Link to Wouter's main folder: https://rockefeller.box.com/s/xclw8qaar6znagu0917bwyh4ybgvxrgq
LC-MS/MS Analysis: Samples were dried on speed-vac, resuspended in lysis buffer (5 % SDS, 8 M urea, 100 mM glycine pH 7.55), reduced (Dithiothreitol 25 mM, 37 ºC, 30 minutes), alkylated (Iodoacetamide 100 mM, room temperature, 30 minutes in darkness) and trypsin digested on S-trap columns (Protifi) using the high recovery protocol (http://www.protifi.com/wp-content/uploads/2018/08/S-Trap-micro-high-recovery-quick-card.pdf). After elution, samples where dried up on speed-vac again and resuspended in 25 uL of 0.1 % (v/v) formic acid in water (MS quality, Thermo). Mass spectral analysis was conducted on a Thermo Scientific Orbitrap Exploris. The mobile phase consisted of 0.1 % (v/v) formic acid in water (A) and 0.1 % (v/v) formic acid in acetonitrile (B). Samples were loaded using a Dionex Ultimate 3000 HPLC system onto a 75 um x 50 cm Acclaim PepMapTM RSLC nanoViper column filled with 2 µm C18 particles (Thermo Scientific) using a 120-minute LC-MS method at a flow rate of 0.3 µL/min as follows: 3 % B over 3 minutes; 3 to 45 % B over 87 minutes; 45 to 80 % B over 1 minute; then wash at 80 % B over 14 minutes, 80 to 3 % B over 1 minutes and then the column was equilibrated with 3 % B for 14 minutes. For precursor peptides and fragmentation detection on the mass spectrometer, MS1 survey scans (m/z 200 to 2000) were performed at a resolution of 120,000 with a 300 % normalized AGC target. Peptide precursors from charge states 2-6 were sampled for MS2 using DDA. For MS2 scan properties, HCD was used and the fragments were analyzed in the orbitrap with a collisional energy of 30 %, resolution of 15000, Standard AGC target, and a maximum injection time of 50 ms.
Raw files and sample list description: https://rockefeller.box.com/s/9pjrsywlu3dybs5ujvjo7gy8zvq596xd
Chromatograms and PD results summary:
First set: https://rockefeller.box.com/s/5oybw4y6cm8pzl3mbmren2i81q92ylz7
Second set (incomplete): https://rockefeller.box.com/s/ck2j9iu0spe5rhc55pk4mwc8yzbk52ad
Second set (completed): https://rockefeller.box.com/s/2jxvii3uvtis77yat8qisjdehuakn0c5