ProLuCID statistics

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ProLuCID specifications


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 Yes


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  • person_outline John R. Yates <>

Publication for ProLuCID

ProLuCID in pipelines

PMCID: 4992702
PMID: 27597932
DOI: 10.3389/fonc.2016.00183

[…] identified proteins with their corresponding peptide identifications is available in table s8 in supplementary material. we make all our raw mass spectrometry files, sepro results and intermediary prolucid/patternlab files available for downloading at, several reports corroborate with our results at the genomic and transcriptomic […]

PMCID: 5042483
PMID: 27684481
DOI: 10.1371/journal.pone.0163500

[…] acquired in the orbitrap analyzer with a resolution of 7,500 at m/z 400., we used two data analysis pipelines; one was proteome discoverer (pd, v.1.3.0. 339, thermo scientific) and the other was prolucid v.1.3.1 for peptide and protein identification [] in conjunction with census 1.57 for quantitation []., in the first pipeline, the raw files were searched against the ipi (international […]

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ProLuCID in publications

PMCID: 5949005
PMID: 29686080
DOI: 10.1073/pnas.1802354115

[…] (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 […]

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

[…] respectively, and maximum injection times of 120 ms and 500 ms for ms and ms/ms scans respectively., tandem mass spectra were extracted from raw files using rawconverter 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 […]

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

[…] identification was done with integrated proteomics pipeline–ip2 (integrated proteomics applications). tandem mass spectra were extracted from raw files using rawextract 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 […]

PMCID: 5834214
PMID: 29462184
DOI: 10.1371/journal.ppat.1006892

[…] gradient., protein and peptide identification were performed with integrated proteomics pipeline—ip2 (integrated proteomics applications, san diego, ca. 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 […]

PMCID: 5810618
PMID: 29441361
DOI: 10.1126/sciadv.aao3424

[…] 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 […]

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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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