New IP2 version 3 is here!!

At Integrated Proteomics Applications we provide research institutions with our powerful proteomics data analysis platform, the Integrated Proteomics Pipeline (IP2). Integrated Proteomics Applications has been helping research hospitals, universities, pharmaceutical companies, and other research institutes with our innovative solutions. At IPA our goal is simple: to give you, the researcher, a complete, comprehensive proteomics software package.

What's new with IP2 version 3

  • Customize the IP2 using IDK
  • Project sharing
  • Improved user interface
  • Improved TMT data analysis (support multi-notch)
  • New TMT QuantCompare to statistically find significant proteins from biological replicates
  • Improved algorithm for MS1-based Quantitative analysis (SILAC, 15N, etc.)
  • Spectral count-based quantitative analysis using PLGEM (NSAF, EMPAI)
  • Gene Ontology Analysis
  • Improved label-free analysis
  • and more

Sign up for our mailing list.


IP2, The Integrated Proteomics Pipeline, provides an elegantly simple user friendly platform for rapid protein identification and quantification for proteomics studies.

Sherry Niessen, Staff Scientist The Scripps Research Institute

More testimonials >>


  • Custom Development Kit
  • Free for licensed users

IP2 Essential

  • Project Management
  • Share Projects
  • Protein/Peptide Identification
  • Spectral Count-based
    Quantitative Analysis on
    multiple samples (NSAF, EMPAI)
  • Statistical Analysis Tools
    (t-test, post-hoc analysis,
    ANOVA, PLGEM, more)
  • PTM Analysis
  • Single Computer Compatible
    (Linux, Mac)
  • Local Parallel Cluster
    Compatible (SGE, PBS, LSF)
  • Cloud Computing Compatible
    (Amazon EC2)

IP2 Quant

  • Stable Isotope Labeling (15N, SILAC,
    Dimethyl, 2H, custom labeling)
  • Isobaric Labeling (TMT, iTRAQ)
  • Protein/Peptide Identification
  • 15N Enrichment Calculation
  • Label-free Analysis
  • PTM Analysis
  • Quantitative Analysis on multiple
    samples with Graphs
  • Statistical Analysis Tools (t-test, post-hoc
    analysis, ANOVA, PLGEM,