PXD011861

PXD011861 is an original dataset announced via ProteomeXchange.

Title	Optimized fragmentation improves the identification of peptides cross-linked using MS-cleavable reagents
Description	Cross-linking mass spectrometry (XLMS) is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by non-specialist laboratories. Specifically, the use of novel mass spectrometry-cleavable (MS-cleavable) reagents dramatically reduces complexity of the data by providing i) characteristic reporter ions and ii) the mass of the individual peptides, rather than that of the cross-linked moiety. However, optimum acquisition strategies to obtain the best quality data for such cross-linkers with higher energy C-trap dissociation (HCD) alone is yet to be achieved. Therefore, we have carefully investigated and optimized MS parameters to facilitate the identification of disuccinimidyl sulfoxide (DSSO)-based cross-links on HCD-equipped mass spectrometers. From the comparison of 9 different fragmentation energies we chose several stepped- HCD fragmentation methods that were evaluated on a variety of cross-linked proteins. The optimal stepped-HCD method was then directly compared with previously described methods using an Orbitrap Fusion™ Lumos™ Tribrid™ instrument using a high-complexity sample. The final results indicate that our stepped-HCD method is able to identify more cross-links than other methods, mitigating the need for multistage MS (MSn) enabled instrumentation and alternative dissociation techniques.
HostingRepository	PRIDE
AnnounceDate	2019-02-01
AnnouncementXML	Submission_2019-02-01_06:38:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Stieger
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Oryctolagus cuniculus (Rabbit); NCBI TaxID: 9986; scientific name: Cicer arietinum (Chickpea) (Garbanzo); NCBI TaxID: 3827; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Streptococcus pyogenes serotype M2; NCBI TaxID: 404330; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-28 00:56:09	ID requested
⏵ 1	2019-02-01 06:38:49	announced

Stieger CE, Doppler P, Mechtler K, Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents. J Proteome Res, 18(3):1363-1370(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: XLMS, cross-linking, stepped-HCD, DSSO, cleavable cross-linking reagents

Karl Mechtler
contact affiliation	Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
contact email	karl.mechtler@imp.ac.at
lab head
Christian Stieger
contact affiliation	Institute of Molecular Pathology
contact email	christian.stieger@imp.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011861
     1. Label: PRIDE project
     2. Name: Optimized fragmentation improves the identification of peptides cross-linked using MS-cleavable reagents