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BioMed Research International
Volume 2016, Article ID 2891918, 13 pages
Research Article

PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data

1Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
2Department of Bioanalytics, University of Applied Sciences and Arts of Coburg, 96450 Coburg, Germany
3Department of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany
4Institute of Clinical Immunology, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
5Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany
6Department of Metabolomics, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
7Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark

Received 30 September 2015; Revised 28 November 2015; Accepted 29 November 2015

Academic Editor: Yudong Cai

Copyright © 2016 Stefan Kalkhof et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

I. Input parameter for the application to the STAT1 interaction network.

The header size of 1 and a single tabulator as field delimiter was chosen to structure the document. The amount of experiments was set to 3 with 6 samples per experiment. The accession number could be retrieved directly with the default extraction pattern “(.*)”, while the gene name was extracted from the description field through the extraction pattern “GN=(.*) P”. The taxonomy id was set manually to “9606” (Homo sapiens). The three experiments have been named manually and the associated sample values could be retrieved directly from appropriate fields. All adjusted parameters have been saved as a template for the ProteomeDiscoverer with three experiments and six samples and therefore can be loaded for upcoming parsing assignments.

Supplementary Table: AP-MS data of all proteins being quantified in this study. Additionally, for each protein the fallowing information are provided: (Quantification frequency, enrichment compared to control, prediction of STAT1 binding, function as chaperon or protease).

  1. Supplementary Material