PEP-Miner protocols

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PEP-Miner specifications


Unique identifier OMICS_23684
Name PEP-Miner
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No


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Publication for PEP-Miner

PEP-Miner in pipelines

PMCID: 3031555
PMID: 21305017
DOI: 10.1371/journal.pone.0016334

[…] (student's test; p<0.05) in all 3 hibm samples versus all 3 controls were identified by ms/ms spectra. peptides from 34 extracted spots were related to 26 different proteins by using sequest and pep-miner softwares with comparison to the human part of nr-ncbi database (, ). when similar proteins were identified at different spots their altered expression was always in the same direction […]

PMCID: 1783643
PMID: 17227583
DOI: 10.1186/1477-5956-5-3

[…] same peptides had very low pairwise similarity. it is thus desirable to find a more robust and stable reference to represent the peptide when a group of spectra for the same peptide are available. pep-miner [] introduced a method to generate a representative for a spectrum cluster which involved a sophisticated procedure to merge peaks, filter noise and identify the significant peaks. another […]

PMCID: 1488847
PMID: 16526958
DOI: 10.1186/1471-2164-7-46

[…] cid using a 4700 maldi-tof-tof mass spectrometer (applied biosystems) or a nano-capillary rp-hplc and esi-qit mass spectrometer (lcq-deca, thermofinnigan). the ms data was analysed using sequest [], pep-miner [] and mascot [] software tools and searching the ncbinr or zfin zebrafish databases. each peptide identified was then manually checked against the corresponding swiss-prot/trembl/pir […]

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PEP-Miner in publications

PMCID: 5931534
PMID: 29717115
DOI: 10.1038/s41467-018-03907-4

[…] followed by collision induced dissociation (cid) of the 5 most dominant ions selected from the first ms scan. the mass spectrometric data was clustered and analyzed using the sequest software and pep-miner, searching against the human sequences within the nr-ncbi database., fragments of the guassia luciferase (referred to as l1 (amino acids 1–93) and l2 (amino acids 94–169)) were fused […]

PMCID: 5645330
PMID: 29042634
DOI: 10.1038/s41598-017-13831-0

[…] data) and mmass., spectral clustering was performed using ms-cluster v2, an open source software for tmt dataset clustering. ms-cluster uses a hierarchical clustering algorithm similar to the pep-miner algorithm, but is optimized for analysis of large numbers of mass spectra. the algorithm clusters spectra in the tmt dataset by similarity using the normalized dot-product, which has shown […]

PMCID: 3391292
PMID: 22792391
DOI: 10.1371/journal.pone.0040636

[…] conditions, as previously described . the ms data were clustered and analyzed using sequest software (version 3.31; j. eng and j. yates, university of washington and finnigan, san jose, ca, usa) and pep-miner searching against the rat part of the uniprot database., before ir and 4, 8 and 12 weeks post-ir, rats were sacrificed and ssgs were removed for rna isolation using the rneasy micro kit […]

PMCID: 3339871
PMID: 22558304
DOI: 10.1371/journal.pone.0036008

[…] full ms scan followed by collision induced dissociation (cid) of the seven most dominant ions selected from the first ms scan. the mass spectrometry data was clustered and analyzed using sequest and pep-miner , searching against the arabidopsis database. in order to compare between the quantities of the different isoforms, several unique peptides were used. as the peak sequence can alter […]

PMCID: 3321617
PMID: 22095288
DOI: 10.1038/cdd.2011.149

[…] fragmentation method. the mass spectrometry data were analyzed using the sequest 3.31 software (j eng and j yates, university of washington, seattle, wa, usa, and finnigan, san jose, ca, usa) and pep-miner searching against the human part of the ncbi-nr database., student's t-test was used to compare the differences between two groups. statistical analysis of the immunogold labeling […]

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PEP-Miner institution(s)
IBM Haifa Research Lab, Haifa, Israel; The Smoler Proteomics Center, Department of Biology, Technion, Haifa, Israel

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