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pLink specifications


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




No version available

Publication for pLink

pLink citations


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

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 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 […]


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

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) ( […]


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

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 […]


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

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

[…] sion,) 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 […]


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

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 […]


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

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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