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Protocols

pLink specifications

Information


Unique identifier OMICS_02404
Name pLink
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for pLink

pLink citations

 (36)
call_split

Mapping disulfide bonds from sub micrograms of purified proteins or micrograms of complex protein mixtures

2018
Biophysics Rep
PMCID: 5937861
PMID: 29756007
DOI: 10.1007/s41048-018-0050-6
call_split See protocol

[…] than pLink, with a friendly graphical interface and some further improvements in accuracy. pLink 2 was officially released on January 1, 2018 and can be downloaded at http://pfind.ict.ac.cn/software/pLink/.Fig. 1 Fig. 2 Fig. 3In this paper, we present a step-by-step disulfide mapping protocol using the method we developed in 2015. As shown in Fig. , this protocol contains three alternative sub-pr […]

library_books

Gcn4 Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein Protein Complex

2018
Cell Rep
PMCID: 5908246
PMID: 29562181
DOI: 10.1016/j.celrep.2018.02.097

[…] the Proteomics facility at the Fred Hutchinson Cancer Research Center, and data were analyzed as described (). Two different database search algorithms were used to identify EDC-crosslinked peptides: pLink () and the in-house-designed Nexus (). A 5% FDR was used for the results from both searches. Spectra were manually evaluated using the COMET/Lorikeet Spectrum Viewer (Trans-Proteomic Pipeline) ( […]

library_books

TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A

2018
Nat Commun
PMCID: 5847541
PMID: 29531219
DOI: 10.1038/s41467-018-03484-6

[…] ther a Thermo QExactive or a Thermo Fusion as above, but over a 4 h 7–37% acetonitrile gradient with charge 2+ or lower masses excluded from fragmentation. Cross-linked peptides were identified using pLink with an FDR of 0.05. Identified cross-links were further filtered to remove matches were either peptide was not ≥5 or ≤40 amino acids in length and with an e-value for the spectral match of ≤0.0 […]

call_split

The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY

2018
Sci Rep
PMCID: 5766551
PMID: 29330529
DOI: 10.1038/s41598-017-19019-w
call_split See protocol

[…] sion 1.5.4.0,) searching against the UniProt E. coli proteome set sequence database (version 2016_03). Identification of cross-linked peptides was performed essentially as described using the program pLink® for searching inter- or intra-molecular cross-links generated by amine-specific cross-linker DSS between peptides from SecY, SecE, SecG and YidC. The resulting set of peptide spectrum matches a […]

library_books

Combining Chemical Cross linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi subunit Protein Assemblies

2017
PMCID: 5755487
PMID: 29286378
DOI: 10.3791/56747

[…] .e., HCD fragmentation is triggered by the presence of peak pairs of defined mass difference in the mass spectra. NOTE: The "peak picking" option might not be available on every mass spectrometer.Use pLink software for identification of cross-linked di-peptides. Use minimized databases for identification. Typical search parameters are: instrument spectra, HCD; enzyme, trypsin; max. missed cleavage […]

library_books

Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites

2017
BMC Genet
PMCID: 5693503
PMID: 29149838
DOI: 10.1186/s12863-017-0557-8

[…] module of Stacks was then run, limiting the output to loci existing in at least 10% of the population with at least 5× coverage, resulting in 219,545 SNPs. The Populations module outputs SNP data in Plink and Structure formats, limited to a single SNP per locus, chosen at random to account for linkage. Inbreeding coefficient and neucleotide diversity were calculated by the populations module of S […]

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pLink institution(s)
College of Biological Sciences, China Agricultural University, Beijing, China

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