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Confetti: A Multi-protease Map of the HeLa Proteome for Comprehensive Proteomics

ABSTRACT: Tryptic digestion proteomics gives limited coverage of many protein sequences as many proteins produce tryptic peptides that cannot be observed easily. Confetti is our comprehensive map of coverage for the HeLa proteome, using 48 different digests and CID/HCD LC-MS/MS analyses. An associated dataset belonging to the same study can be found under the PX identifier PXD001258.

REANALYSED by: PAe005075PAe005072PAe005070PAe005064PAe005063PAe005062PAe005058PAe005048PAe005046PAe005034PAe004980PAe005030PAe005008PAe005000PAe004993PAe004990PAe004986PAe004984PAe005200PAe005199PAe005198PAe005193PAe005185

INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: David Trudgian

LAB HEAD: Hamid Mirzaei

PROVIDER: PXD000900 | Pride | 2014-04-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Confetti_1_1_PSMs.txt	Txt
	Confetti_1_1_Proteins.txt	Txt
	HeLa_ACE_CID_1.mgf	Mgf
	HeLa_ACE_CID_1.raw	Raw
	HeLa_ACE_HCD_1.mgf	Mgf

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Publications

Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics.

Guo Xiaofeng X Trudgian David C DC Lemoff Andrew A Yadavalli Sivaramakrishna S Mirzaei Hamid H

Molecular & cellular proteomics : MCP 20140402 6

Bottom-up proteomics largely relies on tryptic peptides for protein identification and quantification. Tryptic digestion often provides limited coverage of protein sequence because of issues such as peptide length, ionization efficiency, and post-translational modification colocalization. Unfortunately, a region of interest in a protein, for example, because of proximity to an active site or the presence of important post-translational modifications, may not be covered by tryptic peptides. Detec ...[more]

PMID: 24696503

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Correction To - Confetti: A Multi-protease Map of the HeLa Proteome for Comprehensive Proteomics

Project description:Contains corrected HeLa SAX fractionated datasets for the Trypsin, LysC, and Chymotrypsin-Trypsin digests of the Confetti project. Original submission was PXD000900. Together with PXD000900 this submission makes up the dataset used for Confetti build 1.2.

2014-08-28 | PXD001258 | Pride

The Leishmania mexicana promastigote flagellar proteome

Project description:Leishmania are protists (class: Kinetoplastida) with a single multifunctional flagellum used for motility, attachment to the sand fly vector and sensory functions. To discover the protein composition of the L. mexicana promastigote flagellum, we fractionated L. mexicana promastigotes by mechanical shearing and differential centrifugation into four fractions: detergent soluble (Fs) and insoluble (Fi) fractions of isolated flagella and detergent soluble (Cs) and insoluble fractions (Ci) of deflagellated cell body remnants. A label-free quantitation method (SINQ; Trudgian et al., 2011, Proteomics 10.1002) was used to identify proteins enriched in each of the four fractions. This PRIDE upload contains .RAW, .MGF and .XML files, as well as the SINQ quantification output file “SINQ_raw_data” and the genome sequence annotation used for protein identification “MFiebig_20140619” (Fiebig et al., 2015, PLoS Pathogens II:e1005186). XML files are named SUB7467; MSS10859. .RAW and .MGF files are structured as follows (for each fraction there are eight files, corresponding to individual gel pieces): “Ci: C131121_030; C131121_031; C131121_032; C131121_033; C131121_034; C131121_035; C131121_036; C131121_037”, “Cs: C131121_040; C131121_041; C131121_042; C131121_043; C131121_044; C131121_045; C131121_046; C131121_047”, “Fi: C131121_010; C131121_011; C131121_012; C131121_013; C131121_014; C131121_015; C131121_016; C131121_017”, “Fs: C131121_020; C131121_021; C131121_022; C131121_023; C131121_024; C131121_025; C131121_026; C131121_027”.

2018-12-14 | PXD011057 | Pride

Quantative proteomic analysis of teh central amygdala in neuropathic pain model rats

Project description:Neuropathic pain is a major clinic probelm as it is very difficult to treat and mechanism remain unknown. Here, we investigated the differential expression of proteins in the central nuecleus of amygdala (CeA) in neuropathic pain moldel spinal nerve transection (SNT)in rats. CeA was excised from naive, sham, SNTmodels at days 3, 7, 14 and 21 rats. The aim was to quatify the differential proteins in CeA including memebrane proteins. We used gel- and mass spectrometry- based proteomics. For gel-proteomics, total tissue lysate proteins were separated by 2D-PAGE. The 2D gels from different SNT time points against Sham and control rats were compared using Progenesis SameSpot software. The spots with fold change greater then 2 excised for the proteins IDs by LC-MS/MS. Protein spots were digested using trypsin. Extracted peptides were injected on the nano C18 column and measured by a LTQ Orbitrap XL or a LTQ Orbitrap Velos mass spectrometers. For the identification of membrane proteins in CeA, we used 1-SDS-PAGE and cut the gel region of MW 80 kDa and higher for nano-LC-MS/MS analysis. We also quantified membrane proteins by utilising triplex stabel isotope dimethyl labelling at the peptide level. Sham, control and day 3, 7 and 21 after SNT surgery rats CeA membrane proteins were purified and digested by trypsin and labelled with "light", "medium" and "heavy" dimethyl labelling reagents. The resulting peptides were analysed by a nano LC connected to the Q Exactive mass spectrometer. Quantification of peptide was processed using Proteome Discoverer 1.3.

