Diffprot - software for non-parametric statistical analysis of differential proteomics data.
Mass spectrometry-based global proteomics experiments generate large sets of data that can be converted into useful information only with an appropriate statistical approach. We present Diffprot - a software tool for statistical analysis of MS-derived quantitative data. With implemented resampling-based statistical test and local variance estimate, Diffprot allows to draw significant results from small scale experiments and effectively eliminates false positive results. To demonstrate the advantages of this software, we performed two spike-in tests with complex biological matrices, one label-free and one based on iTRAQ quantification; in addition, we performed an iTRAQ experiment on bacterial samples. In the spike-in tests, protein ratios were estimated and were in good agreement with theoretical values; statistical significance was assigned to spiked proteins and single or no false positive results were obtained with Diffprot. We compared the performance of Diffprot with other statistical tests - widely used t-test and non-parametric Wilcoxon test. In contrast to Diffprot, both generated many false positive hits in the spike-in experiment. This proved the superiority of the resampling-based method in terms of specificity, making Diffprot a rational choice for small scale high-throughput experiments, when the need to control the false positive rate is particularly pressing.
Proteomics Laboratory, Biophysics Department, Institute of Biochemistry and Biophysics, Pol. Acad. Sci., ul. Pawinskiego 5A 02-106, Warsaw, Poland. esme@ibb.waw.pl
Agata
A
Malinowska
Michał
M
Kistowski
Magda
M
Bakun
Tymon
T
Rubel
Marta
M
Tkaczyk
Jolanta
J
Mierzejewska
Michał
M
Dadlez
D001426:Bacterial Proteins / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000032:analysis; D013058:Mass Spectrometry / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D011550:Pseudomonas aeruginosa / Q000378:metabolism; D012984:Software; D018709:Statistics, Nonparametric; D053719:Tandem Mass Spectrometry / Q000379:methods
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins