Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry-based proteomic profile of a Silvaner Franken wine

ABSTRACT: The proteomic profile of a Silvaner Franken wine is described here for the first time. Wine proteins were identified via mass spectrometry (MS)-based proteomics through in-solution and in-gel digestion methods to obtain a wide proteomic profile of proteins which survive the vinification processes. Proteins from a Silvaner Franken wine were submitted to size exclusion chromatography (SEC) and subsequently subjected to distinct methods of MS-basedproteomics approaches based on in- solution and in- gel digestion of the proteins. 154 characterized (with described functional information) or so far uncharacterized proteins, mainly from Vitis vinifera and Saccharomyces cerevisiae, were found. A high-score identification of proteins from low to high abundance was obtained.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Vitis Vinifera (grape)

TISSUE(S): Plant Cell

SUBMITTER: Wendell Albuquerque

LAB HEAD: Wendell Albuquerque

PROVIDER: PXD040172 | Pride | 2023-07-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Mass Spectrometry-Based Proteomic Profiling of a Silvaner White Wine.

Albuquerque Wendell W Ghezellou Parviz P Seidel Leif L Burkert Johannes J Will Frank F Schweiggert Ralf R Spengler Bernhard B Zorn Holger H Gand Martin M

Biomolecules 20230404 4

The comprehensive identification of the proteome content from a white wine (cv. Silvaner) is described here for the first time. The wine protein composition isolated from a representative wine sample (250 L) was identified via mass spectrometry (MS)-based proteomics following <i>in-solution</i> and <i>in-gel</i> digestion methods after being submitted to size exclusion chromatographic (SEC) fractionation to gain a comprehensive insight into proteins that survive the vinification processes. In to ...[more]

PMID: 37189397

Similar Datasets

Secretome Processing for Proteomics: A Methods Comparison

Project description:The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: 1. Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); 2. Acetone protein precipitation coupled to IGD; 3. MWCO filter-based protein concentration followed by to in-solution digestion (ISD); 4. Acetone protein precipitation coupled to ISD; 5. Direct ISD; 6. Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reproducibility of protein identification and quantification and detectability of small proteins with important functions in cancer biology such as cytokines, chemokines and growth factors.

2024-02-12 | PXD043014 | Pride

Updated in-gel digestion for protein analysis by mass spectrometry

Project description:The in-gel digestion of proteins for analysis by liquid chromatograph mass spectrometry has been used since the early 1990s. Although several improvements have contributed to increasing the quality of the data obtained, many recent publications still use sub-optimal approaches. We present an updated in-gel digestion protocol. We show that alternative reducing, alkylating agents and tryptic digestion buffers increase peptide and protein identification and reduce incubation times. Our results indicate that a simultaneous and short, high temperature reduction and alkylation reaction using Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) and chloroacetamide (CAA) with a subsequent gel wash improve protein identification and sequence coverage, diminish peptide side reactions. Additionally, use of 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid buffer (HEPES) allows a significant reduction in the digestion time improving trypsin performance and increasing the peptide recovery. The updated in-gel digestion protocol described here is highly efficient and offers flexibility to be incorporated in any proteomic laboratory.

2018-10-02 | PXD009600 | Pride

Human chorionic villus proteome

Project description:We evaluated the effect of the different solubilization techniques on the reproducibility and width of the chorionic proteome characterized using bottom-up proteomics: SDS-based solubilization coupled with in-gel protein digestion after applying self-named 1DE gel-concentration procedure (SDS-PAGE without fractionating in the resolving gel for SDS removal) and in-solution protein digestion of urea-thiourea extracts. These results indicated that 1DE-concentration procedure coupled with in-gel digestion, LC-MS/MS and combinational usage of different bioinformatics tools provides in-depth analysis of a single protein band, including reliable identification and quantification of low-abundant proteins, e.g. FUCA1, PSG7.

2022-06-17 | PXD024759 | Pride

Human_MCF7_membrane - Searching Missing Proteins Based on the Optimization of Membrane Protein Enrichment and Digestion Process

Project description:MCF7 cell was an important stabilized breast cancer cell in cancer research. A membrane proteomic method was developed and compared in this study. A membrane protein enrichment method composed of ultra-centrifugation and detergent-based extraction was first developed. Then in-solution digestion with detergents and eFASP (enhanced filter aided sample preparation) with detergents were compared with the time consuming in-gel digestion method. Our data indicated that ultra-centrifugation combined detergent-based extraction can effectively enrich membrane proteins with higher purity. Among the in-solution digestion methods, the eFASP combined with RapiGest method identified 1125 membrane proteins. Similarly, the eFASP combined with SDC identified 1069 membrane proteins, however, the in-gel digestion characterized 1091 membrane proteins. Totally, with the 5 digestion methods, 1390 membrane proteins were identified with ≥1 unique peptides, among which 1345 membrane proteins contain unique peptides ≥2. This is the biggest membrane protein datasets for MCF7 cell line and even breast cancer tissue samples. Interestingly, we realized that 9 missing proteins (MPs) present with one or more unique peptides. After verification, 4 of them were validated by synthesized peptide with amino acids larger than 9.

2016-10-07 | PXD004131 | Pride

Quantitative Proteomics of different truffle species

Project description:Truffles of the Tuber species as expensive foods are predestined for food fraud. To find markers for distinguishing different truffle species the proteomes as phenotype determining basis were investigated. First, established sample preparation protocols subsequent to LC-MS/MS analysis for a bottom up proteomic approach were tested on a truffle sample. The sample preparation included protein extraction and in-solution tryptic digestion. For protein extraction sodium deoxycholate (SDC), sodium dodecylsulfate (SDS) and urea were tested, followed by direct tryptic digestion in solution (SDC extracted proteins) and a tryptic digestion utilizing the FASP approach with molecular cut-off filters (SDS and urea extracted proteins). By this approach the SDC sample preparation protocol was classified as the most suited one to prepare truffle samples. It resulted in a high protein identification rate, had a high reproducibility, was cost efficient and most easy to handle. By a quantitative proteomic approach using label-free and non-targeted bottom up LC-MS/MS the species T. magnatum (n=13), T. aestivum (n=16), T. uncinatum (n=4) and T. melanosporum (n=7) were compared and truffle species specific markers were identified.

2021-12-19 | PXD017901 | Pride

Proteomic Profile of Daphnia pulex using Data-Independent Acquisition Mass Spectrometry and Ion Mobility Separation

Project description:In this study, various sample preparation and mass spectrometry acquisition methods were performed for the purpose of improving Daphnia pulex proteome exploration. We observed benefits for employing both in-gel and in-solution methods of trypsin digestion. Furthermore, data independent acquisition methods employing ion-mobility separation greatly increased peptide identification and more than doubled our proteome coverage.

2018-07-11 | PXD008455 | Pride

Extracellular Vesicles released by Leishmania donovani infected mouse macrophages

Project description:Extracellular vesicles (EVs) released by Leishmania donovani infected RAW264.7 murine macrophages were evaluated for their proteomic composition and potential function in pathogenesis. EVs were collected after 72 hours infection and analyzed by LC-MS/MS using both in gel and in solution digestion approaches to identify protein composition of both host and parasite origin.

2020-10-26 | PXD021769 | Pride

Profiling of cow urinary proteins using various extraction methods reveals more than 1550 proteins

Project description:Urine can help in diagnosis of different diseases including cancer and other patho-physiological conditions. Urine proteome studies have been mainly human- centric. No information is available on urinary proteome from bovine till date. In the present study, we have used 3 protein extraction methods such as ammonium sulphate precipitation, ProteoSpin column and diafiltration method from bovine urine for identification of urinary proteome. The tryptic peptides generated after In-gel and In-solution method were identified using LC/MS/MS (ESI-qTOF) which resulted in identification of 1582 proteins. In-gel trypsin digestion method revealed more protein (1191) in comparison to in-solution digestion method (541). Maximum proteins were identified in ammonium sulphate precipitation method (938) followed by ProteoSpin (606) and diafiltration (444) methods respectively. The profile of the identified proteins were compared with human urinary proteome of which 311 bovine urinary proteins matched with human. An exclusive list of 38 bovine urinary proteins with high protein scores were listed which are absent in human urine. All identified proteins were analyzed according to Gene Ontology which were classified according to cellular component, biological processes and molecular functions. This study reports for the first time an exclusive evidence of more than 1550 proteins in urine of healthy cow donors.

2023-03-22 | PXD002038 | Pride

Comparison of in-gel digestion methods for histone PTM analysis

Project description:In order to optimize the histone digestion procedure for low-abundance clinical samples, we compared different in-gel digestion protocols. Histones are usually digested in-gel using “Arg-C-like” strategies, which involve chemical acylation of lysines followed by trypsin digestion (17). Acylated lysines are not recognized by trypsin, which -as a consequence- cuts only at the C-terminus of arginines and generates peptides of suitable length for MS analysis. We compared four Arg-C-like protocols: 1) D3 protocol (deuterated acetic anhydride as acylating agent); 2) PRO protocol (propionic anhydride as acylating agent); 3) PRO-PRO protocol (propionic anhydride as acylating agent and peptide N-terminal derivatization); 4) PRO-PIC protocol (propionic anhydride as acylating agent and phenyl-isocyanate as peptide N-terminal derivatization). We also used an Arg-C in solution digestion as a reference, and tested the performance of the methods with decreasing sample amounts.

2021-09-09 | PXD024745 | Pride

Assessment of sample preparation bias in mass spectrometry-based proteomics

Project description:For mass spectrometry-based proteomics, the selected sample preparation strategy is a key determinant for information that will be obtained. However, the corresponding selection is often not based on a fit-for-purpose evaluation. Here we report a comparison of in-gel (IGD), in-solution (ISD), on-filter (OFD), and on-pellet digestion (OPD) workflows on the basis of targeted (QconCAT-multiple reaction monitoring (MRM) method for mitochondrial proteins) and discovery proteomics (data dependent acquisition, DDA) analyses using three different human head and neck tissues (i.e. nasal polyps, parotid gland, and palatine tonsils). Our study reveals differences between the sample preparation methods, for example with respect to protein and peptide losses, quantification variability, protocol-induced methionine oxidation and asparagine/glutamine deamidation as well as identification of cysteine containing peptides. Moreover, none of the methods performed best for all types of tissues, which seemingly argues against the existence of a universal sample preparation method for proteome analysis.

2018-04-06 | PXD008493 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data