetrey JP, Kalaitzakis A, Poisat J, Romdhani A, Burlet-Schiltz O, Cianférani S, Garin J, Bruley C. Proline: an efficient and user-friendly software suite for large-scale proteomics. Bioinformatics 2020; 36:3148-3155. [PMID: 32096818 PMCID: PMC7214047 DOI: 10.1093/bioinformatics/btaa118] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/10/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022] Open
Abstract
Motivation The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study. Results Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline’s ability to provide high quantification accuracy in a user-friendly interface for datasets of any size. Availability and implementation Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client–server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne-Marie Hesse
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Charlotte Macron
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yohann Couté
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | | | - Alexandre Burel
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | | | - Andrea Kalaitzakis
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | - Julie Poisat
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Aymen Romdhani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Jerome Garin
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | - Christophe Bruley
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| |
Collapse
|
8
|
Couté Y, Bruley C, Burger T. Beyond Target-Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics. Anal Chem 2020; 92:14898-14906. [PMID: 32970414 DOI: 10.1021/acs.analchem.0c00328] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In bottom-up discovery proteomics, target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control. Despite unquestionable statistical foundations, this method has drawbacks, including its hitherto unknown intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinterpreted. This article provides evidence that TDC has become less reliable as the accuracy of modern mass spectrometers improved. We therefore propose to replace TDC by a totally different method to control the FDR at the spectrum, peptide, and protein levels, while benefiting from the theoretical guarantees of the Benjamini-Hochberg framework. As this method is simpler to use, faster to compute, and more stable than TDC, we argue that it is better adapted to the standardization and throughput constraints of current proteomic platforms.
Collapse
Affiliation(s)
- Yohann Couté
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Thomas Burger
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| |
Collapse
|
9
|
Crespo M, Damont A, Blanco M, Lastrucci E, Kennani SE, Ialy-Radio C, Khattabi LE, Terrier S, Louwagie M, Kieffer-Jaquinod S, Hesse AM, Bruley C, Chantalat S, Govin J, Fenaille F, Battail C, Cocquet J, Pflieger D. Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes. Nucleic Acids Res 2020; 48:4115-4138. [PMID: 32182340 PMCID: PMC7192594 DOI: 10.1093/nar/gkaa163] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/30/2020] [Accepted: 03/07/2020] [Indexed: 12/17/2022] Open
Abstract
Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. We investigated the dynamics of lysine acetylation and crotonylation on histones H3 and H4 during mouse spermatogenesis. Lysine crotonylation appeared to be of significant abundance compared to acetylation, particularly on Lys27 of histone H3 (H3K27cr) that accumulates in sperm in a cleaved form of H3. We identified the genomic localization of H3K27cr and studied its effects on transcription compared to the classical active mark H3K27ac at promoters and distal enhancers. The presence of both marks was strongly associated with highest gene expression. Assessment of their co-localization with transcription regulators (SLY, SOX30) and chromatin-binding proteins (BRD4, BRDT, BORIS and CTCF) indicated systematic highest binding when both active marks were present and different selective binding when present alone at chromatin. H3K27cr and H3K27ac finally mark the building of some sperm super-enhancers. This integrated analysis of omics data provides an unprecedented level of understanding of gene expression regulation by H3K27cr in comparison to H3K27ac, and reveals both synergistic and specific actions of each histone modification.
Collapse
Affiliation(s)
- Marion Crespo
- Univ. Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France
| | - Annelaure Damont
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Melina Blanco
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, 75014 Paris, France
| | | | - Sara El Kennani
- Univ. Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France.,CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, 38000 Grenoble, France
| | - Côme Ialy-Radio
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, 75014 Paris, France
| | - Laila El Khattabi
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, 75014 Paris, France
| | - Samuel Terrier
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, 91191 Gif-sur-Yvette, France
| | | | | | - Anne-Marie Hesse
- Univ. Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France
| | | | - Sophie Chantalat
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 2 rue Gaston Crémieux, CP 5706, 91057 Evry Cedex, France
| | - Jérôme Govin
- Univ. Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France.,CNRS UMR 5309, Inserm U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, 38000 Grenoble, France
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, 91191 Gif-sur-Yvette, France
| | - Christophe Battail
- Univ. Grenoble Alpes, CEA, INSERM, Biosciences and Biotechnology Institute of Grenoble, Biology of Cancer and Infection UMR_S 1036, 38000 Grenoble, France
| | - Julie Cocquet
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, 75014 Paris, France
| | - Delphine Pflieger
- Univ. Grenoble Alpes, CEA, Inserm, IRIG-BGE, 38000 Grenoble, France.,CNRS, IRIG-BGE, 38000 Grenoble, France
| |
Collapse
|
10
|
Couté Y, Kraut A, Zimmermann C, Büscher N, Hesse AM, Bruley C, De Andrea M, Wangen C, Hahn F, Marschall M, Plachter B. Mass Spectrometry-Based Characterization of the Virion Proteome, Phosphoproteome, and Associated Kinase Activity of Human Cytomegalovirus. Microorganisms 2020; 8:microorganisms8060820. [PMID: 32486127 PMCID: PMC7357008 DOI: 10.3390/microorganisms8060820] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
The assembly of human cytomegalovirus (HCMV) virions is an orchestrated process that requires, as an essential prerequisite, the complex crosstalk between viral structural proteins. Currently, however, the mechanisms governing the successive steps in the constitution of virion protein complexes remain elusive. Protein phosphorylation is a key regulator determining the sequential changes in the conformation, binding, dynamics, and stability of proteins in the course of multiprotein assembly. In this review, we present a comprehensive map of the HCMV virion proteome, including a refined view on the virion phosphoproteome, based on previous publications supplemented by new results. Thus, a novel dataset of viral and cellular proteins contained in HCMV virions is generated, providing a basis for future analyses of individual phosphorylation steps and sites involved in the orchestrated assembly of HCMV virion-specific multiprotein complexes. Finally, we present the current knowledge on the activity of pUL97, the HCMV-encoded and virion-associated kinase, in phosphorylating viral and host proteins.
Collapse
Affiliation(s)
- Yohann Couté
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France; (A.K.); (A.-M.H.); (C.B.)
- Correspondence: (Y.C.); (B.P.); Tel.: +33-4-38789461 (Y.C.); +49-6131-179232 (B.P.)
| | - Alexandra Kraut
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France; (A.K.); (A.-M.H.); (C.B.)
| | - Christine Zimmermann
- Institute for Virology and Forschungszentrum für Immuntherapie, University Medical Center of the Johannes Gutenberg-University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany; (C.Z.); (N.B.)
| | - Nicole Büscher
- Institute for Virology and Forschungszentrum für Immuntherapie, University Medical Center of the Johannes Gutenberg-University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany; (C.Z.); (N.B.)
| | - Anne-Marie Hesse
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France; (A.K.); (A.-M.H.); (C.B.)
| | - Christophe Bruley
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France; (A.K.); (A.-M.H.); (C.B.)
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, Turin Medical School, University of Turin, 10126 Turin, and CAAD – Center for Translational Research on Autoimmune and Allergic Disease, Novara Medical School, 28100 Novara, Italy;
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (F.H.); (M.M.)
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (F.H.); (M.M.)
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (F.H.); (M.M.)
| | - Bodo Plachter
- Institute for Virology and Forschungszentrum für Immuntherapie, University Medical Center of the Johannes Gutenberg-University Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany; (C.Z.); (N.B.)
- Correspondence: (Y.C.); (B.P.); Tel.: +33-4-38789461 (Y.C.); +49-6131-179232 (B.P.)
| |
Collapse
|
11
|
Salvi D, Bournais S, Moyet L, Bouchnak I, Kuntz M, Bruley C, Rolland N. AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins. Methods Mol Biol 2019; 1829:395-406. [PMID: 29987736 DOI: 10.1007/978-1-4939-8654-5_26] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO ( http://at-chloro.prabi.fr/at_chloro/ ) is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins.
