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Protocols

PEAKS specifications

Information


Unique identifier OMICS_02475
Name PEAKS
Alternative name PEAKS Online
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Input format RAW, YEP, D, BAF, LIFT, WIFF, RUN, SMS, XMS, DAT, mzData, pepXML, DTA, mzML, PKL, MGF, mzXML, XML
Output data Amino acid sequences with confidence scores for the entire sequences
Operating system Windows
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PEAKS

Versioning


No version available

Documentation


Maintainer


  • person_outline B. Ma

Additional information


An online version is available at: http://www.bioinfor.com/peaks-online/

Publication for PEAKS

PEAKS citations

 (9)
library_books

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random

2018
Genome Biol Evol
PMCID: 5786225
PMID: 29325123
DOI: 10.1093/gbe/evy005

[…] se gene, was identified in the D. shibae genome at position 98.7–102.8 kb, just outside peak 1 (, online). Genes encoding transposable elements or tRNAs were also not found within the DsGTA coverage peaks (, online). The origin and terminus of replication showed a higher frequency of methylated adenosines (m6A) (), whereas the frequency of methylated cytosines (m4C) lacked such a pattern (, onl […]

call_split

Plasma degradome affected by variable storage of human blood

2016
PMCID: 5037888
PMID: 27708557
DOI: 10.1186/s12014-016-9126-9
call_split See protocol

[…] Sequence interpretation of MS/MS spectra of naturally occurred peptides was performed by the interrogation of UniProt Homo Sapiens database using PEAKS Online v7.5 (Bioinformatics Solutions Inc.) with an FDR of 1 % and imported into the Progenesis QI software for quantitation. Average normalised abundance values were obtained via quantile norma […]

library_books

Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation

2015
Nat Genet
PMCID: 4626279
PMID: 26390058
DOI: 10.1038/ng.3402

[…] ve transcriptional enhancers. When we overlaid CTCF ChIP-seq from the ENCODE lymphoblastoid cell line GM12878 with ubiquitous DHSs, we saw dramatic enrichment of CTCF signal at low H3K4me3 ubiquitous peaks (, Online Methods), suggesting their a role in 3D chromatin structure. An early ENCODE study of 1% of the human genome across 6 unrelated cell types found that almost all ubiquitous DNase peaks […]

library_books

Sb2Se3 under pressure

2013
Sci Rep
PMCID: 3776230
PMID: 24045363
DOI: 10.1038/srep02665

[…] ef. . It should be noted, however, that the Raman spectra obtained with M/E/W and M/E exhibit also distinct differences between each other, e.g. completely different relative intensities of the Raman peaks [ online]. Therefore, it becomes clear that the choice of PTM affects the Raman response of Sb2Se3. Since the Raman response of Sb2Se3 at ambient conditions matches that of Sb2Se3 embedded in th […]

library_books

Temperature and species richness effects in phytoplankton communities

2012
PMCID: 3548109
PMID: 22847329
DOI: 10.1007/s00442-012-2419-4

[…] t complementary processes other than light use efficiency influenced nutrient uptake in phytoplankton communities of higher species richness. However, a clear increase in C:P ratios after temperature peaks (Online Resource Fig. S4) suggests that the complementary effects of light use may be more pronounced compared to potential other complementary processes involved in nutrient uptake. […]

library_books

Tbx2 and Tbx3 induce atrioventricular myocardial development and endocardial cushion formation

2011
PMCID: 3314179
PMID: 22130515
DOI: 10.1007/s00018-011-0884-2

[…] directly regulate these genes (Fig. b, c; Online Fig. 7). Two genes that are not influenced by Tbx3 in the myocardium but indirectly in the endocardium, Has2 and Sox9, were indeed devoid of any Tbx3 peaks (Online Fig. 7).Fig. 6Closer inspection of the Bmp2 locus revealed one particular genomic site with which Tbx3 interacts (Fig. c). In the developing heart, enhancer associated co-factor p300 was […]

Citations

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PEAKS institution(s)
Bioinformatics Solutions Inc; Waterloo, ON, Canada; Department of Biochemistry, The University of Western Ontario, London, ON, Canada; School of Computer Science, University of Waterloo, Waterloo, ON, Canada
PEAKS funding source(s)
This work was supported by funds from Natural Sciences and Engineering Research Council of Canada Discovery program and by Bioinformatics Solutions Inc.

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