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iPRG 2011: A Study on the Identification of Electron Transfer Dissociation (ETD) Mass Spectra

Askenazi, M.; Bandeira, N.; Chalkley, R.J.; Clauser, K.R.; Deutsch, E.; Lam, H.H.N.; McDonald, W.H.; Neubert, T.; Rudnick, P.A.; Martens, L.
Fonte: Association of Biomolecular Resource Facilities Publicador: Association of Biomolecular Resource Facilities
Tipo: Artigo de Revista Científica
Publicado em /10/2011 Português
Relevância na Pesquisa
274.2957%
The field of mass spectrometry based proteomics has seen several key innovations over the last several years, including novel experimental methods, new instruments, and unique fragmentation strategies. The latter, in the form of electron capture dissociation (ECD) and electron transfer dissociation (ETD) have captured the imaginations of many researchers, expanding their ability to identify and analyze peptides and proteins. However, since ECD/ETD spectra differ substantial from more traditional collision induced dissociation (CID) spectra in both their prominent ion series as well as their preferred bond-breaking characteristics, the (automatic) interpretation of ECD/ETD spectra requires novel algorithm optimizations. Efficient identification of ECD/ETD spectra thus remains an active and exciting field of proteomics informatics research. In this work, the ABRF Proteome Informatics Research Group (iPRG) presents the results of a collaborative study focusing on the analysis of an LC-MS/MS dataset from a yeast lysate digested with Lys-C and enriched for highly charged peptides using strong cation exchange fractionation. The data derived from one fraction analyzed exclusively by ETD was distributed to participants for analysis in several equivalent formats...

GlycoMaster — Software for Glycopeptide Identification with Combined ETD and CID/HCD Spectra

Xin, L.; Shan, P.
Fonte: Association of Biomolecular Resource Facilities Publicador: Association of Biomolecular Resource Facilities
Tipo: Artigo de Revista Científica
Publicado em /10/2011 Português
Relevância na Pesquisa
276.1078%
Objective: To automate the data analysis for the identification of glycopeptides with combined ETD and CID/HCD fragmentation. The inputs for GlycoMaster software include the raw mass spectrometry data of a Thermo Orbitrap instrument and the list of proteins in the sample. The list of proteins can be identified from the same mass spectrometry data by using a database search method. The software uses the signature ions of simple sugars in the HCD spectra to identify the HCD-ETD spectrum pairs of glycopeptides. Then the ETD spectrum in each pair is used to identify the glycopeptides sequence, the glycosylation site and glycan mass. The output of the software is an excel file that contains information about the identified glycopeptides, including glycan composition, mass error, glycan components, glycosylation site and glycopeptide sequence. A score is associated with each identification result that can be used to sort the identifications according to confidence. GlycoMaster was tested with an ETD-CID dataset containing 3561 MS and 2738 MS/MS spectra from tryptic digest of reduced and alkylated 12 standard protein mixture containing 3 glycoproteins (human serotransferrin, chicken ovalabumin and ovomucoid) from Sigma. Glycopeptides were enriched on cellulose column or by using ZIC-HILIC spin columns from EMD. Purified glycopeptides were analyzed by LTQ Orbitrap Velos ETD. PEAKSTM Studio Suite was used for spectral preprocessing and protein identification. GlycoMaster reported 161 identified HCD-ETD spectrum pairs of glycopeptides. 95 of 161 were manually validated. 68 glycopeptides were reported by GlycoMaster...

ETD Performance and Complementarity to Other Fragmentation Methods for Proteomic Analysis

Chalkley, R.
Fonte: Association of Biomolecular Resource Facilities Publicador: Association of Biomolecular Resource Facilities
Tipo: Artigo de Revista Científica
Publicado em /10/2011 Português
Relevância na Pesquisa
274.2957%
Radical-driven fragmentation approaches present an alternative to the well-established collisional cleavage approaches that have dominated proteomic research up until now. With the recent availability of electron transfer dissociation (ETD) in commercial quadrupole ion trap and hybrid instruments, this technology is now accessible to many researchers. It has been described as a complementary approach to CID, and decision tree approaches have been employed where a choice between CID or ETD is made depending on the precursor m/z and charge. In this presentation I will discuss the performance of ETD for peptide identification, drawing heavily on data acquired as part of the 2011 iPRG study ‘Identification of Electron Transfer Dissocation (ETD) Mass Spectra’. Results will be compared to analyses of the same sample using CID and HCD, decision tree approaches and the difference in measuring data in the ion trap versus in the orbitrap detector. A comparison of search engine performance will be presented and methods for improving database search engine analysis of ETD data will also be discussed.