Collapse
Affiliation(s)
- Daniel Salvi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Sylvain Bournais
- Laboratoire de Biologie à Grande Echelle, Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Santé et de la Recherche Médicale, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Imen Bouchnak
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Christophe Bruley
- Laboratoire de Biologie à Grande Echelle, Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Santé et de la Recherche Médicale, Grenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France.
| |
Collapse
|
12
|
Kraut A, Louwagie M, Bruley C, Masselon C, Couté Y, Brun V, Hesse AM. Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry. Methods Mol Biol 2019; 1959:129-150. [PMID: 30852820 DOI: 10.1007/978-1-4939-9164-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In discovery proteomics experiments, tandem mass spectrometry and data-dependent acquisition (DDA) are classically used to identify and quantify peptides and proteins through database searching. This strategy suffers from known limitations such as under-sampling and lack of reproducibility of precursor ion selection in complex proteomics samples, leading to somewhat inconsistent analytical results across large datasets. Data-independent acquisition (DIA) based on fragmentation of all the precursors detected in predetermined isolation windows can potentially overcome this limitation. DIA promises reproducible peptide and protein quantification with deeper proteome coverage and fewer missing values than DDA strategies. This approach is particularly attractive in the field of clinical biomarker discovery, where large numbers of samples must be analyzed. Here, we describe a DIA workflow for non-depleted serum analysis including a straightforward approach through which to construct a dedicated spectral library, and indications on how to optimize chromatographic and mass spectrometry analytical methods to produce high-quality DIA data and results.
Collapse
Affiliation(s)
- Alexandra Kraut
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France
| | | | | | | | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France
| | - Anne-Marie Hesse
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France.
| |
Collapse
|
13
|
Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V. Proteomic characterization of human exhaled breath condensate. J Breath Res 2018; 12:021001. [PMID: 29189203 DOI: 10.1088/1752-7163/aa9e71] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To improve biomedical knowledge and to support biomarker discovery studies, it is essential to establish comprehensive proteome maps for human tissues and biofluids, and to make them publicly accessible. In this study, we performed an in-depth proteomics characterization of exhaled breath condensate (EBC), a sample obtained non-invasively by condensation of exhaled air that contains submicron droplets of airway lining fluid. Two pooled samples of EBC, each obtained from 10 healthy donors, were processed using a straightforward protocol based on sample lyophilization, in-gel digestion and liquid chromatography tandem-mass spectrometry analysis. Two 'technical' control samples were processed in parallel to the pooled samples to correct for exogenous protein contamination. A total of 229 unique proteins were identified in EBC among which 153 proteins were detected in both EBC pooled samples. A detailed bioinformatics analysis of these 153 proteins showed that most of the proteins identified corresponded to proteins secreted in the respiratory tract (lung, bronchi). Eight proteins were salivary proteins. Our dataset is described and has been made accessible through the ProteomeXchange database (dataset identifier: PXD007591) and is expected to be useful for future MS-based biomarker studies using EBC as the diagnostic specimen.
Collapse
Affiliation(s)
- Maud Lacombe
- Université Grenoble-Alpes, F-38000, Grenoble, France. CEA, BIG, Biologie à Grande Echelle, F-38054, Grenoble, France. Inserm, Unité 1038, F-38054, Grenoble, France
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Giai Gianetto Q, Couté Y, Bruley C, Burger T. Uses and misuses of the fudge factor in quantitative discovery proteomics. Proteomics 2017; 16:1955-60. [PMID: 27272648 DOI: 10.1002/pmic.201600132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/02/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
Selecting proteins with significant differential abundance is the cornerstone of many relative quantitative proteomics experiments. To do so, a trade-off between p-value thresholding and fold-change thresholding can be performed because of a specific parameter, named fudge factor, and classically noted s0 . We have observed that this fudge factor is routinely turned away from its original (and statistically valid) use, leading to important distortion in the distribution of p-values, jeopardizing the protein differential analysis, as well as the subsequent biological conclusion. In this article, we provide a comprehensive viewpoint on this issue, as well as some guidelines to circumvent it.
Collapse
Affiliation(s)
| | - Yohann Couté
- BIG-BGE (Université Grenoble-Alpes, CNRS, CEA, INSERM), Grenoble, France
| | - Christophe Bruley
- BIG-BGE (Université Grenoble-Alpes, CNRS, CEA, INSERM), Grenoble, France
| | - Thomas Burger
- BIG-BGE (Université Grenoble-Alpes, CNRS, CEA, INSERM), Grenoble, France
| |
Collapse
|
15
|
Gloaguen P, Bournais S, Alban C, Ravanel S, Seigneurin-Berny D, Matringe M, Tardif M, Kuntz M, Ferro M, Bruley C, Rolland N, Vandenbrouck Y, Curien G. ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. Plant Physiol 2017; 174:922-934. [PMID: 28442501 PMCID: PMC5462031 DOI: 10.1104/pp.17.00242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/24/2017] [Indexed: 05/07/2023]
Abstract
Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (stoichiometry matrices) and pathway databases are extremely useful, they cannot describe the complexity of the metabolic context, and new tools are required to visually represent integrated biocurated knowledge for use by both humans and computers. Here, we describe ChloroKB, a Web application (http://chlorokb.fr/) for visual exploration and analysis of the Arabidopsis (Arabidopsis thaliana) metabolic network in the chloroplast and related cellular pathways. The network was manually reconstructed through extensive biocuration to provide transparent traceability of experimental data. Proteins and metabolites were placed in their biological context (spatial distribution within cells, connectivity in the network, participation in supramolecular complexes, and regulatory interactions) using CellDesigner software. The network contains 1,147 reviewed proteins (559 localized exclusively in plastids, 68 in at least one additional compartment, and 520 outside the plastid), 122 proteins awaiting biochemical/genetic characterization, and 228 proteins for which genes have not yet been identified. The visual presentation is intuitive and browsing is fluid, providing instant access to the graphical representation of integrated processes and to a wealth of refined qualitative and quantitative data. ChloroKB will be a significant support for structural and quantitative kinetic modeling, for biological reasoning, when comparing novel data with established knowledge, for computer analyses, and for educational purposes. ChloroKB will be enhanced by continuous updates following contributions from plant researchers.
Collapse
Affiliation(s)
- Pauline Gloaguen
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Sylvain Bournais
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Claude Alban
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Stéphane Ravanel
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Daphné Seigneurin-Berny
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Michel Matringe
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Marianne Tardif
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Marcel Kuntz
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Myriam Ferro
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Christophe Bruley
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Norbert Rolland
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Yves Vandenbrouck
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| | - Gilles Curien
- Laboratoire de Biologie à Grande Echelle (BGE), CEA, INSERM, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (P.G., S.B., M.T., M.F., C.B, Y.V.); Laboratoire de Physiologie Cellulaire et Végétale (LPCV), CNRS, CEA, INRA, BIG, Université Grenoble-Alpes, 38000, Grenoble, France (C.A., S.R., D.S.-B., M.M., M.K., N.R., G.C.)
| |
Collapse
|
16
|
El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics Chromatin 2017; 10:2. [PMID: 28096900 PMCID: PMC5223428 DOI: 10.1186/s13072-016-0109-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. RESULTS We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. CONCLUSIONS Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.
Collapse
Affiliation(s)
- Sara El Kennani
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Annie Adrait
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Saadi Khochbin
- CNRS UMR 5309 INSERM U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Christophe Bruley
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Delphine Pflieger
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Jérôme Govin
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| |
Collapse
|
17
|
Giai Gianetto Q, Combes F, Ramus C, Bruley C, Couté Y, Burger T. Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics 2016; 16:29-32. [PMID: 26572953 DOI: 10.1002/pmic.201500189] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 10/14/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022]
Abstract
In MS-based quantitative proteomics, the FDR control (i.e. the limitation of the number of proteins that are wrongly claimed as differentially abundant between several conditions) is a major postanalysis step. It is classically achieved thanks to a specific statistical procedure that computes the adjusted p-values of the putative differentially abundant proteins. Unfortunately, such adjustment is conservative only if the p-values are well-calibrated; the false discovery control being spuriously underestimated otherwise. However, well-calibration is a property that can be violated in some practical cases. To overcome this limitation, we propose a graphical method to straightforwardly and visually assess the p-value well-calibration, as well as the R codes to embed it in any pipeline. All MS data have been deposited in the ProteomeXchange with identifier PXD002370 (http://proteomecentral.proteomexchange.org/dataset/PXD002370).
