Datasets
This page provides a list of examples that have been used to test ProteoSuite and X-Tracker Software.
Datasets:
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:
- ksl_1_10.mzML (45.2 MB)
- ksl_1_20.mzML (33.5 MB)
- ksl_1_50.mzML (28.2 MB)
- ksl_1_100re.mzML (19.5 MB)
- ksl_1_10.mzid (16.5 MB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
- ksl_1_20.mzid (14.3 MB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
- ksl_1_50.mzid (15.0 MB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
- ksl_1_100re.mzid (14.8 MB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
Other available formats:
- ks1_1_10.mgf (82.9 MB)
- ks1_1_20.mgf (58.7 MB)
- ks1_1_50.mgf (45.5 MB)
- ks1_1_100re.mgf (25.5 MB)
- ksl_1_10.xml (1.14 MB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
- ksl_1_20.xml (1.04 MB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
- ksl_1_50.xml (891 KB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
- ksl_1_100re.xml (923 KB) - Peptide identifications against the UniProtKB/Swiss-Prot database using Mascot.
Database:
- ksl_itraq.fasta (2.13 KB) - You can use this artificial database to perform peptide identification via MSGFPlus.
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