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Gomes FA, Souza Junior DR, Massafera MP, Ronsein GE. Robust assessment of sample preparation protocols for proteomics of cells and tissues. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141030. [PMID: 38944097 DOI: 10.1016/j.bbapap.2024.141030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
In proteomic studies, the reliability and reproducibility of results hinge on well-executed protein extraction and digestion protocols. Here, we systematically compared three established digestion methods for macrophages, namely filter-assisted sample preparation (FASP), in-solution, and in-gel digestion protocols. We also compared lyophilization and manual lysis for liver tissue protein extraction, each of them tested using either sodium deoxycholate (SDC)- or RIPA-based lysis buffer. For the macrophage cell line, FASP using passivated filter units outperformed the other tested methods regarding the number of identified peptides and proteins. However, a careful standardization has shown that all three methods can yield robust results across a wide range of starting material (even starting with 1 μg of proteins). Importantly, inter and intra-day coefficients of variance (CVs) were determined for all sample preparation protocols. Thus, the median inter-day CVs for in-solution, in-gel and FASP protocols were respectively 10, 8 and 9%, very similar to the median CVs obtained for the intra-day analysis (9, 8 and 8%, respectively). Moreover, FASP digestion presented 80% of proteins with a CV lower than 25%, followed closely by in-gel digestion (78%) and in-solution sample preparation (72%) protocols. For tissue proteomics, both manual lysis and lyophilization presented similar proteome coverage and reproducibility, but the efficiency of protein extraction depended on the lysis buffer used, with RIPA buffer showing better results. In conclusion, although each sample preparation method has its own particularity, they are all suited for successful proteomic experiments if a careful standardization of the sample preparation workflow is carried out.
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Affiliation(s)
- Francielle Aguiar Gomes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | | | - Graziella Eliza Ronsein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
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2
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Influence of different sample preparation strategies on hypothesis-driven shotgun proteomic analysis of human saliva. OPEN CHEM 2022. [DOI: 10.1515/chem-2022-0216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
This research aimed to find an efficient and repeatable bottom-up proteolytic strategy to process the unstimulated human saliva. The focus is on monitoring immune system activation via the cytokine and interleukin signaling pathways. Carbohydrate metabolism is also being studied as a possible trigger of inflammation and joint damage in the context of the diagnostic procedure of temporomandibular joint disorder. The preparation of clean peptide mixtures for liquid chromatography–mass spectrometry analysis was performed considering different aspects of sample preparation: the filter-aided sample preparation (FASP) with different loadings of salivary proteins, the unfractionated saliva, amylase-depleted, and amylase-enriched salivary fractions. To optimize the efficiency of the FASP method, the protocols with the digestion in the presence of 80% acetonitrile and one-step digestion in the presence of 80% acetonitrile were used, omitting protein reduction and alkylation. The digestion procedures were repeated in the standard in-solution mode. Alternatively, the temperature of 24 and 37°C was examined during the trypsin digestion. DyNet analysis of the hierarchical networks of Gene Ontology terms corresponding to each sample preparation method for the bottom-up assay revealed the wide variability in protein properties. The method can easily be tailored to the specific samples and groups of proteins to be examined.
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3
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Loroch S, Kopczynski D, Schneider AC, Schumbrutzki C, Feldmann I, Panagiotidis E, Reinders Y, Sakson R, Solari FA, Vening A, Swieringa F, Heemskerk JWM, Grandoch M, Dandekar T, Sickmann A. Toward Zero Variance in Proteomics Sample Preparation: Positive-Pressure FASP in 96-Well Format (PF96) Enables Highly Reproducible, Time- and Cost-Efficient Analysis of Sample Cohorts. J Proteome Res 2022; 21:1181-1188. [PMID: 35316605 PMCID: PMC8981309 DOI: 10.1021/acs.jproteome.1c00706] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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As novel liquid chromatography–mass
spectrometry (LC-MS)
technologies for proteomics offer a substantial increase in LC-MS
runs per day, robust and reproducible sample preparation emerges as
a new bottleneck for throughput. We introduce a novel strategy for
positive-pressure 96-well filter-aided sample preparation (PF96) on
a commercial positive-pressure solid-phase extraction device. PF96
allows for a five-fold increase in throughput in conjunction with
extraordinary reproducibility with Pearson product-moment correlations
on the protein level of r = 0.9993, as demonstrated
for mouse heart tissue lysate in 40 technical replicates. The targeted
quantification of 16 peptides in the presence of stable-isotope-labeled
reference peptides confirms that PF96 variance is barely assessable
against technical variation from nanoLC-MS instrumentation. We further
demonstrate that protein loads of 36–60 μg result in
optimal peptide recovery, but lower amounts ≥3 μg can
also be processed reproducibly. In summary, the reproducibility, simplicity,
and economy of time provide PF96 a promising future in biomedical
and clinical research.