Collapse
Affiliation(s)
- Quentin Giai Gianetto
- Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.,CEA, iRTSV-BGE, Grenoble, France.,INSERM, BGE, Grenoble, France
| | - Florence Combes
- Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.,CEA, iRTSV-BGE, Grenoble, France.,INSERM, BGE, Grenoble, France
| | - Claire Ramus
- Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.,CNRS, iRTSV-BGE, Grenoble, France.,CEA, iRTSV-BGE, Grenoble, France.,INSERM, BGE, Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.,CEA, iRTSV-BGE, Grenoble, France.,INSERM, BGE, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.,CEA, iRTSV-BGE, Grenoble, France.,INSERM, BGE, Grenoble, France
| | - Thomas Burger
- Univ. Grenoble Alpes, iRTSV-BGE, Grenoble, France.,CNRS, iRTSV-BGE, Grenoble, France.,CEA, iRTSV-BGE, Grenoble, France.,INSERM, BGE, Grenoble, France
| |
Collapse
|
18
|
Hesse AM, Dupierris V, Adam C, Court M, Barthe D, Emadali A, Masselon C, Ferro M, Bruley C. hEIDI: An Intuitive Application Tool To Organize and Treat Large-Scale Proteomics Data. J Proteome Res 2016; 15:3896-3903. [PMID: 27560970 DOI: 10.1021/acs.jproteome.5b00853] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Advances in high-throughput proteomics have led to a rapid increase in the number, size, and complexity of the associated data sets. Managing and extracting reliable information from such large series of data sets require the use of dedicated software organized in a consistent pipeline to reduce, validate, exploit, and ultimately export data. The compilation of multiple mass-spectrometry-based identification and quantification results obtained in the context of a large-scale project represents a real challenge for developers of bioinformatics solutions. In response to this challenge, we developed a dedicated software suite called hEIDI to manage and combine both identifications and semiquantitative data related to multiple LC-MS/MS analyses. This paper describes how, through a user-friendly interface, hEIDI can be used to compile analyses and retrieve lists of nonredundant protein groups. Moreover, hEIDI allows direct comparison of series of analyses, on the basis of protein groups, while ensuring consistent protein inference and also computing spectral counts. hEIDI ensures that validated results are compliant with MIAPE guidelines as all information related to samples and results is stored in appropriate databases. Thanks to the database structure, validated results generated within hEIDI can be easily exported in the PRIDE XML format for subsequent publication. hEIDI can be downloaded from http://biodev.extra.cea.fr/docs/heidi .
Collapse
Affiliation(s)
- Anne-Marie Hesse
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Véronique Dupierris
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Claire Adam
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Magali Court
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Damien Barthe
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Anouk Emadali
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Christophe Masselon
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Myriam Ferro
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, BIG-BGE, F-38000 Grenoble, France.,CEA, BIG-BGE, F-38000 Grenoble, France.,Inserm U1038, BGE, F-38000 Grenoble, France
| |
Collapse
|
19
|
Wieczorek S, Combes F, Lazar C, Giai Gianetto Q, Gatto L, Dorffer A, Hesse AM, Couté Y, Ferro M, Bruley C, Burger T. DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. Bioinformatics 2016; 33:135-136. [PMID: 27605098 PMCID: PMC5408771 DOI: 10.1093/bioinformatics/btw580] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 07/05/2016] [Accepted: 09/02/2016] [Indexed: 11/30/2022] Open
Abstract
Summary DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser. Availability and implementation DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages.
Collapse
Affiliation(s)
- Samuel Wieczorek
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Florence Combes
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Cosmin Lazar
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Quentin Giai Gianetto
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Laurent Gatto
- Computational Proteomics Unit, Cambridge, CB2 1GA, UK.,Cambridge Center for Proteomics, Cambridge, CB2 1GA, UK
| | - Alexia Dorffer
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Anne-Marie Hesse
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Yohann Couté
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Myriam Ferro
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Christophe Bruley
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France
| | - Thomas Burger
- Université Grenoble Alpes, BIG-BGE, Grenoble, 38000, France.,CEA, BIG-BGE, Grenoble, 38000, France.,INSERM, BGE, Grenoble, 38000, France.,CNRS, BIG-BGE, Grenoble, 38000, France
| |
Collapse
|
20
|
Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. J Proteome Res 2016; 15:3998-4019. [PMID: 27444420 DOI: 10.1021/acs.jproteome.6b00400] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome.
Collapse
Affiliation(s)
- Yves Vandenbrouck
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Lydie Lane
- Department of Human Protein Sciences, Faculty of Medicine, University of Geneva , 1, rue Michel-Servet, 1211 Geneva 4, Switzerland.,CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Paula Duek
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Karine Rondel
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Christophe Bruley
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Charlotte Macron
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Yohann Couté
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Karima Chaoui
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Emmanuelle Com
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Alain Gateau
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Anne-Marie Hesse
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Marlene Marcellin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Loren Méar
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Thibault Robin
- Proteome Informatics Group, Centre Universitaire d'Informatique , Route de Drize 7, 1227 Carouge, CH, Switzerland
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Myriam Ferro
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Thomas Fréour
- Service de Médecine de la Reproduction, CHU de Nantes , 38 boulevard Jean Monnet, 44093 Nantes cedex, France.,INSERM UMR1064 , Nantes 44093, France
| | - Cecilia Lindskog
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France
| | - Jérôme Garin
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Charles Pineau
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| |
Collapse
|
21
|
Lazar C, Gatto L, Ferro M, Bruley C, Burger T. Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies. J Proteome Res 2016; 15:1116-25. [DOI: 10.1021/acs.jproteome.5b00981] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Cosmin Lazar
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Laurent Gatto
- Computational Proteomics Unit, Cambridge CB2 1GA, United Kingdom
- Cambridge Center for Proteomics, Cambridge CB2 1GA, United Kingdom
| | - Myriam Ferro
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| | - Thomas Burger
- Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France
- CNRS, iRTSV-BGE, F-38000 Grenoble, France
- CEA, iRTSV-BGE, F-38000 Grenoble, France
- INSERM, BGE, F-38000 Grenoble, France
| |
Collapse
|
22
|
Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Van Dorssaeler A, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A. Benchmarking quantitative label-free LC–MS data processing workflows using a complex spiked proteomic standard dataset. J Proteomics 2016; 132:51-62. [DOI: 10.1016/j.jprot.2015.11.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/04/2015] [Accepted: 11/08/2015] [Indexed: 10/22/2022]
|
23
|
Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief 2015; 6:286-94. [PMID: 26862574 PMCID: PMC4706616 DOI: 10.1016/j.dib.2015.11.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 11/23/2015] [Indexed: 11/30/2022] Open
Abstract
This data article describes a controlled, spiked proteomic dataset for which the “ground truth” of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.
Collapse
Affiliation(s)
- Claire Ramus
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Agnès Hovasse
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Marlène Marcellin
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Anne-Marie Hesse
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Emmanuelle Mouton-Barbosa
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - David Bouyssié
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Sebastian Vaca
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Christine Carapito
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Karima Chaoui
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Christophe Bruley
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Jérôme Garin
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Sarah Cianférani
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Myriam Ferro
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Alain Van Dorssaeler
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Odile Burlet-Schiltz
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Christine Schaeffer
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Yohann Couté
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Anne Gonzalez de Peredo
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| |
Collapse
|
24
|
Carapito C, Lane L, Benama M, Opsomer A, Mouton-Barbosa E, Garrigues L, Gonzalez de Peredo A, Burel A, Bruley C, Gateau A, Bouyssié D, Jaquinod M, Cianferani S, Burlet-Schiltz O, Van Dorsselaer A, Garin J, Vandenbrouck Y. Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14. J Proteome Res 2015; 14:3621-34. [PMID: 26132440 DOI: 10.1021/pr5010345] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last 4 years, the French proteomics infrastructure has collected high-quality data sets from 40 human samples, including a series of rarely studied cell lines, tissue types, and sample preparations. Here we described a step-by-step strategy based on the use of bioinformatics screening and subsequent mass spectrometry (MS)-based validation to identify what were up to now missing proteins in these data sets. Screening database search results (85,326 dat files) identified 58 of the missing proteins (36 on chromosome 2 and 22 on chromosome 14) by 83 unique peptides following the latest release of neXtProt (2014-09-19). PSMs corresponding to these peptides were thoroughly examined by applying two different MS-based criteria: peptide-level false discovery rate calculation and expert PSM quality assessment. Synthetic peptides were then produced and used to generate reference MS/MS spectra. A spectral similarity score was then calculated for each pair of reference-endogenous spectra and used as a third criterion for missing protein validation. Finally, LC-SRM assays were developed to target proteotypic peptides from four of the missing proteins detected in tissue/cell samples, which were still available and for which sample preparation could be reproduced. These LC-SRM assays unambiguously detected the endogenous unique peptide for three of the proteins. For two of these, identification was confirmed by additional proteotypic peptides. We concluded that of the initial set of 58 proteins detected by the bioinformatics screen, the consecutive MS-based validation criteria led to propose the identification of 13 of these proteins (8 on chromosome 2 and 5 on chromosome 14) that passed at least two of the three MS-based criteria. Thus, a rigorous step-by-step approach combining bioinformatics screening and MS-based validation assays is particularly suitable to obtain protein-level evidence for proteins previously considered as missing. All MS/MS data have been deposited in ProteomeXchange under identifier PXD002131.
