Mushan Li, Jian Liu, Qian Wang, Yuannyu Zhang, Jian Xu, Yijing Zhang, Feng Zhou and Zhen Shao (2018) MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes. (under review)

MAP

Version 1
Usage:
MAP.pl -text_data -strategy -window_size -step_size -fraction_of_proteins
opts:
-text_data              This tab-delimited text file is expected to be a table with 3 columns: (1) Gene symbols, (2) MS                                         intensities of sample 1 and (3) MS intensities of sample 2.
-strategy               Trimmed_total_count/Total_count/Pass
-window_size        Size of the sliding window to scan the ratio-intensity plot (similar to the M-A plot widely used for                                     microarray data analysis). By default: 400 proteins.
-step_size              Step size of the sliding window. By default: 100 proteins.
-fraction_of_proteins   The fraction of proteins with the weakest intensity changes of each window used to model                                             technical variations. They are assumed to be predominantly comprised of non-differentially                                             expressed proteins. By default: 50 (values higher than 60 or lower than 30 is not recommended).