This page provides a list of examples that have been used to test ProteoSuite and X-Tracker Software.





Dataset 1

ID: D1-iTRAQ-4plex

Sample details:

All samples are an artificial mix of four proteins. Relative abundance is shown in the table below.

Sample Yeast Enolase (ENO) Rabbit Phosphorylase b (PHO) Bovine Heart Cytochrome C (CYT) Bovine serum abumin (BSA)
114 0.40 0.25 0.25 0.10
115 0.30 0.25 0.25 0.20
116 0.20 0.25 0.25 0.30
117 0.10 0.25 0.25 0.40

There are four experiments:

  • ksl_1_10
  • ksl_1_20
  • ksl_1_50
  • ksl_1_100

Experimental description:

Four samples were created using a combination of four different standard proteins (i.e. yeast Enolase, rabbit Phosphorilase b, bovine heart Cytochrome C and bovine Serum albumin) of known quantities. Peptides were separated and analyzed using an Ultimate Plus nano-LC system (Dionex) coupled to a QSTAR XL quadrupole TOF hybrid mass spectrometer (Applied Biosystems, Foster City, CA). Samples (60 μl) were loaded onto an Acclaim PA C16 pre-column (5 mm × 300 μm internal diameter, Dionex) at 20 μl/minute and washed with 0.1% formic acid (FA; also at 20 μl/minute) for 25 minutes to desalt the samples. Peptides were then eluted onto a PepMap C18 analytical column (15 cm × 75 μm internal diameter, Dionex) at 150 nl/minute and separated using a 165 minute gradient of 5-32% ACN (0.1% FA). The QSTAR XL was operated in information-dependent acquisition (IDA) mode, in which a 1 second TOF-MS scan from 400- 1,600 m/z was performed, followed by 3 second product ion scans from 100-1,580 m/z on the two most intense doubly (2+) or triply (3+) charged ions. Mass spectrometry data files were processed using the wiff2DTA software to generate centroided and uncentroided peak lists.


PSI Standard files:


Other available formats:




Other datasets




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