Collapse
Affiliation(s)
- Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178 , 25 Rue Becquerel, 67087 Strasbourg, France
| | - Lydie Lane
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland.,Department of Human Protein Sciences, Faculty of Medicine, rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Mohamed Benama
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble, F-38054, France.,INSERM U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université Grenoble , Grenoble F-38054, France
| | - Alisson Opsomer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178 , 25 Rue Becquerel, 67087 Strasbourg, France
| | - Emmanuelle Mouton-Barbosa
- CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 118 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse , 205, route de Narbonne, 31077 Toulouse, France
| | - Luc Garrigues
- CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 118 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse , 205, route de Narbonne, 31077 Toulouse, France
| | - Anne Gonzalez de Peredo
- CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 118 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse , 205, route de Narbonne, 31077 Toulouse, France
| | - Alexandre Burel
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178 , 25 Rue Becquerel, 67087 Strasbourg, France
| | - Christophe Bruley
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble, F-38054, France.,INSERM U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université Grenoble , Grenoble F-38054, France
| | - Alain Gateau
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland.,Department of Human Protein Sciences, Faculty of Medicine, rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - David Bouyssié
- CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 118 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse , 205, route de Narbonne, 31077 Toulouse, France
| | - Michel Jaquinod
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble, F-38054, France.,INSERM U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université Grenoble , Grenoble F-38054, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178 , 25 Rue Becquerel, 67087 Strasbourg, France
| | - Odile Burlet-Schiltz
- CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 118 route de Narbonne, 31077 Toulouse, France.,Université de Toulouse , 205, route de Narbonne, 31077 Toulouse, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178 , 25 Rue Becquerel, 67087 Strasbourg, France
| | - Jérôme Garin
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble, F-38054, France.,INSERM U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université Grenoble , Grenoble F-38054, France
| | - Yves Vandenbrouck
- CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble, F-38054, France.,INSERM U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université Grenoble , Grenoble F-38054, France
| |
Collapse
|
25
|
Trauchessec M, Jaquinod M, Bonvalot A, Brun V, Bruley C, Ropers D, de Jong H, Garin J, Bestel-Corre G, Ferro M. Mass spectrometry-based workflow for accurate quantification of Escherichia coli enzymes: how proteomics can play a key role in metabolic engineering. Mol Cell Proteomics 2014; 13:954-68. [PMID: 24482123 DOI: 10.1074/mcp.m113.032672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metabolic engineering aims to design high performance microbial strains producing compounds of interest. This requires systems-level understanding; genome-scale models have therefore been developed to predict metabolic fluxes. However, multi-omics data including genomics, transcriptomics, fluxomics, and proteomics may be required to model the metabolism of potential cell factories. Recent technological advances to quantitative proteomics have made mass spectrometry-based quantitative assays an interesting alternative to more traditional immuno-affinity based approaches. This has improved specificity and multiplexing capabilities. In this study, we developed a quantification workflow to analyze enzymes involved in central metabolism in Escherichia coli (E. coli). This workflow combined full-length isotopically labeled standards with selected reaction monitoring analysis. First, full-length (15)N labeled standards were produced and calibrated to ensure accurate measurements. Liquid chromatography conditions were then optimized for reproducibility and multiplexing capabilities over a single 30-min liquid chromatography-MS analysis. This workflow was used to accurately quantify 22 enzymes involved in E. coli central metabolism in a wild-type reference strain and two derived strains, optimized for higher NADPH production. In combination with measurements of metabolic fluxes, proteomics data can be used to assess different levels of regulation, in particular enzyme abundance and catalytic rate. This provides information that can be used to design specific strains used in biotechnology. In addition, accurate measurement of absolute enzyme concentrations is key to the development of predictive kinetic models in the context of metabolic engineering.
Collapse
Affiliation(s)
- Mathieu Trauchessec
- Commisariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologie et Sciences pour le Vivant (iRTSV), Biologie à Grande Echelle, F-38054 Grenoble, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 2013; 341:281-6. [PMID: 23869018 DOI: 10.1126/science.1239181] [Citation(s) in RCA: 379] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study.
Collapse
Affiliation(s)
- Nadège Philippe
- Structural and Genomic Information Laboratory, UMR 7256 CNRS Aix-Marseille Université, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Emadali A, Rousseaux S, Bruder-Costa J, Rome C, Duley S, Hamaidia S, Betton P, Debernardi A, Leroux D, Bernay B, Kieffer-Jaquinod S, Combes F, Ferri E, McKenna CE, Petosa C, Bruley C, Garin J, Ferro M, Gressin R, Callanan MB, Khochbin S. Identification of a novel BET bromodomain inhibitor-sensitive, gene regulatory circuit that controls Rituximab response and tumour growth in aggressive lymphoid cancers. EMBO Mol Med 2013; 5:1180-95. [PMID: 23828858 PMCID: PMC3944460 DOI: 10.1002/emmm.201202034] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 12/13/2022] Open
Abstract
Immuno-chemotherapy elicit high response rates in B-cell non-Hodgkin lymphoma but heterogeneity in response duration is observed, with some patients achieving cure and others showing refractory disease or relapse. Using a transcriptome-powered targeted proteomics screen, we discovered a gene regulatory circuit involving the nuclear factor CYCLON which characterizes aggressive disease and resistance to the anti-CD20 monoclonal antibody, Rituximab, in high-risk B-cell lymphoma. CYCLON knockdown was found to inhibit the aggressivity of MYC-overexpressing tumours in mice and to modulate gene expression programs of biological relevance to lymphoma. Furthermore, CYCLON knockdown increased the sensitivity of human lymphoma B cells to Rituximab in vitro and in vivo. Strikingly, this effect could be mimicked by in vitro treatment of lymphoma B cells with a small molecule inhibitor for BET bromodomain proteins (JQ1). In summary, this work has identified CYCLON as a new MYC cooperating factor that autonomously drives aggressive tumour growth and Rituximab resistance in lymphoma. This resistance mechanism is amenable to next-generation epigenetic therapy by BET bromodomain inhibition, thereby providing a new combination therapy rationale for high-risk lymphoma. The nuclear factor CYCLON is a new MYC cooperating factor that drives tumor growth and Rituximab resistance in lymphoma. This resistance mechanism can be targeted by next-generation epigenetic therapy by BET bromodomain inhibition downstream of MYC.
Collapse
Affiliation(s)
- Anouk Emadali
- CEA, iRTSV, Biologie à Grande Echelle, Grenoble, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Chapel A, Kieffer-Jaquinod S, Sagné C, Verdon Q, Ivaldi C, Mellal M, Thirion J, Jadot M, Bruley C, Garin J, Gasnier B, Journet A. An extended proteome map of the lysosomal membrane reveals novel potential transporters. Mol Cell Proteomics 2013; 12:1572-88. [PMID: 23436907 PMCID: PMC3675815 DOI: 10.1074/mcp.m112.021980] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 02/01/2013] [Indexed: 12/22/2022] Open
Abstract
Lysosomes are membrane-bound endocytic organelles that play a major role in degrading cell macromolecules and recycling their building blocks. A comprehensive knowledge of the lysosome function requires an extensive description of its content, an issue partially addressed by previous proteomic analyses. However, the proteins underlying many lysosomal membrane functions, including numerous membrane transporters, remain unidentified. We performed a comparative, semi-quantitative proteomic analysis of rat liver lysosome-enriched and lysosome-nonenriched membranes and used spectral counts to evaluate the relative abundance of proteins. Among a total of 2,385 identified proteins, 734 proteins were significantly enriched in the lysosomal fraction, including 207 proteins already known or predicted as endo-lysosomal and 94 proteins without any known or predicted subcellular localization. The remaining 433 proteins had been previously assigned to other subcellular compartments but may in fact reside on lysosomes either predominantly or as a secondary location. Many membrane-associated complexes implicated in diverse processes such as degradation, membrane trafficking, lysosome biogenesis, lysosome acidification, signaling, and nutrient sensing were enriched in the lysosomal fraction. They were identified to an unprecedented extent as most, if not all, of their subunits were found and retained by our screen. Numerous transporters were also identified, including 46 novel potentially lysosomal proteins. We expressed 12 candidates in HeLa cells and observed that most of them colocalized with the lysosomal marker LAMP1, thus confirming their lysosomal residency. This list of candidate lysosomal proteins substantially increases our knowledge of the lysosomal membrane and provides a basis for further characterization of lysosomal functions.
