TMT
Ensure empty channels/ TMT labels are set as "none" under the column Label.
Example for an IP-MS TMT10 run of 3 baits and 1 control with two repeats per condition.
Sample file (IP-MS)Example for an IP-MS TMT10 run for cancer driver fusion FUS-ERG and 1 control with two repeats per condition.
Sample file (Fusion IP-MS)Example for benchmarking dataset (downsampled) of a TMT9 run of human yeast proteome with a yeast proteome spike-in at specific ratios. Run on Orbitrap Fusion Lumos.
Sample file (Whole-proteome)Example for phospho-proteome benchmarking dataset (downsampled) of a TMT10 run of human with a yeast proteome spike-in at specific ratios. Published by Hogrebe et al. Nature Communications 2018 as TMT MS3 OTMC.
Sample file (Phospho-proteome)SILAC
Example for an IP-MS (heavy and light - two channels) run on METTL3 with a forward and reverse repeat.
Sample file (IP-MS - Protein level)DIA-LFQ
Example for an IP-MS run on Bruker of 4 conditions with 3 repeats each.
Sample file (IP-MS)Example for benchmarking dataset (downsampled) of human yeast proteome with a yeast proteome spike-in at specific ratios. Run on Bruker timsTOF with 80 min gradient.
Sample file (Whole-proteome)TMT
IP-MS TMT10 run (downsampled) of 3 baits and 1 control with two repeats per condition.
Sample file (IP-MS) S/N file for Proteome Discoverer searchIP-MS TMT10 run for cancer driver fusion FUS-ERG and 1 control with two repeats per condition.
Sample file (Fusion IP-MS) S/N file for Proteome Discoverer searchBenchmarking dataset (downsampled) of a TMT9 run of human yeast proteome with a yeast proteome spike-in at specific ratios. Run on Orbitrap Fusion Lumos.
Sample file (whole proteome) S/N file for Proteome Discoverer searchBenchmarking phosphoproteome dataset (downsampled) of a TMT9 run of human with a yeast proteome spike-in at specific ratios. Published by Hogrebe et al. Nature Communications 2018.
Sample file (phospho proteome) S/N file for Proteome Discoverer searchSILAC
IP-MS run on METTL3 (light and heavy) Wild Type -vs- Control Forward run.
Sample file (IP-MS) COMET searchIP-MS run on METTL3 (light and heavy) Wild Type -vs- Control Reverse run.
Sample file (IP-MS) COMET searchDIA-LFQ
IP-MS run on Bruker of 4 conditions with 3 repeats each.
Sample file (IP-MS - Protein level)Benchmarking dataset (downsampled) of human yeast proteome with a yeast proteome spike-in at specific ratios. Run on Bruker timsTOF with 80 min gradient.
Sample file (Whole Proteome - Protein level)