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Protocols

ProLuCID specifications

Information


Unique identifier OMICS_13626
Name ProLuCID
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Input data Protein FASTA databases or pre-processed databases
Input format FASTA
Output data Peptide identification
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for ProLuCID

ProLuCID citations

 (119)
library_books

Systemic surfaceome profiling identifies target antigens for immune based therapy in subtypes of advanced prostate cancer

2018
Proc Natl Acad Sci U S A
PMCID: 5949005
PMID: 29686080
DOI: 10.1073/pnas.1802354115

[…] er (Thermo Fisher Scientific). RAW-Xtract (Version 1.8) was used to extract peak list information from Xcalibur-generated RAW files. Database searching of the MS/MS spectra was performed by using the ProLuCID algorithm (Version 1.0). Other database search parameters included (i) precursor ion mass tolerance of ±20 ppm; (ii) fragment ion mass tolerance of ±400 ppm; (iii) only peptides with fully tr […]

library_books

The influence of transcript assembly on the proteogenomics discovery of microproteins

2018
PLoS One
PMCID: 5870951
PMID: 29584760
DOI: 10.1371/journal.pone.0194518

[…] Tandem mass spectra were extracted from raw files using RawConverter 1.0.0.0 and searched with ProLuCID using Integrated Proteomics Pipeline–IP2 (Integrated Proteomics Applications). We used four custom databases created from the in silico 3-frame translation of RNA-Seq data from HEK293 cells d […]

library_books

A proteomic insight into vitellogenesis during tick ovary maturation

2018
Sci Rep
PMCID: 5856802
PMID: 29549327
DOI: 10.1038/s41598-018-23090-2

[…] tide identification was done with Integrated Proteomics Pipeline–IP2 (Integrated Proteomics Applications). Tandem mass spectra were extracted from raw files using RawExtract 1.9.9.2 and searched with ProLuCID against a local R. microplus protein database (Rm-INCT-EM) containing 22,010 sequences previously produced by our research group using Illumina Sequencing technology (BioProject ID PRJNA23200 […]

call_split

Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na+/K+ transporting subunit Alpha 1 and prohibitin as host cell factors involved in the life cycle of mammarenaviruses

2018
PLoS Pathog
PMCID: 5834214
PMID: 29462184
DOI: 10.1371/journal.ppat.1006892
call_split See protocol

[…] Protein and peptide identification were performed with Integrated Proteomics Pipeline—IP2 (Integrated Proteomics Applications, San Diego, CA. http://www.integratedproteomics.com/) using ProLuCID and DTASelect2 algorithms. DTASelect parameters were—p 2 -y 1—trypstat—pfp .01 –extra-pI-DB-dm-in. Spectrum raw files were extracted into ms2 files from raw files using open source RawExtract […]

library_books

Increased proteomic complexity in Drosophila hybrids during development

2018
Sci Adv
PMCID: 5810618
PMID: 29441361
DOI: 10.1126/sciadv.aao3424

[…] bitrap Velos mass spectrometer (Thermo Fisher Scientific; fig. S5A) in biological triplicate. Relative ion abundance was extracted with Census () using tandem mass spectra of peptides identified with ProLuCID () in a search against a combined database of D. melanogaster and D. simulans proteomes (fig. S5B). All peptide spectrum matches and associated quantitative values as well as identified prote […]

call_split

Integrated omics dissection of proteome dynamics during cardiac remodeling

2018
Nat Commun
PMCID: 5760723
PMID: 29317621
DOI: 10.1038/s41467-017-02467-3
call_split See protocol

[…] ccumulation targets were 1.0E4 and 1.0E6, respectively. MS1 lock mass (m/z 425.120025) and dynamic exclusion (90 s) were used. Peptide identification was performed using the database search algorithm ProLuCID against a reverse-decoyed protein sequence database (Uniprot Reference Proteome, reviewed, accessed April-08–2014, 16,672 forward entries). Static cysteine carboxyamidomethylation (57.02146 D […]

Citations

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ProLuCID institution(s)
Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA; Dow AgroSciences LLC, Indianapolis, IN, USA
ProLuCID funding source(s)
The work is supported by NIH Grant 5U01 DE016267-04, 5R01 HL079442-04, R01 MH067880, P41 GM103533 and NHLBI contract # HHSN268201000035C.

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