Collapse
Affiliation(s)
- Agnès Chapel
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Sylvie Kieffer-Jaquinod
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Corinne Sagné
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Quentin Verdon
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
- §§Graduate School ED 419, Université Paris-Sud 11, Hôpital Bicêtre, F-94276 Le Kremlin Bicêtre France, and
| | - Corinne Ivaldi
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Mourad Mellal
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jaqueline Thirion
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Michel Jadot
- the **Unité de Recherche en Physiologie Moléculaire, Namur Research Institute for Life Sciences, University of Namur (FUNDP), 61, Rue de Bruxelles B,-5000, Namur, Belgium
| | - Christophe Bruley
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jérôme Garin
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Bruno Gasnier
- the ‖Université Paris Descartes, Sorbonne Paris Cité, CNRS, UMR 8192, Centre Universitaire des Saints-Pères, 45 Rue des Saints-Pères, F-75006 Paris, France
| | - Agnès Journet
- From the ‡Commissariat à l'Energie Atomique, Institut de Recherches en Technologies et Sciences du Vivant, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France
- §INSERM, U1038, F-38054 Grenoble, France
- the ¶Université Joseph Fourier, Grenoble 1, F-38000, France
| |
Collapse
|
29
|
Zaccaria A, Bouamrani A, Selek L, El Atifi M, Hesse AM, Juhem A, Ratel D, Mathieu H, Coute Y, Bruley C, Garin J, Benabid AL, Chabardes S, Piallat B, Berger F. A micro-silicon chip for in vivo cerebral imprint in monkey. ACS Chem Neurosci 2013; 4:385-92. [PMID: 23509975 DOI: 10.1021/cn300116g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Access to cerebral tissue is essential to better understand the molecular mechanisms associated with neurodegenerative diseases. In this study, we present, for the first time, a new tool designed to obtain molecular and cellular cerebral imprints in the striatum of anesthetized monkeys. The imprint is obtained during a spatially controlled interaction of a chemically modified micro-silicon chip with the brain tissue. Scanning electron and immunofluorescence microscopies showed homogeneous capture of cerebral tissue. Nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) analysis of proteins harvested on the chip allowed the identification of 1158 different species of proteins. The gene expression profiles of mRNA extracted from the imprint tool showed great similarity to those obtained via the gold standard approach, which is based on post-mortem sections of the same nucleus. Functional analysis of the harvested molecules confirmed the spatially controlled capture of striatal proteins implicated in dopaminergic regulation. Finally, the behavioral monitoring and histological results establish the safety of obtaining repeated cerebral imprints in striatal regions. These results demonstrate the ability of our imprint tool to explore the molecular content of deep brain regions in vivo. They open the way to the molecular exploration of brain in animal models of neurological diseases and will provide complementary information to current data mainly restricted to post-mortem samples.
Collapse
Affiliation(s)
- Affif Zaccaria
- Institut des Neurosciences Team 7 Brain Nanomedicine, INSERM U836, UJF, CHU, Grenoble, France
| | | | - Laurent Selek
- Institut des Neurosciences Team 7 Brain Nanomedicine, INSERM U836, UJF, CHU, Grenoble, France
- Department of Neurosurgery, Centre Hospitalier Universitaire, Grenoble, France
| | - Michelle El Atifi
- Institut des Neurosciences Team 7 Brain Nanomedicine, INSERM U836, UJF, CHU, Grenoble, France
| | - Anne Marie Hesse
- Biologie à Grande Echelle, IRTSV, CEA, Grenoble, France, and INSERM, U1038, Grenoble, France
| | - Aurélie Juhem
- Ecrins therapeutics, BIOPOLIS, 38700 La Tronche, France
| | | | - Herve Mathieu
- Institut des Neurosciences Team 5 Functional and Metabolic Neuroimaging, INSERM U836, UJF, CHU, Grenoble, France
| | - Yohann Coute
- Biologie à Grande Echelle, IRTSV, CEA, Grenoble, France, and INSERM, U1038, Grenoble, France
| | - Christophe Bruley
- Biologie à Grande Echelle, IRTSV, CEA, Grenoble, France, and INSERM, U1038, Grenoble, France
| | - Jerome Garin
- Biologie à Grande Echelle, IRTSV, CEA, Grenoble, France, and INSERM, U1038, Grenoble, France
| | | | - Stephan Chabardes
- Institut des Neurosciences Team 11 Brain Function and Modulation, INSERM U836, UJF, CHU, Grenoble, France
- Department of Neurosurgery, Centre Hospitalier Universitaire, Grenoble, France
| | - Brigitte Piallat
- Institut des Neurosciences Team 11 Brain Function and Modulation, INSERM U836, UJF, CHU, Grenoble, France
| | - François Berger
- Institut des Neurosciences Team 7 Brain Nanomedicine, INSERM U836, UJF, CHU, Grenoble, France
- Clinatec, CEA-LETI, Grenoble, France
| |
Collapse
|
30
|
Picard G, Lebert D, Louwagie M, Adrait A, Huillet C, Vandenesch F, Bruley C, Garin J, Jaquinod M, Brun V. PSAQ™ standards for accurate MS-based quantification of proteins: from the concept to biomedical applications. J Mass Spectrom 2012; 47:1353-63. [PMID: 23019168 DOI: 10.1002/jms.3106] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Absolute protein quantification, i.e. determining protein concentrations in biological samples, is essential to our understanding of biological and physiopathological phenomena. Protein quantification methods based on the use of antibodies are very effective and widely used. However, over the last ten years, absolute protein quantification by mass spectrometry has attracted considerable interest, particularly for the study of systems biology and as part of biomarker development. This interest is mainly linked to the high multiplexing capacity of MS analysis, and to the availability of stable-isotope-labelled standards for quantification. This article describes the details of how to produce, control the quality and use a specific type of standard: Protein Standard Absolute Quantification (PSAQ™) standards. These standards are whole isotopically labelled proteins, analogues of the proteins to be assayed. PSAQ standards can be added early during sample treatment, thus they can correct for protein losses during sample prefractionation and for incomplete sample digestion. Because of this, quantification of target proteins is very accurate and precise using these standards. To illustrate the advantages of the PSAQ method, and to contribute to the increase in its use, selected applications in the biomedical field are detailed here.
Collapse
Affiliation(s)
- Guillaume Picard
- CEA, IRTSV, Biologie à Grande Echelle, F-38054, Grenoble, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugière S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O, Cournac L. PredAlgo: a new subcellular localization prediction tool dedicated to green algae. Mol Biol Evol 2012; 29:3625-39. [PMID: 22826458 DOI: 10.1093/molbev/mss178] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a prime model for deciphering processes occurring in the intracellular compartments of the photosynthetic cell. Organelle-specific proteomic studies have started to delineate its various subproteomes, but sequence-based prediction software is necessary to assign proteins subcellular localizations at whole genome scale. Unfortunately, existing tools are oriented toward land plants and tend to mispredict the localization of nuclear-encoded algal proteins, predicting many chloroplast proteins as mitochondrion targeted. We thus developed a new tool called PredAlgo that predicts intracellular localization of those proteins to one of three intracellular compartments in green algae: the mitochondrion, the chloroplast, and the secretory pathway. At its core, a neural network, trained using carefully curated sets of C. reinhardtii proteins, divides the N-terminal sequence into overlapping 19-residue windows and scores the probability that they belong to a cleavable targeting sequence for one of the aforementioned organelles. A targeting prediction is then deduced for the protein, and a likely cleavage site is predicted based on the shape of the scoring function along the N-terminal sequence. When assessed on an independent benchmarking set of C. reinhardtii sequences, PredAlgo showed a highly improved discrimination capacity between chloroplast- and mitochondrion-localized proteins. Its predictions matched well the results of chloroplast proteomics studies. When tested on other green algae, it gave good results with Chlorophyceae and Trebouxiophyceae but tended to underpredict mitochondrial proteins in Prasinophyceae. Approximately 18% of the nuclear-encoded C. reinhardtii proteome was predicted to be targeted to the chloroplast and 15% to the mitochondrion.
