An example of a database search report from Scaffold (Proteome Software). These reports provide a convenient mechanism for viewing information on protein identifications, GO annotations for all identified proteins, sequence coverage maps, and MS/MS spectra. In addition, Scaffold files can be used to provide data analysis information necessary for publication of results in a scientific journals.
An example of SWATH 2.0 data analysis. A complex protein mixture was digested with trypsin, then spiked with β-galactosidase (Ecoli) digestion in variable concentrations (1, 2.5, 5, 10, 15, 30 fmol/ul), triplicate runs for each sample. The graph of principle component analysis is shown below. The up panel shows PC values of each run (left) and each protein (right); (A) All 18 runs were divided into 6 groups which shows a good reproducibility of DIA runs; (B) shows the protein changes among samples, which is far away from (0, 0); (C) shows β-galactosidase response changes with samples’ concentration.
A t test for the experiment from last page. (A) statistic values for proteins between every two groups comparison; (B) the Christmas tree graph for the comparison between group 1 (1fmol/ul β-galactosidase) to group 3 (5fmol/ul β-galactosidase), where t=-24.04, p=1.78x10E-5; (C) the Christmas tree graph for the comparison between group 1 to group 4, where t=-83.60; p=1.22x10E-7.
Scaffold version 4.4.8: Scaffold is used to report results of proteomics experiments in a format that is easy for researchers to understand. In addition, Scaffold facilitates publication of experimental results by providing a description of the data analysis protocol and tools for exporting results in a format that is appropriate for publication.
PEAKS Studio, version 7.5:PEAKS is a tool which provides cutting-edge capabilities for identification and quantification of bottom-up proteomics data. Its search algorithm is complementary to Mascot in that it performs de novo sequencing and uses these results for database searching. In addition, PEAKS has been shown in various ABRF studies to perform very strongly in the identification of single amino acid variants and unexpected post-translational modifications.
Progenesis QI for proteomics, version 2.0: This software is used for label-free quantification based on MS1 peak volumes. LC-MS data files for multiple experimental conditions and analytical replicates are aligned by accurate mass and retention time, and then database searching is performed in order to assign peptide sequences to features identified by the software. The software provides multiple options for using the resulting peptide assignments to infer protein-level quantification. In addition, information for features without spectral identification can be exported and used to drive targeted LC-MS methods in order to gain additional peptide assignments.
Mass Profiler Pro. version 12.6.1: This data analysis software tool provides advanced quantification, statistical analysis and visualization tools for proteomics, transcriptomics, lipidomics and metabolomics experiments.
Skyline: This open source software, from the MacCoss laboratory at the University of Washington, is valuable in the analysis of data from all varieties of quantitative experiments – including MS1-based quantification from DDA experiments, SRM, PRM and DIA.
Ingenuity Pathway Analysis: Our laboratory has a license for this web-based tool, which is a useful hypothesis-generating tool for the analysis of quantitative data. It can also be useful in the integration of data from multi-omics experiments.