PXD014523

PXD014523 is an original dataset announced via ProteomeXchange.

Title	Comparison of OpenPepXL and xQuest on a Labeled Cross-Linking MS dataset
Description	These data sets are part of a large study aimed at the comparison of experimental and computational workflows used in chemical cross-linking coupled to mass spectrometry. Bovine serum albumin (BSA) was used as a model protein. Two different cross-linking chemistries were used: disuccinimidyl suberate (DSS) and a combination of pimelic acid dihydrazide (PDH) and the coupling reagent, DMTMM. See related publication: Iacobucci et al., First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study, Analytical Chemistry, 91 (2019) 6953-6961, DOI: 10.1021/acs.analchem.9b00658 This project is a reanalysis of these datasets with the two Labeled Cross-Linking MS identification tools OpenPepXL and xQuest.
HostingRepository	PRIDE
AnnounceDate	2020-10-20
AnnouncementXML	Submission_2020-10-19_22:44:40.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eugen Netz
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-08 09:11:37	ID requested
⏵ 1	2020-10-19 22:44:41	announced

Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O, OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS. Mol Cell Proteomics, 19(12):2157-2168(2020) [pubmed]

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, G, ö, tze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kuka, č, ka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Nov, á, k P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A, First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem, 91(11):6953-6961(2019) [pubmed]

submitter keyword: Chemical cross-linking

DSS

PDH

DMTMM

structural proteomics

bovine serum albumin

Alexander Leitner
contact affiliation	Institute of Molecular Systems Biology, ETH Zürich, Switzerland
contact email	leitner@imsb.biol.ethz.ch
lab head
Eugen Netz
contact affiliation	Biomolecular Interactions, Max Planck Institute for Developmental Biology
contact email	eugen.netz@gmail.com
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/2020/10/PXD014523

PRIDE project URI

• PRIDE
  1. PXD014523
     1. Label: PRIDE project
     2. Name: Comparison of OpenPepXL and xQuest on a Labeled Cross-Linking MS dataset