Collapse
|
32
|
Louwagie M, Kieffer-Jaquinod S, Dupierris V, Couté Y, Bruley C, Garin J, Dupuis A, Jaquinod M, Brun V. Introducing AAA-MS, a Rapid and Sensitive Method for Amino Acid Analysis Using Isotope Dilution and High-Resolution Mass Spectrometry. J Proteome Res 2012; 11:3929-36. [DOI: 10.1021/pr3003326] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mathilde Louwagie
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Sylvie Kieffer-Jaquinod
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Véronique Dupierris
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Yohann Couté
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Christophe Bruley
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Jérôme Garin
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Alain Dupuis
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Michel Jaquinod
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| | - Virginie Brun
- CEA, IRTSV, Biologie à Grande Echelle,
F-38054 Grenoble, France
- INSERM, U1038, F-38054 Grenoble, France
- Université Joseph Fourier, Grenoble 1, F-38000, France
| |
Collapse
|
33
|
Adrait A, Lebert D, Trauchessec M, Dupuis A, Louwagie M, Masselon C, Jaquinod M, Chevalier B, Vandenesch F, Garin J, Bruley C, Brun V. Development of a Protein Standard Absolute Quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum. J Proteomics 2012; 75:3041-9. [DOI: 10.1016/j.jprot.2011.11.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 11/23/2011] [Accepted: 11/26/2011] [Indexed: 10/14/2022]
|
34
|
Jaquinod M, Trauchessec M, Huillet C, Louwagie M, Lebert D, Picard G, Adrait A, Dupuis A, Garin J, Brun V, Bruley C. Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of “noncanonical” proteotypic peptides. Proteomics 2012; 12:1217-21. [DOI: 10.1002/pmic.201100538] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Michel Jaquinod
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Mathieu Trauchessec
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Céline Huillet
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Mathilde Louwagie
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Dorothée Lebert
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
- Promise Advanced Proteomics; Grenoble France
| | - Guillaume Picard
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
- Promise Advanced Proteomics; Grenoble France
| | - Annie Adrait
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Alain Dupuis
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Jérôme Garin
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Virginie Brun
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| | - Christophe Bruley
- CEA; IRTSV; Biologie à Grande Echelle; Grenoble France
- INSERM; U1038 Grenoble France
- Université Joseph Fourier; Grenoble France
| |
Collapse
|
35
|
Bruley C, Dupierris V, Salvi D, Rolland N, Ferro M. AT_CHLORO: A Chloroplast Protein Database Dedicated to Sub-Plastidial Localization. Front Plant Sci 2012; 3:205. [PMID: 22973284 PMCID: PMC3438710 DOI: 10.3389/fpls.2012.00205] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/14/2012] [Indexed: 05/20/2023]
Abstract
AT_CHLORO (www.grenoble.prabi.fr/at_chloro) is a database dedicated to sub-plastidial localization of A. thaliana chloroplast proteins. This information was infered from proteomics experiments obtained from a comprehensive study that allowed the identification of proteins from envelope, stroma, and thylakoid sub-compartments Ferro et al., 2010. In addition to current knowledge regarding sub-plastidial localization, AT_CHLORO provides experimental data that allowed curated information regarding subcellular localizations of chloroplast proteins to be given. A specific focus was given to proteins that were identified in envelope fractions and for which expert functional annotation was provided. The present mini review shows the specificities of AT_CHLORO with respect to available information, data export options and recent improvements in data representation.
Collapse
Affiliation(s)
- Christophe Bruley
- CEA, DSV, IRTSV, Laboratoire Biologie à Grande Echelle, Institut de Recherches en Technologie et Sciences pour le VivantGrenoble, France
- INSERM, U1038Grenoble, France
- Université Joseph Fourier, Grenoble 1Grenoble, France
| | - Véronique Dupierris
- CEA, DSV, IRTSV, Laboratoire Biologie à Grande Echelle, Institut de Recherches en Technologie et Sciences pour le VivantGrenoble, France
- INSERM, U1038Grenoble, France
- Université Joseph Fourier, Grenoble 1Grenoble, France
| | - Daniel Salvi
- Université Joseph Fourier, Grenoble 1Grenoble, France
- CEA, DSV, IRTSV, Laboratoire de Physiologie Cellulaire et VégétaleGrenoble, France
- CNRS, UMR5168Grenoble, France
- INRA, USC1359Grenoble, France
| | - Norbert Rolland
- Université Joseph Fourier, Grenoble 1Grenoble, France
- CEA, DSV, IRTSV, Laboratoire de Physiologie Cellulaire et VégétaleGrenoble, France
- CNRS, UMR5168Grenoble, France
- INRA, USC1359Grenoble, France
- *Correspondence: Norbert Rolland, Laboratoire de Physiologie Cellulaire et Végétale, Institut de Recherches en Technologies et Sciences pour le Vivant, CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France. e-mail:
| | - Myriam Ferro
- CEA, DSV, IRTSV, Laboratoire Biologie à Grande Echelle, Institut de Recherches en Technologie et Sciences pour le VivantGrenoble, France
- INSERM, U1038Grenoble, France
- Université Joseph Fourier, Grenoble 1Grenoble, France
| |
Collapse
|
36
|
Journet A, Klein G, Brugière S, Vandenbrouck Y, Chapel A, Kieffer S, Bruley C, Masselon C, Aubry L. Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry. Proteomics 2011; 12:241-5. [PMID: 22120990 DOI: 10.1002/pmic.201100313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/22/2011] [Accepted: 11/03/2011] [Indexed: 12/21/2022]
Abstract
The cellular slime mold Dictyostelium discoideum is a soil-living eukaryote, which feeds on microorganisms engulfed by phagocytosis. Axenic laboratory strains have been produced that are able to use liquid growth medium internalized by macropinocytosis as the source of food. To better define the macropinocytosis process, we established the inventory of proteins associated with this pathway using mass spectrometry-based proteomics. Using a magnetic purification procedure and high-performance LC-MS/MS proteome analysis, a list of 2108 non-redundant proteins was established, of which 24% featured membrane-spanning domains. Bioinformatics analyses indicated that the most abundant proteins were linked to signaling, vesicular trafficking and the cytoskeleton. The present repertoire validates our purification method and paves the way for a future proteomics approach to study the dynamics of macropinocytosis.
Collapse
Affiliation(s)
- Agnès Journet
- CEA, IRTSV, Laboratoire Biologie à Grande Echelle, Grenoble, France
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Huillet C, Adrait A, Lebert D, Picard G, Trauchessec M, Louwagie M, Dupuis A, Hittinger L, Ghaleh B, Le Corvoisier P, Jaquinod M, Garin J, Bruley C, Brun V. Accurate quantification of cardiovascular biomarkers in serum using Protein Standard Absolute Quantification (PSAQ™) and selected reaction monitoring. Mol Cell Proteomics 2011; 11:M111.008235. [PMID: 22080464 DOI: 10.1074/mcp.m111.008235] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Development of new biomarkers needs to be significantly accelerated to improve diagnostic, prognostic, and toxicity monitoring as well as therapeutic follow-up. Biomarker evaluation is the main bottleneck in this development process. Selected Reaction Monitoring (SRM) combined with stable isotope dilution has emerged as a promising option to speed this step, particularly because of its multiplexing capacities. However, analytical variabilities because of upstream sample handling or incomplete trypsin digestion still need to be resolved. In 2007, we developed the PSAQ™ method (Protein Standard Absolute Quantification), which uses full-length isotope-labeled protein standards to quantify target proteins. In the present study we used clinically validated cardiovascular biomarkers (LDH-B, CKMB, myoglobin, and troponin I) to demonstrate that the combination of PSAQ and SRM (PSAQ-SRM) allows highly accurate biomarker quantification in serum samples. A multiplex PSAQ-SRM assay was used to quantify these biomarkers in clinical samples from myocardial infarction patients. Good correlation between PSAQ-SRM and ELISA assay results was found and demonstrated the consistency between these analytical approaches. Thus, PSAQ-SRM has the capacity to improve both accuracy and reproducibility in protein analysis. This will be a major contribution to efficient biomarker development strategies.
