PXD002779

PXD002779 is an original dataset announced via ProteomeXchange.

Title	Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome.
Description	A common problem encountered when performing large-scale mass spectrometry proteome analysis is the loss of information due to the high percentage of unassigned spectra. To determine the causes behind this loss we have analyzed the proteome of one of the smallest living bacteria that can be grown axenically, Mycoplasma pneumoniae (729 ORFs). M. pneumoniae cultures were grown in defined media, and their proteomes were analyzed by mass spectrometry. An initial database search with a curated M. pneumoniae protein database left around 78% of the acquired spectra without an assignment. After re-analysis of the data with the PEAKS software and a larger protein database, the percentage of non-assigned spectra was reduced to 27%, thereby increasing the proteome coverage of M. pneumoniae from the initial 60% to over 76%. Nonetheless, 33413 of spectra with assigned amino acid sequences, could not be mapped in any NCBInr database protein sequence. Approximately, 1% of these unassigned peptides corresponded to post-translational modifications and 4% to protein variants. We found that deamidation of Asn affected preferentially to integral membrane proteins and that about 1% of the peptides had repetitions of the same aromatic/hydrophobic amino acid at the N-terminus, or Arg/Lys at the C-terminus. Thus, in an ideal system, we maximized the level of assignment to 73% of the spectra (51453 out of 70040 initial acquired spectra).
HostingRepository	PRIDE
AnnounceDate	2016-01-05
AnnouncementXML	Submission_2016-01-05_14:27:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Francesco Mattia Mancuso
SpeciesList	scientific name: Mycoplasma pneumoniae (strain ATCC 29342 / M129); NCBI TaxID: 272634;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-24 01:31:53	ID requested
⏵ 1	2016-01-05 14:27:43	announced

Lluch-Senar M, Mancuso FM, Climente-Gonz, á, lez H, Pe, ñ, a-Paz MI, Sabido E, Serrano L, Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome. Proteomics, 16(4):554-63(2016) [pubmed]

curator keyword: Technical

submitter keyword: : Mass Spectroscopy, Proteome coverage, translation errors, Post-translational modifications (PTMs), Protein identification, Unassigned spectra

Eduard Sabidò
contact affiliation	Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
contact email	eduard.sabido@crg.eu
lab head
Francesco Mattia Mancuso
contact affiliation	CRG/UPF Proteomics Unit
contact email	francescomattia.mancuso@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002779
     1. Label: PRIDE project
     2. Name: Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome.