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Protocols

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


No version available

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 citations

 (26)
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

[…] 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. 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 […]

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 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 c […]

call_split

O GlcNAcylation of SIRT1 enhances its deacetylase activity and promotes cytoprotection under stress

2017
Nat Commun
PMCID: 5684413
PMID: 29133780
DOI: 10.1038/s41467-017-01654-6
call_split See protocol

[…] ypically 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–. […]

library_books

Structure based biophysical characterization of the PROPPIN Atg18 shows Atg18 oligomerization upon membrane binding

2017
Sci Rep
PMCID: 5656675
PMID: 29070817
DOI: 10.1038/s41598-017-14337-5

[…] d peptides. 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: fragment […]

library_books

pGlyco 2.0 enables precision N glycoproteomics with comprehensive quality control and one step mass spectrometry for intact glycopeptide identification

2017
Nat Commun
PMCID: 5585273
PMID: 28874712
DOI: 10.1038/s41467-017-00535-2

[…] pGlyco 2.0 program and the source code, as well as a manual for the program: http://pfind.ict.ac.cn/download/pGlyco/pGlyco2-stable.zip The RAW MS data of yeast and mouse glycoproteome analysis, as well as the original search results of pGlyco 2.0 have been uploaded to the PRIDE partn […]

library_books

Proteome wide acetylation dynamics in human cells

2017
Sci Rep
PMCID: 5579049
PMID: 28860605
DOI: 10.1038/s41598-017-09918-3

[…] with the Orbitrap as the detector. Dynamic exclusion was set to 60 seconds. HCD collision energy was set to 27, AGC target to 5e4 and maximum injection time to 200 msec.MS raw files were analyzed by pFind. MS/MS spectra were searched against the Human UniProt FASTA database [9606]. The modifications considered included acetylation and oxidation, and the fixed modification was carbamidomethylation […]

Citations

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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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