Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tetrahymena thermophila ciliary proteome fractionated by SEC and IEX

ABSTRACT: Cilia were isolated from Tetrahymena thermophila SB715 by pH shock. Soluble ciliary proteins were extracted in buffer containing 1% NP40 and fractionated by HPLC SEC or mixed bed IEX. All fractions were reduced/alkylated and digested with trypsin for LC-MS/MS on an Orbitrap Fusion using a DDA 75 minute top speed CID method. Data were processed using MS Blender.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Tetrahymena Thermophila (ncbitaxon:5911)

SUBMITTER: Edward Marcotte

PROVIDER: MSV000091648 | MassIVE | Wed Apr 05 09:35:00 BST 2023

SECONDARY ACCESSION(S): PXD050671

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteome of Deciliated Tetrahymena thermophila "Bodies" Fractionated by IEX or SEC.

Project description:Tetrahymena thermophil SB715 were deciliated by pH shock, collected by centrifugation, washed once and flash frozen. Lysate was made by grinding in liquid nitrogen and resuspension in buffer containing 0.2% NP40 with pipetting. Lysate was clarified by sequential centrifugations including 1 hour 130,000 x g 4C. Clarified lysate was fractionated by HPLC SEC or diluted to reduce salts to 22mM NaCl prior to fractionation by mixed-bed IEX. Fractions were reduced/alkylated and digested with trypsin for DDA LC-MS/MS. Data from SEC fractions was collected on an Orbitrap Fusion Lumos using a 75 minute top speed HCD method. Data from IEX fractions was collected on an Orbitrap Fusion using a 75 minute Topspeed CID method.

2023-04-07 | MSV000091661 | MassIVE

WT and FAP256-KO Cilia Proteome from Tetrahymena thermophila

Project description:Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. By analysing Tetrahymena thermophila cells lacking a ciliary tip-enriched protein CEP104/FAP256 by mass spectrometry, we discovered candidates for the central pair cap complex and explained the potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and the mechanisms of ciliary assembly and length regulation.

2023-09-01 | PXD042582 | Pride

Protein Identification in Tetrahymena thermophila cilia IEX fractions used for XL-MS

Project description:Tetrahymena thermophila SB715 were deciliated by pH shock substituting HEPES for Tris in all subsequent buffers. Ciliry proteins were solubilized with buffer containing 1%NP40, and fractionated by HPLC on a mixed-bed IEX column. DSSO was added to 0.5 mM to all collected fractions. Crosslinking was quenched with Tris pH 8.0 at 28 mM and fractions were reduced, alkylated, and digested with trypsin for mass spectrometry. Spectra were collected on an Orbitrap Fusion Lumos using a DDA MS2-MS3 method for both protein and crosslink identification. Data in this deposition include the RAW files and MSBlender pipeline files used for protein identification. Crosslink analysis will be deposited separately.

2023-04-13 | MSV000091710 | MassIVE

IEX fractionated proteome of pig tracheal cilia extract

Project description:Cilia from two fresh pig tracheas (Sus scrofa) were removed by calcium shock and proteins extracted in buffer containing 1% NP40. Extract was diluted to reduce salts and fractionated by HPLC on a mixed bed ion exchange column. Fractions were reduced/alkylated and digested with trypsin for analysis by LC-MS/MS on an orbitrap fusion Lumos using a 75 minute top speed DDA method and HCD.

2023-05-04 | MSV000091856 | MassIVE

Proteomics of SEC and IEX fractionated Mouse Embryonic Stem Cells

Project description:Mouse embryonic stem cells were lysed in Pierce IP Lysis buffer and 2 mg of the clarified extract was fractionated on an HPLC SEC column and 2 mg was fractionated on an HPLC IEX mixed bed column. All fractions were reduced, alkylated, and trypsin digested for mass spectrometry as in Mallam et al. 2019 (PMID: 31665645). Data were collected on an Orbitrap Fusion mass spectrometer using a data dependent 75 minute topspeed method. Dissociation for SEC fractions was by CID, and for IEX fractions was by HCD. RAW files were converted to mzXML and searched using an MSBlender analysis pipeline.

2023-05-01 | MSV000091831 | MassIVE

DSSO Crosslinking of Partially Purified IFT-A from Tetrahymena thermophila

Project description:DSSO crosslinking data from two Tetrahymena thermophila samples: IEX fractions from chromatography of a cilia extract, and IFT-A-enriched fractions from preparative SEC of cilia extract.

2022-03-25 | MSV000089131 | MassIVE

DSSO Crosslinking of IEX column fractions from Tetrahymena cilia extract fractionation.

Project description:Procedure details are reported in McCafferty et al. eLife2022;11e81977. Briefly cilia extract from Tetrahymena thermophila SB715 was fractionated on a mixed bed IEX HPLC column and all resulting fractions were crosslinked by addition of DSSO to 0.5mM. Following reduction, alkylation, trypsin digestion, and desalting, mass spectra were collected on an Orbitrap Fusion Lumos using a DDA MS2-MS3 method and spectra were processed in ProteomeDiscoverer 2.3 using the Xlinkx node to identify crosslinks. The look-up database for crosslink identification was generated from the same .RAW files using a standard Basic workflow to identify proteins present in the fractions.

2023-04-20 | MSV000091761 | MassIVE

SEC-IEX fractionation of Naja ashei venom

Project description:The aim of the study was to separate the proteins from Naja ashei venom with the use of SEC followed by IEX in order to obtain and functionally characterize purified toxins.

2024-08-12 | PXD033540 | Pride

Phaeodactylum tricornutum proteome from SEC and IEX fractionation of native extract

Project description:Phaeodactylum tricornutum (UTEX 646) grown without silica were used to generate a native protein extract. Extraction involved multiple freeze/thaw cycles, sonication, and solubilization in buffer containing 1% NP40. Following chromatographic separation by SEC or IEX the fractions were reduced/alkylated and digested with trypsin for LC-MS/MS on an orbitrap fusion. Data were collected using a 75 minute top speed DDA method with CID.

2023-04-03 | MSV000091621 | MassIVE

Constitutive secretion in Tetrahymena thermophila.

Project description:The growth, survival, and life cycle progression of the freshwater ciliated protozoan Tetrahymena thermophila are responsive to protein signals thought to be released by constitutive secretion. In addition to providing insights about ciliate communication, studies of constitutive secretion are of interest for evaluating the utility of T. thermophila as a platform for the expression of secreted protein therapeutics. For these reasons, we undertook an unbiased investigation of T. thermophila secreted proteins using wild-type and secretion mutant strains. Extensive tandem mass spectrometry analyses of secretome samples were performed. We identified a total of 207 secretome proteins, most of which were not detected in a set of abundant whole-cell protein identifications. Numerous proteases and other hydrolases were secreted from cells grown in rich medium but not cells transferred to a nutrient starvation condition. On the other hand, we detected the starvation-enhanced secretion of a small number of cytosolic proteins, suggestive of an exosome-like pathway in T. thermophila. Subsets of proteins from the T. thermophila regulated secretion pathway were detected with differential representation across strains and culture conditions. Finally, many secretome proteins had a predicted N-terminal signal sequence but no other annotated characteristic or functional classification. Our work provides the first comprehensive analysis of secreted proteins in T. thermophila and establishes the groundwork for future studies of constitutive protein secretion biology and biotechnology in ciliates.

| S-EPMC2863955 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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