Followed by two times 0.5 ml of 5 mg/mL a-cyano-4-hydroxy-cinnamic acid in 50 ACN and 0.5 TFA. Mass-to-charge (m/z) spectra were generated using MALDI-TOF MS (Microflex LT with software flexControl Version 3.0, Bruker Daltonics) in positive, linear ion mode and 350 laser shots. Initial laser power; 50 for 1?0 kDa and 60 for 10?60 kDa measurements, Laser Attenuator; Offset 25 and Range 20 . Pulsed ion extraction was set to 250 ns. Samples prepared with the WCX support beads were measured in the 1?0 kDa mass range and those prepared with the C8 beads were measured in both the 1?0 kDa and 10?160 kDa mass range. Calibration was performed using protein calibration standard I for 1?0 kDa measurements and protein calibration standard II (both Bruker Daltonics) for 10?60 kDa measurements.inhibitor described elsewhere [18,19]. Single C8 pretreated urine samples were used to identify specific protein masses smaller than 4 
kDa directly with vMALDI LTQ. Proteins larger than 4 kDa were identified using 1D-gelelectrophoresis with a 15 SDS gel and silver-blue staining. Bands were excised and subjected to reduction, alkylation and trypsin digestion before being measured on the vMALDI-LTQ. For LC-MS/MS two pooled urine samples were used to identify differentially excreted proteins between control (n = 5) and APAP-induced liver injury (n = 5; plasma ALT.5000 U/L). Urine samples were in-solution digested, after reduction and alkylation. The digested samples were loaded on stagetips for desalting and concentrating, and eluted to a final volume of 20 mL, 8 mL of which was used for analysis. To avoid contamination with polymers, an extra strong cation exchange purification step was performed. Database searches were performed using the Mus musculus RefSeq36 protein database supplemented with known contaminant proteins. For vMALDI LTQ the data search was performed using SEQUEST (v. 28 BioworksTM), for LC-MS/MS protein identifications were extracted from the data by means of the search program Mascot (v2.2; Matrix Science). The following modifications were allowed in the search: carbamidomethylation of cysteines (fixed), oxidation of methionine (variable) and acetylation of the N-terminus (variable). When appropriate, searches Autophagy specified tryptic specificity, allowing a single missed cleavage site. Additional parameters for vMALDI LTQ were 1.4 Da precursor ion mass tolerance and 1 Da fragment ion mass tolerance. For LC-MS/MS precursor ion mass tolerance was set to 10 ppm, and fragment ion mass tolerance was set to 0.8 Da. Proteins identified using vMALDI LTQ were considered significant with a peptide probability .1e-002, and a protein probability .1e-003. Validation of proteins identified using LC-MS/MS was performed by an in-house developed script (PROTON) as described elsewhere [19].ImmunoprecipitationUrine samples were pretreated with C8 beads and incubated overnight with PBS and 0.1 Triton containing 2 mM CaCl2 and CaM antibody at 4uC. Subsequently, magnetic beads that bind IgG (MagnabindTM Protein G Magnetic beads, Thermo scientific, Rockford USA) were added and incubated for two hours at RT. After removal of the unbound fraction, proteins were eluted from the beads using 50 ACN and 0.5 TFA. The eluted fraction was measured using MALDI-TOF MS, as described. To correct for non-specific binding to the magnetic IgG beads, a urine sample was analyzed as described without CaM antibody.Western blotUrine samples were normalized to creatinine (mouse samples) or prot.Followed by two times 0.5 ml of 5 mg/mL a-cyano-4-hydroxy-cinnamic acid in 50 ACN and 0.5 TFA. Mass-to-charge (m/z) spectra were generated using MALDI-TOF MS (Microflex LT with software flexControl Version 3.0, Bruker Daltonics) in positive, linear ion mode and 350 laser shots. Initial laser power; 50 for 1?0 kDa and 60 for 10?60 kDa measurements, Laser Attenuator; Offset 25 and Range 20 . Pulsed ion extraction was set to 250 ns. Samples prepared with the WCX support beads were measured in the 1?0 kDa mass range and those prepared with the C8 beads were measured in both the 1?0 kDa and 10?160 kDa mass range. Calibration was performed using protein calibration standard I for 1?0 kDa measurements and protein calibration standard II (both Bruker Daltonics) for 10?60 kDa measurements.described elsewhere [18,19]. Single C8 pretreated urine samples were used to identify specific protein masses smaller than 4 kDa directly with vMALDI LTQ. Proteins larger than 4 kDa were identified using 1D-gelelectrophoresis with a 15 SDS gel and silver-blue staining. Bands were excised and subjected to reduction, alkylation and trypsin digestion before being measured on the vMALDI-LTQ. For LC-MS/MS two pooled urine samples were used to identify differentially excreted proteins between control (n = 5) and APAP-induced liver injury (n = 5; plasma ALT.5000 U/L). Urine samples were in-solution digested, after reduction and alkylation. The digested samples were loaded on stagetips for desalting and concentrating, and eluted to a final volume of 20 mL, 8 mL of which was used for analysis. To avoid contamination with polymers, an extra strong cation exchange purification step was performed. Database searches were performed 
using the Mus musculus RefSeq36 protein database supplemented with known contaminant proteins. For vMALDI LTQ the data search was performed using SEQUEST (v. 28 BioworksTM), for LC-MS/MS protein identifications were extracted from the data by means of the search program Mascot (v2.2; Matrix Science). The following modifications were allowed in the search: carbamidomethylation of cysteines (fixed), oxidation of methionine (variable) and acetylation of the N-terminus (variable). When appropriate, searches specified tryptic specificity, allowing a single missed cleavage site. Additional parameters for vMALDI LTQ were 1.4 Da precursor ion mass tolerance and 1 Da fragment ion mass tolerance. For LC-MS/MS precursor ion mass tolerance was set to 10 ppm, and fragment ion mass tolerance was set to 0.8 Da. Proteins identified using vMALDI LTQ were considered significant with a peptide probability .1e-002, and a protein probability .1e-003. Validation of proteins identified using LC-MS/MS was performed by an in-house developed script (PROTON) as described elsewhere [19].ImmunoprecipitationUrine samples were pretreated with C8 beads and incubated overnight with PBS and 0.1 Triton containing 2 mM CaCl2 and CaM antibody at 4uC. Subsequently, magnetic beads that bind IgG (MagnabindTM Protein G Magnetic beads, Thermo scientific, Rockford USA) were added and incubated for two hours at RT. After removal of the unbound fraction, proteins were eluted from the beads using 50 ACN and 0.5 TFA. The eluted fraction was measured using MALDI-TOF MS, as described. To correct for non-specific binding to the magnetic IgG beads, a urine sample was analyzed as described without CaM antibody.Western blotUrine samples were normalized to creatinine (mouse samples) or prot.