2020-02-21 | PXD017473 | Pride

Proteomic dissection of CFAP44 deficient axonemes

Project description:Leishmania are protists (class: Kinetoplastida) with a single multifunctional flagellum, which forms a canonical motile 9+2 microtubule axoneme in the promastigote forms. Deletion of gene CFAP44 (LmxM.14.1430) caused a reduction in promastigote motility (Beneke et al., PLoS Pathogens, 2019; accepted). To study the changes in protein composition in CFAP44 deficient axonemes, flagellar skeletons were isolated from CFAP44 knockout mutants and the parental cell line L. mex Cas9 T7 (Beneke et al., R Soc Open Sci. 2017; 4(5):170095) using a modified version of the method by Robinson et al., (Methods Enzymol. 1991; 196:285-99). Liquid chromatography tandem mass spectrometry and a label-free quantitation method (SINQ; Trudgian et al., 2011, Proteomics 10.1002) were used to identify proteins enriched in each fraction. This PRIDE upload contains .RAW and .XML files, as well as the SINQ quantification output file “SINQ_raw_data”. XML files are named SUB9810; MSS11680. .RAW files are structured as follows: “CFAP44 mutants: Qex01_SVH_180422_TomBeneke_B29_F_001”; “Cas9 T7 parentals: Qex01_SVH_180422_TomBeneke_Cas9_F_005”.

2020-01-20 | PXD014077 | Pride

Confetti: A Multi-protease Map of the HeLa Proteome for Comprehensive Proteomics

Project description:Tryptic digestion proteomics gives limited coverage of many protein sequences as many proteins produce tryptic peptides that cannot be observed easily. Confetti is our comprehensive map of coverage for the HeLa proteome, using 48 different digests and CID/HCD LC-MS/MS analyses. An associated dataset belonging to the same study can be found under the PX identifier PXD001258.

2017-10-12 | MSV000081607 | MassIVE

TMT-switch assay for the detection of SNO

Project description:To maximize SNO-proteome coverage and ensure capture of all modified sites, different experimental configurations using both iodo- and cysTMT were evaluated.

2016-12-23 | PXD000741 | Pride

Human lamin B1: stress-induced phosphorylation

Project description:This is a small scale study of the phosphorylation state of human lamin B1 immunoprecipitated from control cells or cells treated with methyl methane sulphonate (MMS, acting as a DNA damage stressor agent)

2017-05-30 | PXD006459 | Pride

Human Treg LC-MSMS - Foxp3 drives oxidative phosphorylation and protection from lipotoxicity

Project description:Regulatory T cells (Treg) have been shown to adopt a catabolic metabolic programme with increased capacity for fatty acid oxidation fuelled oxidative phosphorylation (OXPHOS). The role of Foxp3 in this metabolic shift is poorly understood. Here we show that Foxp3 was sufficient to induce a significant increase in the spare respiratory capacity of the cell, the extra OXPHOS capacity available to a cell to meet increased demands on energy in response to work. Foxp3-expressing cells were enhanced in their ability to utilise palmitate for respiration and, in addition, the activity of electron transport complexes I, II and IV were enhanced following Foxp3 expression. Foxp3 also imparts a selective advantage in ATP generation capacity, one that might be exploited as a source of adenosine for functional immunomodulation. In order to explore possible mechanisms for these differences in metabolism we conducted a quantitative proteomics study to compare the contribution of TGFβ and the transcription factor Foxp3 to the Treg proteome. We used quantitative mass spectrometry to examine differences between proteomes of nuclear and cytoplasmic Foxp3-containing CD4+ T cells from various sources with Foxp3- activated CD4 T cells, as well as Treg from human peripheral blood. Gene set enrichment analysis of our proteomic datasets demonstrated that Foxp3 expression is associated with a significant up regulation of several members of the mitochondrial electron transport chain. Not only does Foxp3 influence genes directly concerned with immune function, but also with the energy generating functions of Treg.

2017-02-15 | PXD001906 | Pride

Ultraviolet Photodissociation of tryptic peptide backbones at 213 nm

Project description:We analyzed the backbone fragmentation behavior of tryptic peptides of a four protein mixture and of E. coli lysate subjected to Ultraviolet Photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass spectrometer. We obtained 15,178 high-confidence peptide-spectrum matches by additionally recording a reference beam-type collision-induced dissociation (HCD) spectrum of each precursor. Type a, b and y ions were most prominent in UVPD spectra and median sequence coverage ranged from 5.8% (at 5 ms laser excitation time) to 45.0% (at 100 ms). Overall sequence fragment intensity remained relatively low (median: 0.4% (5 ms) to 16.8% (100 ms) of total intensity) and remaining precursor intensity high. Sequence coverage and sequence fragment intensity ratio correlated with precursor charge density, suggesting that UVPD at 213 nm may suffer from newly formed fragments sticking together due to non-covalent interactions. UVPD fragmentation efficiency therefore might benefit from supplemental activation, as was shown for ETD. Aromatic amino acids, most prominently tryptophan, facilitated UVPD. This points at aromatic tags as possible enhancers of UVPD. Data are available via ProteomeXchange and on spectrumviewer.org/db/UVPD_213nm_trypPep

2020-05-07 | PXD018176 | Pride

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