pFind protocols

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pFind specifications

Information


Unique identifier OMICS_02467
Name pFind
Alternative name pFind Studio
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 3.1.3
Stability Stable
Requirements
NET framework
Maintained Yes

Subtool


  • Open-pFind

Versioning


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Documentation


Maintainers


  • person_outline Wen Gao <>
  • person_outline Si-Min He <>
  • person_outline pFind Team <>

Additional information


http://pfind.ict.ac.cn/software/pFind/pFind_2.wmv

Publications for pFind

pFind in pipeline

2014
PMCID: 3963859
PMID: 24664103
DOI: 10.1371/journal.pone.0091380

[…] a final concentration of 0.1%., to determine protein compositions of the cross-linked samples, we used maxquant software (as described above). to search for the cross-linked peptides, we used plink (pfind studio) . the following parameters were used: precursor mass tolerance, 50 ppm; fragment mass tolerance, 20 ppm; cross-linker, light [d0]-bs3 and heavy [d4]-bs3 (cross-linking sites, k […]


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pFind in publications

 (25)
PMCID: 5937861
PMID: 29756007
DOI: 10.1007/s41048-018-0050-6

[…] ink 2 is ~40 times faster 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. 3, in this paper, we present a step-by-step disulfide mapping protocol using the method we developed in 2015. as shown in fig. , this protocol contai […]

PMCID: 5755487
PMID: 29286378
DOI: 10.3791/56747

[…] searching note: there is different software available for database searching. maxquant, for instance, is freely available. convert .raw-files into .mgf-files using a pxtract conversion tool (http://pfind.ict.ac.cn/downloads.html).perform database search using typical search parameters: database, swissprot; peptide mass tolerance, 10 ppm; fragment mass tolerance, 0.5 da; enzyme, trypsin; missed […]

PMCID: 5684413
PMID: 29133780
DOI: 10.1038/s41467-017-01654-6

[…] 2500 v in the nano-lc (liquid chromatography) esi ms/ms mode. for ltq orbitrap xl™ etd mass spectrometer analysis, the ion source voltage is set to 1500 v. ms/ms data were searched using the pfind program for o-glcnacylated peptides, and the spectra were annotated using plabel–., the collected purified proteins (300 ng) were incubated with gst fusion proteins (100–200 ng) bound on gs4b […]

PMCID: 5656675
PMID: 29070817
DOI: 10.1038/s41598-017-14337-5

[…] internal calibration of the orbitrap was performed using the lock mass option (lock mass: m/z 445.120025)., raw data files were converted into mgf format using pxtract software tool (http://pfind.ict.ac.cn/software.html). potential cross-links were then identified by database searching against a reduced database containing atg18 using plink search engine. search parameters were: […]

PMCID: 5585273
PMID: 28874712
DOI: 10.1038/s41467-017-00535-2

[…] fine-scoring step., the second step is fine-scoring, which was a scoring scheme for a gsm. for each valid glycan candidate after coarse scoring, the corresponding candidate peptides were searched by pfind based only on the peptide backbone mass, . pfind has been compiled into a static link library that could be called automatically by pglyco 2.0 without installing pfind studio. after peptide […]


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pFind institution(s)
Key Laboratory of Intelligent Information Processing of the Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; National Institute of Biological Sciences, Beijing, Beijing, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China; State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China

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