Table 1

Quality report. An example of a quality report, generated by the software, when a profile matrix is created.

Experimentid: 1

experimentname : cerebrospinal fluid tryptic peptide profiles to diagnose leptomeningeal metastasis in breast cancer patients

Find maxima within distance (Da) : 0.50

Quantile threshold peak finding : 0.98

Combine peaks within distance (Da) : 0.50

Noisy spectra contain peak numbers > : 450

Maximum mass spectra per sample : 4

threshold binary table 0 < 1 > = : 2


Minimum mass (Da) : 800

Maximum mass (Da) : 4000

Calibration : yes

ALBMASSES(4)


number of masses in matrix : 1949


group : control group without breast cancer(group1_control)

total number of samples : 45

number of samples in matrix : 32

number of samples with too low number of replicates : 12

number of samples not in matrix that because all spectra cannot not be calibrated or are all too noisy : 1

(total number of 6 sample(s) with at least one noisy spectrum)


group : breast cancer without leptomeningeal metastasis(group2_breast_cancer)

total number of samples : 52

number of samples in matrix : 39

number of samples with too low number of replicates : 13

number of samples not in matrix that because all spectra cannot not be calibrated or are all too noisy : 0

(total number of 5 sample(s) with at least one noisy spectrum)


group : breast cancer with leptomeningeal metastasis(group3_leptomeningeal_metastasis)

total number of samples : 54

number of samples in matrix : 40

number of samples with too low number of replicates : 12

number of samples not in matrix that because all spectra cannot not be calibrated or are all too noisy : 2

(total number of 8 sample(s) with at least one noisy spectrum)


The profile matrix consists of peptide masses in all spectra of the samples on the columns against the number of occurrences of these masses in replicate spectra of the samples on the rows. The software stores the contents of the quality report as a text file, e.g. with the name 0.98_1_ALBMASSES(4)_sample4_binary2_quality.txt in the windows document root of the client workstation, namely in C:\Documents and Settings\username}\.

Titulaer et al. BMC Bioinformatics 2006 7:403   doi:10.1186/1471-2105-7-403

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