PXD000118

PXD000118 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of Mycoplasma hyopneumoniae virulent strain 232
Description	The experiment consists of M.hyp 232 cultures digests analyzed on two mass specs, LTQ Velos Pro and LTQ FT Ultra LTQ Velos Pro: Six cell culture replicates of M.hyo 232 were hydrophobically separated using tree detergents: Digitonin, Tween, and SDS. Each francion, including the insoluble pellet, was trypsin digested and then cleaned using an SCX trap follwed by a RP trap to remove detergents. Each fraction was sepated using a Dionex U3000 splitless nanoflow system operating at 333 nl per minute using a gradient of 2% ACN to 50% ACN in 4 hours. Eluate was analyzed using an LTQ Velos Pro mass spectrometer with 20 MS/MS scans of the 20 most intense peaks from each MS scan. Dynamic exclusion was enable for 3 minutes for each m/z with a repeat count of 1. LTQ FT Ultra: Two cell pellets for high resolution analysis were lysed and trypsin digested. Digested peptides were dried, resuspended in 20 mM KH2PO4, 20% ACN, pH 3 (Buffer A) in 2.5 µL and transferred to low retention vials in preparation for separation using an Ultimate 3000 configured for 2D-LC. Each sample was loaded at 15 µl/min onto an SCX microtrap for the first dimension of separation, involving SCX steps of Buffer A + 0, 5, 10, 15, 20, 25, 30, 40, 50, 100, 250, 500, and 1000 mM KCl. For the second dimension of separation, each eluted salt step was desalted with an inline peptide microtrap with 2% ACN, 0.1% FA at 5 µl/min. Once desalted, the microtrap was switched into line with a fritless nano column (75µm x ~10cm) containing C18 media (5µ, 200 Å Magic, Michrom). Peptides were eluted using a gradient of 2% to 36% ACN, 0.1% FA at 350 nl/min over 60 min and electrospray ionized for analysis using an LTQ FT Ultra mass spectrometer. A survey scan m/z 350-1750 was acquired in the FT ICR cell (Resolution = 100,000 at m/z 400, with an accumulation target value of 1,000,000 ions). Up to the 6 most abundant ions (>3,000 counts) with charge states > +2 were sequentially isolated and fragmented within the linear ion trap using collisionally induced dissociation with an activation q = 0.25 and activation time of 30 ms at a target value of 30,000 ions. M/z ratios selected for MS/ MS were dynamically excluded for 30 seconds. Analysis: X!tandem searches were performed using the Mycoplasma hyopneumoniae strain 232 reference protein set from NCBI. The only difference between the searches for the LTQ Velos and LTQ FT was the precursor mass tolenance being set to +-1500ppm and +-24ppm respectively. Decoy searches were performed and the data filtered at e-value <= 0.01 with single peptide proteins discarded. These results are included in the submission as two tab-delimited text files.
HostingRepository	PRIDE
AnnounceDate	2018-01-11
AnnouncementXML	Submission_2018-01-11_00:30:19.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000118
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ken Pendarvis
SpeciesList	scientific name: Mycoplasma hyopneumoniae (strain 232); NCBI TaxID: 295358;
ModificationList	dihydroxylated residue; dehydrated residue; phosphorylated residue; deaminated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	instrument model: LTQ FT Ultra; LTQ FT Ultra; LTQ Orbitrap Velos; instrument model: LTQ Velos Pro

Revision	Datetime	Status	ChangeLog Entry
0	2013-01-04 03:32:07	ID requested
1	2018-01-10 05:30:08	announced
⏵ 2	2018-01-11 00:30:20	announced	Updated project metadata.

Pendarvis K, Padula MP, Tacchi JL, Petersen AC, Djordjevic SP, Burgess SC, Minion FC, Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232. BMC Genomics, 15(1):576(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: Mycoplasma hyopneumoniae 232 LTQ Velos FT mass spec proteomics

Ken Pendarvis
contact affiliation	University of Arizona
contact email	jkpendarvis@email.arizona.edu
lab head
Ken Pendarvis
contact affiliation	Veterinary Science and Microbiology
contact email	jkpendarvis@email.arizona.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD000118

PRIDE project URI

• PRIDE
  1. PXD000118
     1. Label: PRIDE project
     2. Name: Proteomic analysis of Mycoplasma hyopneumoniae virulent strain 232