MS Bioworks IP-works service enables researchers to visualize the wealth of biological information captured in an immuno-precipitation (IP) experiment.   Your precipitated samples are fractionated by SDS-PAGE and analyzed by nanoscale LC-MS/MS using state-of-the-art mass spectrometry.  Samples can be submitted in singlet and protein abundance compared within a sample or duplicate submission can be used to determine which events are germane to your experiment.

Studying circadian rhythm using the IP-works service
Circadian Locomotor Output Cycles Kaput (CLOCK) was tagged in-vivo and used for an immuno-precipitation from D. melanogaster brain lysate.  As a control the same IP was performed in the untagged wild type (WT).  Samples were fractionated using SDS-PAGE, digested using sequencing grade trypsin and analyzed by reverse phase nanoscale LC-MS/MS using state-of-the-art high resolution mass spectrometry.  Data were processed using Mascot (Matrix Science) and compiled for reporting purposes using Scaffold (Proteome Software)

Total Proteins 1274 1324
Sum of spectral counts 26613 24564
Sum of unique peptides 11483 10867
% FDR 0.3 0.5

A total of 1493 proteins to D. melanogaster were detected with two or more unique peptides at a false discovery rate of 0.3% (WT) and 0.5% (CLOCK).

230 proteins were observed as unique to the CLOCK test sample. These proteins were used to search known D. melanogaster pathways in KEGG. The circadian rhythm pathway dme04710 was populated with 5 known members, the Wnt signaling pathway dme04310 was populated with 16 known members

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