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Affiliation(s)
- Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Adriana C Schneider
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany.,Faculty of Biochemical and Chemical Engineering, Technical University of Dortmund, 44227 Dortmund, Germany
| | - Cornelia Schumbrutzki
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Ingo Feldmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | | | - Yvonne Reinders
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Roman Sakson
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Alicia Vening
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Frauke Swieringa
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Johan W M Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Maria Grandoch
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany.,Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, AB24 3FX Aberdeen, United Kingdom
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Sandbaumhüter FA, Nezhyva M, Eriksson O, Engberg A, Kreuger J, Andrén PE, Jansson ET. Well-Plate μFASP for Proteomic Analysis of Single Pancreatic Islets. J Proteome Res 2022; 21:1167-1174. [PMID: 35293755 PMCID: PMC8981318 DOI: 10.1021/acs.jproteome.2c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Filter-aided sample preparation (FASP) is widely used in bottom-up proteomics for tryptic digestion. However, the sample recovery yield of this method is limited by the amount of the starting material. While ∼100 ng of digested protein is sufficient for thorough protein identification, proteomic information gets lost with a protein content <10 μg due to incomplete peptide recovery from the filter. We developed and optimized a flexible well-plate μFASP device and protocol that is suitable for an ∼1 μg protein sample. In 1 μg of HeLa digest, we identified 1295 ± 10 proteins with μFASP followed by analysis with liquid chromatography-mass spectrometry. In contrast, only 524 ± 5 proteins were identified with the standard FASP protocol, while 1395 ± 4 proteins were identified in 20 μg after standard FASP as a benchmark. Furthermore, we conducted a combined peptidomic and proteomic study of single pancreatic islets with well-plate μFASP. Here, we separated neuropeptides and digested the remaining on-filter proteins for bottom-up proteomic analysis. Our results indicate inter-islet heterogeneity for the expression of proteins involved in glucose catabolism, pancreatic hormone processing, and secreted peptide hormones. We consider our method to provide a useful tool for proteomic characterization of samples where the biological material is scarce. All proteomic data are available under DOI: 10.6019/PXD029039.
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Affiliation(s)
| | - Mariya Nezhyva
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
| | - Olle Eriksson
- Department of Medical Cell Biology, Uppsala University, Uppsala 751 23, Sweden
| | - Adam Engberg
- Department of Medical Cell Biology, Uppsala University, Uppsala 751 23, Sweden
| | - Johan Kreuger
- Department of Medical Cell Biology, Uppsala University, Uppsala 751 23, Sweden
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden.,Science for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala 751 24, Sweden
| | - Erik T Jansson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
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Araújo MJ, Sousa ML, Felpeto AB, Turkina MV, Fonseca E, Martins JC, Vasconcelos V, Campos A. Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species. Proteomes 2021; 9:proteomes9040046. [PMID: 34842808 PMCID: PMC8628934 DOI: 10.3390/proteomes9040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/07/2023] Open
Abstract
Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC–MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).
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Affiliation(s)
- Mário Jorge Araújo
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria Lígia Sousa
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Aldo Barreiro Felpeto
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden;
| | - Elza Fonseca
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - José Carlos Martins
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Vítor Vasconcelos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Alexandre Campos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Correspondence:
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