Collapse
Affiliation(s)
- Céline Huillet
- CEA, IRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Nguyen HM, Baudet M, Cuiné S, Adriano JM, Barthe D, Billon E, Bruley C, Beisson F, Peltier G, Ferro M, Li-Beisson Y. Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: With focus on proteins involved in lipid metabolism. Proteomics 2011; 11:4266-73. [DOI: 10.1002/pmic.201100114] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/10/2011] [Accepted: 08/04/2011] [Indexed: 11/07/2022]
|
39
|
Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL. MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol 2011; 155:259-70. [PMID: 21075962 PMCID: PMC3075751 DOI: 10.1104/pp.110.168195] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 11/10/2010] [Indexed: 05/18/2023]
Abstract
Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level. Proteomics-based studies have also contributed to the ever-expanding array of data in modern biology, with many generating Web portals and online resources that contain incrementally expanding and updated information. Many of these resources reflect specialist research areas with significant and novel information that is not currently captured by centralized repositories. The Arabidopsis (Arabidopsis thaliana) community is well served by a number of online proteomics resources that hold an abundance of functional information. These sites can be difficult to locate among a multitude of online resources. Furthermore, they can be difficult to navigate in order to identify specific features of interest without significant technical knowledge. Recently, members of the Arabidopsis proteomics community involved in developing many of these resources decided to develop a summary aggregation portal that is capable of retrieving proteomics data from a series of online resources on the fly. The Web portal is known as the MASCP Gator and can be accessed at the following address: http://gator.masc-proteomics.org/. Significantly, proteomics data displayed at this site retrieve information from the data repositories upon each request. This means that information is always up to date and displays the latest data sets. The site also provides hyperlinks back to the source information hosted at each of the curated databases to facilitate more in-depth analysis of the primary data.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (H.J.J., J.L.H.); Department of Biology, Eidgenössisch Technische Hochschule Zurich, CH–8092 Zurich, Switzerland (M.H.-H., K.B., W.G.); Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.); Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (R.S., W.X.S.); Department of Plant Biology, Cornell University, Ithaca, New York 14853 (Q.S., K.J.v.W.); Molecular Systems Biology, University of Vienna, 1090 Vienna, Austria (V.E., S.W., W.W.); Institut National de la Santé et de la Recherche Médicale, Laboratoire d’Etude de la Dynamique des Protéomes, U880, F–38000 Grenoble, France (C.B.); Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F–38000 Grenoble, France (C.B., N.R.); Université Joseph Fourier, F–38000 Grenoble, France (C.B., N.R.); CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, F–38000 Grenoble, France (N.R.); INRA, UMR1200, F–38000 Grenoble, France (N.R.); RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Tsurumi-ku, Yokohama 230–0045, Japan (T.T., H.N.); The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A.M.J.); Division of Biology, University of California San Diego, La Jolla, California 92093 (S.P.B.); Centre of Excellence for Computational Systems Biology (I.C.) and Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (I.C., S.K.T., A.H.M.), University of Western Australia, Crawley 6009, Western Australia, Australia
| |
Collapse
|
40
|
Abstract
In the field of analytical chemistry, stable isotope dilution assays are extensively used in combination with liquid chromatography-mass spectrometry (LC-MS) to provide confident quantification results. Over the last decade, the principle of isotope dilution has been adopted by the proteomic community in order to accurately quantify proteins in biological samples. In these experiments, a protein's concentration is deduced from the ratio between the MS signal of a tryptic peptide and that of a stable isotope-labeled analog, which serves as an internal standard. The first isotope dilution standards introduced in proteomics were chemically synthesized peptides incorporating a stable isotope-tagged amino acid. These isotopically labeled peptide standards, which are currently widely used, are generally added to samples after protein isolation and digestion. Thus, if protein enrichment is necessary, they do not allow correction for protein losses that may occur during sample pre-fractionation, nor do they allow the tryptic digestion yield to be taken into account. To reduce these limitations we have developed the PSAQ (Protein Standard Absolute Quantification) strategy using full-length stable isotope-labeled proteins as quantification standards. These standards and the target proteins share identical biochemical properties. This allows standards to be spiked into samples at an early stage of the analytical process. Thanks to this possibility, the PSAQ method provides highly accurate quantification results, including for samples requiring extensive biochemical pre-fractionation. In this chapter, we describe the production of full-length stable isotope-labeled proteins (PSAQ standards) using cell-free expression devices. The purification and quality control of protein standards, crucial for good-quality and accurate measurements, are also detailed. Finally, application of the PSAQ method to a typical protein quantification assay is presented.
Collapse
Affiliation(s)
- Dorothée Lebert
- CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, Grenoble, France
| | | | | | | | | |
Collapse
|
41
|
Ferro M, Brugière S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, Kieffer-Jaquinod S, Bruley C, Garin J, Joyard J, Masselon C, Rolland N. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics 2010; 9:1063-84. [PMID: 20061580 DOI: 10.1074/mcp.m900325-mcp200] [Citation(s) in RCA: 356] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further validated as the compartmentation of well known pathways (for instance, photosynthesis and amino acid, fatty acid, or glycerolipid biosynthesis) within chloroplasts could be dissected. It also allowed revisiting the compartmentation of the chloroplast metabolism and functions.
Collapse
Affiliation(s)
- Myriam Ferro
- INSERM, Laboratoire d'Etude de Dynamique des Protéomes, U880, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Kraut A, Marcellin M, Adrait A, Kuhn L, Louwagie M, Kieffer-Jaquinod S, Lebert D, Masselon CD, Dupuis A, Bruley C, Jaquinod M, Garin J, Gallagher-Gambarelli M. Peptide Storage: Are You Getting the Best Return on Your Investment? Defining Optimal Storage Conditions for Proteomics Samples. J Proteome Res 2009; 8:3778-85. [DOI: 10.1021/pr900095u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandra Kraut
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Marlène Marcellin
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Annie Adrait
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Lauriane Kuhn
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Mathilde Louwagie
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Sylvie Kieffer-Jaquinod
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Dorothée Lebert
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Christophe D. Masselon
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Alain Dupuis
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Christophe Bruley
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Michel Jaquinod
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Jérôme Garin
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Maighread Gallagher-Gambarelli
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| |
Collapse
|
43
|
Dupierris V, Masselon C, Court M, Kieffer-Jaquinod S, Bruley C. A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. ACTA ACUST UNITED AC 2009; 25:1980-1. [PMID: 19420053 DOI: 10.1093/bioinformatics/btp301] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY The IRMa toolbox provides an interactive application to assist in the validation of Mascot search results. It allows automatic filtering of Mascot identification results as well as manual confirmation or rejection of individual PSM (a match between a fragmentation mass spectrum and a peptide). Dynamic grouping and coherence of information are maintained by the software in real time. Validated results can be exported under various forms, including an identification database (MSIdb). This allows biologists to compile search results from a whole study in a unique repository in order to provide a summarized view of their project. IRMa also features a fully automated version that can be used in a high-throughput pipeline. Given filter parameters, it can delete hits with no significant PSM, regroup hits identified by the same peptide(s) and export the result to the specified format without user intervention. AVAILABILITY http://biodev.extra.cea.fr/docs/irma (java 1.5 or higher needed).
Collapse
|
44
|
Ferro M, Tardif M, Reguer E, Cahuzac R, Bruley C, Vermat T, Nugues E, Vigouroux M, Vandenbrouck Y, Garin J, Viari A. PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J Proteome Res 2008; 7:1873-83. [PMID: 18348511 DOI: 10.1021/pr070415k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PepLine is a fully automated software which maps MS/MS fragmentation spectra of trypsic peptides to genomic DNA sequences. The approach is based on Peptide Sequence Tags (PSTs) obtained from partial interpretation of QTOF MS/MS spectra (first module). PSTs are then mapped on the six-frame translations of genomic sequences (second module) giving hits. Hits are then clustered to detect potential coding regions (third module). Our work aimed at optimizing the algorithms of each component to allow the whole pipeline to proceed in a fully automated manner using raw nucleic acid sequences (i.e., genomes that have not been "reduced" to a database of ORFs or putative exons sequences). The whole pipeline was tested on controlled MS/MS spectra sets from standard proteins and from Arabidopsis thaliana envelope chloroplast samples. Our results demonstrate that PepLine competed with protein database searching softwares and was fast enough to potentially tackle large data sets and/or high size genomes. We also illustrate the potential of this approach for the detection of the intron/exon structure of genes.
Collapse
Affiliation(s)
- Myriam Ferro
- CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, Grenoble, F-38054, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Marmagne A, Ferro M, Meinnel T, Bruley C, Kuhn L, Garin J, Barbier-Brygoo H, Ephritikhine G. A High Content in Lipid-modified Peripheral Proteins and Integral Receptor Kinases Features in the Arabidopsis Plasma Membrane Proteome. Mol Cell Proteomics 2007; 6:1980-96. [PMID: 17644812 DOI: 10.1074/mcp.m700099-mcp200] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proteomics of plasma membrane has brought to date only scarce and partial information on the actual protein repertoire. In this work, the plant plasma membrane proteome of Arabidopsis thaliana was investigated. A highly purified plasma membrane fraction was washed by NaCl and Na2CO3 salts, and the insoluble fractions were further analyzed by nano-LC-MS/MS. With 446 proteins identified, we hereby describe the largest plasma membrane proteome diversity reported so far. Half of the proteins were predicted to display transmembrane domains and/or to be anchored to the membrane, validating a posteriori the pertinence of the approach. A fine analysis highlighted two main specific and novel features. First, the main functional category is represented by a majority of as yet unreported signaling proteins, including 11% receptor-like kinases. Second, 16% of the identified proteins are predicted to be lipid-modified, specifically involving double lipid linkage through N-terminal myristoylation, S-palmitoylation, C-terminal prenylation, or glycosylphosphatidylinositol anchors. Thus, our approach led for the first time to the identification of a large number of peripheral proteins as part of the plasma membrane and allowed the functionality of the plasma membrane in the cell context to be reconsidered.
