Protocols

PAnalyzer specifications

Information


Unique identifier OMICS_27839
Name PAnalyzer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C#
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
NET, GTK#
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Gorka Prieto

Publication for PAnalyzer

PAnalyzer citations

 (2)
library_books

In Depth Proteomic Characterization of Classical and Non Classical Monocyte Subsets

2018
Proteomes
PMCID: 5874767
PMID: 29401756
DOI: 10.3390/proteomes6010008

[…] vel and protein level using Mayu [] were calculated, and protein identifications were obtained by applying the criteria of PSM FDR < 1% and protein FDR < 1%. Protein inference was performed using the PAnalyzer algorithm []. Those proteins not labelled as non-conclusive by this algorithm were considered to be observed proteins in the sample.The quantification of proteins was performed using a spect […]

call_split

Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence

2016
J Proteome Res
PMCID: 5099979
PMID: 27581094
DOI: 10.1021/acs.jproteome.6b00437
call_split See protocol

[…] PSM level and protein level using Mayu were calculated, and protein identifications were obtained applying the criteria of PSM FDR < 1% and protein FDR < 1%. Protein inference was performed using the PAnalyzer algorithm. Only those missing proteins labeled as conclusive by this algorithm and with at least 2 proteotypic peptides were considered as observed missing proteins in the sample. […]

PAnalyzer institution(s)
Department of Communications Engineering, University of the Basque Country (UPV/EHU), Bilbao, Spain; Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain; Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain; Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Proteolysis in diseases, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
PAnalyzer funding source(s)
Supported by UPV/EHU, MCINN, GV/EJ, ERDF and ESF; by the Department of Industry of the Basque Government (ETORTEK grant IE09-256); by Fundacao para a Ciencia e a Tecnologia (FCT) Ciencia 2007 and by European Social Fund; by FCT and by FCT grants (PTDC/QUI-BIQ/099457/2008 and PTDC/EIA-EIA/099458/2008).

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