Latin Square Data

This page contains links to the Latin Sqaure data set from the manuscript "SuperHirn - a novel tool for high resolution LC-MS based peptide/protein profiling". The available data spans the raw as well as preprocessed LC-MS runs (e.g. detected MS1 features), collected MS2 peptide identifications processed on the TransProteomicsPipeline (TPP) and the constructed MasterMaps.

Preprocessed LC-MS runs: The Latin Square data dilution outline is perfomed over 6 LC-MS runs over which the concentrations of 6 standart proteins are alterated (see table 1 in the manuscript for details). Each of the LC-MS runs is anaylzed in triplicates. LC-MS runs obtained from high resolution FT mass spectrometer are converted to mzXML format ( see below of the page a detailed table of the mzXML runs). The LC-MS runs are processed by a feature extraction routine and then stored in a novel XML format called Annotated Peptide Markup Language (APML, Vitek et al, 2006).
[Download files via this link ]

MS2 peptide identifications: MS2 scans are collected during every LC-MS run and processed on the TPP to obtain validated peptide assignments, which are formated in pepXML.
[Download files via this link ]

LC-MS MasterMaps: For every replicate set, the 6 LC-MS runs are combined into a MasterMap by multi dimensional LC-MS alignment. The MasterMaps contain the NOT intensity normalized MS1 aligned features together with their MS2 peptide assignments. The MasterMaps are stored in APML format.
[Download files via this link ]

LC-MS MasterMaps of all Replicates: The link below contains the MasterMap of all 18 replicates. The MasterMap contains the NOT intensity normalized MS1 aligned features together with heir MS2 peptide assignments. The MasterMaps is stored in tab-delimited format.
[Download files via this link ]

Reference:
Vitek, O., Brusniak, M.-Y., Garbutt, A., Campbell, D., Eddes, J., Letarte, S., Mueller, L.N., Martin, D., Watts, J., Zhang, N. and Aebersold, R. (2006)
A combined LC-MS and LC-MS/MS inferential framework for reliable and reproducible discovery of candidate biomarkers. ASMS Conference on Mass Spectrometry. Seattle.

Further weblinks:
SuperHirn home page

Contact:
Contact Lukas Mueller for questions reagrding this data set.


mzXML LC-MS runs:

LC-MS name

Dilution number

Replicate set

download

B06-8004_p.mzXML

1

1

save this linked file

B06-8010_p.mzXML

2

1

save this linked file

B06-8006_p.mzXML

3

1

save this linked file

B06-8012_p.mzXML

4

1

save this linked file

B06-8008_p.mzXML

5

1

save this linked file

B06-8014_p.mzXML

6

1

save this linked file

B06-8034_p.mzXML

1

2

save this linked file

B06-8016_p.mzXML

2

2

save this linked file

B06-8024_p.mzXML

3

2

save this linked file

B06-8030_p.mzXML

4

2

save this linked file

B06-8036_p.mzXML

5

2

save this linked file

B06-8032_p.mzXML

6

2

save this linked file

B06-8022_p.mzXML

1

3

save this linked file

B06-8038_p.mzXML

2

3

save this linked file

B06-8028_p.mzXML

3

3

save this linked file

B06-8018_p.mzXML

4

3

save this linked file

B06-8026_p.mzXML

5

3

save this linked file

B06-8020_p.mzXML

6

3

save this linked file