Collapse
Affiliation(s)
- Anne Marmagne
- Institut des Sciences du Végétal, CNRS-UPR 2355, Bât 22, avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J. A Proteomics Approach Highlights a Myriad of Transporters in the Arabidopsis thaliana Vacuolar Membrane. Plant Signal Behav 2007; 2:413-5. [PMID: 19704618 PMCID: PMC2634231 DOI: 10.4161/psb.2.5.4415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 05/10/2007] [Indexed: 05/09/2023]
Abstract
To better understand plant vacuolar functions and identify new transporters present on the tonoplast, a proteomic work was initiated on Arabidopsis thaliana. A procedure was developed to prepare highly purified vacuoles from protoplasts isolated from Arabidopsis cell cultures, and a proteomics approach was designed to identify the protein components present in both the membrane and soluble fractions of the vacuoles. This procedure allowed the identification of 650 proteins, 2/3 of which copurify with the hydrophobic membrane fraction and 1/3 with the soluble fraction. With regard to function, only 20% of the proteins identified were previously known to be associated with vacuolar activities.
Collapse
Affiliation(s)
- Michel Jaquinod
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Florent Villiers
- Laboratoire de Physiologie Cellulaire Végétale; Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Sylvie Kieffer-Jaquinod
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire Végétale; Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Christophe Bruley
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Jérôme Garin
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Jacques Bourguignon
- Laboratoire de Physiologie Cellulaire Végétale; Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| |
Collapse
|
47
|
Lanquar V, Kuhn L, Lelièvre F, Khafif M, Espagne C, Bruley C, Barbier-Brygoo H, Garin J, Thomine S. 15N-Metabolic labeling for comparative plasma membrane proteomics in Arabidopsis cells. Proteomics 2007; 7:750-4. [PMID: 17285564 DOI: 10.1002/pmic.200600791] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
An important goal for proteomic studies is the global comparison of proteomes from different genotypes, tissues, or physiological conditions. This has so far been mostly achieved by densitometric comparison of spot intensities after protein separation by 2-DE. However, the physicochemical properties of membrane proteins preclude the use of 2-DE. Here, we describe the use of in vivo labeling by the stable isotope 15N as an alternative approach for comparative membrane proteomic studies in plant cells. We confirm that 15N-metabolic labeling of proteins is possible and efficient in Arabidopsis suspension cells. Quantification of 14N versus 15N MS signals reflects the relative abundance of 14N and 15N proteins in the sample analyzed. We describe the use of 15N-metabolic labeling to perform a partial comparative analysis of Arabidopsis cells following cadmium exposure. By focusing our attention on plasma membrane proteins, we were able to confidently identify proteins showing up to 5-fold regulation compared to unexposed cells. This study provides a proof of principle that 15N-metabolic labeling is a useful technique for comparative membrane proteome studies.
Collapse
Affiliation(s)
- Viviane Lanquar
- Institut des Sciences du Végétal, CNRS, Gif-sur-Yvette, France
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J. A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture. Mol Cell Proteomics 2006; 6:394-412. [PMID: 17151019 PMCID: PMC2391258 DOI: 10.1074/mcp.m600250-mcp200] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
To better understand the mechanisms governing cellular traffic, storage of various metabolites, and their ultimate degradation, Arabidopsis thaliana vacuole proteomes were established. To this aim, a procedure was developed to prepare highly purified vacuoles from protoplasts isolated from Arabidopsis cell cultures using Ficoll density gradients. Based on the specific activity of the vacuolar marker alpha-mannosidase, the enrichment factor of the vacuoles was estimated at approximately 42-fold with an average yield of 2.1%. Absence of significant contamination by other cellular compartments was validated by Western blot using antibodies raised against specific markers of chloroplasts, mitochondria, plasma membrane, and endoplasmic reticulum. Based on these results, vacuole preparations showed the necessary degree of purity for proteomics study. Therefore, a proteomics approach was developed to identify the protein components present in both the membrane and soluble fractions of the Arabidopsis cell vacuoles. This approach includes the following: (i) a mild oxidation step leading to the transformation of cysteine residues into cysteic acid and methionine to methionine sulfoxide, (ii) an in-solution proteolytic digestion of very hydrophobic proteins, and (iii) a prefractionation of proteins by short migration by SDS-PAGE followed by analysis by liquid chromatography coupled to tandem mass spectrometry. This procedure allowed the identification of more than 650 proteins, two-thirds of which copurify with the membrane hydrophobic fraction and one-third of which copurifies with the soluble fraction. Among the 416 proteins identified from the membrane fraction, 195 were considered integral membrane proteins based on the presence of one or more predicted transmembrane domains, and 110 transporters and related proteins were identified (91 putative transporters and 19 proteins related to the V-ATPase pump). With regard to function, about 20% of the proteins identified were known previously to be associated with vacuolar activities. The proteins identified are involved in ion and metabolite transport (26%), stress response (9%), signal transduction (7%), and metabolism (6%) or have been described to be involved in typical vacuolar activities, such as protein and sugar hydrolysis. The subcellular localization of several putative vacuolar proteins was confirmed by transient expression of green fluorescent protein fusion constructs.
Collapse
Affiliation(s)
- Michel Jaquinod
- Développement de la protéomique comme outil d'investigation fonctionelle et d'annotation des génomes
INSERM : ERM0201CEA17, rue des Martyrs 38054 Grenoble Cedex,FR
- * Correspondence should be adressed to: Michel Jaquinod
| | - Florent Villiers
- LPCV, Laboratoire de physiologie cellulaire végétale
CNRS : UMR5168INRA : UR1200CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble Ibat. C2
17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
| | - Sylvie Kieffer-Jaquinod
- Développement de la protéomique comme outil d'investigation fonctionelle et d'annotation des génomes
INSERM : ERM0201CEA17, rue des Martyrs 38054 Grenoble Cedex,FR
| | - Véronique Hugouvieux
- LPCV, Laboratoire de physiologie cellulaire végétale
CNRS : UMR5168INRA : UR1200CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble Ibat. C2
17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
| | - Christophe Bruley
- Développement de la protéomique comme outil d'investigation fonctionelle et d'annotation des génomes
INSERM : ERM0201CEA17, rue des Martyrs 38054 Grenoble Cedex,FR
| | - Jérôme Garin
- Développement de la protéomique comme outil d'investigation fonctionelle et d'annotation des génomes
INSERM : ERM0201CEA17, rue des Martyrs 38054 Grenoble Cedex,FR
| | - Jacques Bourguignon
- LPCV, Laboratoire de physiologie cellulaire végétale
CNRS : UMR5168INRA : UR1200CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble Ibat. C2
17 Rue des martyrs
38054 GRENOBLE CEDEX 9,FR
- * Correspondence should be adressed to: Jacques Bourguignon
| |
Collapse
|
49
|
Hoeflich A, Nedbal S, Schmidt S, Elmlinger MW, Renne U, Blum WF, Bruley C, Bünger L, Wolf E. Growth Control In Vivo – Lessons From Growth Selected Mouse Lines. Exp Clin Endocrinol Diabetes 2004. [DOI: 10.1055/s-2004-819225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
50
|
Burt DW, Bruley C, Dunn IC, Jones CT, Ramage A, Law AS, Morrice DR, Paton IR, Smith J, Windsor D, Sazanov A, Fries R, Waddington D. The dynamics of chromosome evolution in birds and mammals. Nature 1999; 402:411-3. [PMID: 10586880 DOI: 10.1038/46555] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparative mapping, which compares the location of homologous genes in different species, is a powerful tool for studying genome evolution. Comparative maps suggest that rates of chromosomal change in mammals can vary from one to ten rearrangements per million years. On the basis of these rates we would expect 84 to 600 conserved segments in a chicken comparison with human or mouse. Here we build comparative maps between these species and estimate that numbers of conserved segments are in the lower part of this range. We conclude that the organization of the human genome is closer to that of the chicken than the mouse and by adding comparative mapping results from a range of vertebrates, we identify three possible phases of chromosome evolution. The relative stability of genomes such as those of the chicken and human will enable the reconstruction of maps of ancestral vertebrates.
Collapse
Affiliation(s)
- D W Burt
- Roslin Institute (Edinburgh), Roslin, Midlothian, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|