PatternLab statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

PatternLab specifications

Information


Unique identifier OMICS_27885
Name PatternLab
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Maintainers


  • person_outline Diogo B. Lima
  • person_outline Paulo Carvaho
  • person_outline Marlon Santos
  • person_outline Valmir Barbosa

Publications for PatternLab

PatternLab citations

 (40)
library_books

Embryonic stem cell derived cardiomyocytes for the treatment of doxorubicin induced cardiomyopathy

2018
PMCID: 5799903
PMID: 29402309
DOI: 10.1186/s13287-018-0788-2

[…] of 1 × 10–6 ions. The 14 most intense ions were subjected to MS2 acquisition in the LTQ using normalized collision-induced dissociation (CID) of previously fragmented ions.MS data were analyzed with PatternLab (version 4.0.0.62) using a Uniprot Mus Musculus database downloaded in June 2017. Search parameters were semi-tryptic hydrolysis, two missed cleavages, oxidation of methionine as variable a […]

library_books

The PEG responding desiccome of the alder microsymbiont Frankia alni

2018
Sci Rep
PMCID: 5768760
PMID: 29335550
DOI: 10.1038/s41598-017-18839-0

[…] resented as percentage of the NSAF sum considering all proteins. Proteome comparison between both conditions was done taking into account the five biological replicates with the TFold module from the PatternLab software and standard normalisation, as previously described. […]

library_books

Tick Host Range Adaptation: Changes in Protein Profiles in Unfed Adult Ixodes scapularis and Amblyomma americanum Saliva Stimulated to Feed on Different Hosts

2017
PMCID: 5742094
PMID: 29312895
DOI: 10.3389/fcimb.2017.00517

[…] In order to investigate if shared proteins were differentially secreted I. scapularis and A. americanum when stimulated to start feeding on different hosts, pairwise comparison analyses using the PatternLab's TFold module (Carvalho et al., ) were conducted (Figure , Tables , ). This analysis demonstrated that some of the shared proteins were secreted at equivalent levels (red dots), not signif […]

library_books

Construction of Mycobacterium tuberculosis cdd knockout and evaluation of invasion and growth in macrophages

2017
PMCID: 5661903
PMID: 29091140
DOI: 10.1590/0074-02760170105

[…] ependent CID MS/MS spectra of the eight most intense ions in the ion trap, with dynamic exclusion applied. Mass spectra were searched for candidate peptides with the software Comet () in the platform PatternLab for Proteomics (). The database contained a non-redundant M. tuberculosis reference proteome (ID UP000001584, www.uniprot.org) and the reverse sequences of all entries. The validity of the […]

library_books

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

2017
Sci Rep
PMCID: 5595786
PMID: 28900110
DOI: 10.1038/s41598-017-10132-4

[…] e in cross-correlation scores (DeltaCN) larger than 0.08. Proteins with more than two peptides were identified as detected and were recorded, . The differential expression proteins were identified by PatternLab with TFold module between two samples, . The blue-dot proteins which have p-values of  < 0.05 and an absolute fold change >2.5 were classified as differentially expressed proteins. In the d […]

library_books

The EAL domain protein FcsR regulates flagella, chemotaxis and type III secretion system in Pseudomonas aeruginosa by a phosphodiesterase independent mechanism

2017
Sci Rep
PMCID: 5579053
PMID: 28860517
DOI: 10.1038/s41598-017-09926-3

[…] LC-MS/MS data analysis was performed in accordance to the PatternLab for proteomics 4.0 software (http://www.patternlabforproteomics.org) data analysis protocol.The proteome from P. aeruginosa strain K was downloaded from UniProt (May 2015) (http://www.unipr […]

Citations

Looking to check out a full list of citations?

PatternLab institution(s)
Computational Mass Spectrometry Group, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil; Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil; Department of Pathology, University of Michigan, MI, Ann Arbor, USA; Leonidas e Maria Deane Institute, Fiocruz Amazonas, Manaus, Brazil; Laboratory for Biological Mass Spectrometry, The Scripps Research Institute, La Jolla, USA; Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
PatternLab funding source(s)
Supported the National Institutes of Health (P41 GM103533, R01 MH067880, and R01 MH100175) and the UCLA/NHLBI Proteomics Centers (HHSN268201000035C). JJM acknowledges NIH Research Resources (5P41RR011823) and the National Institute of General Medical Sciences (8 P41 GM103533).

PatternLab reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PatternLab