Additional file 2: of Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum

Protein identification results from using ProteinPilot™ to search a composite (Bos taurus, Ovis aries and Carpra hircus) UniProtKB protein sequence database of serum samples derived from the first, second and third in-gel and in-solution digestion with a results quality of FDR ≤1%; ≥ 2 peptides for the highest scoring member of the protein group to be considered confidently identified. Each tab contains a list of protein IDs based on the quantity of protein loaded (μg), digestion workflow or sample conditions as follows: 1st_In-gel_digestion_2 μg = first in-gel (2 μg); 1st_In-gel_digestion_10 μg = first in-gel (10 μg); 1st_In-gel_digestion_22 μg = first in-gel (22 μg); All_1st_In-gel_digestion_IDs = all first in-gel samples; 2nd_In-gel_digestion_100 μgGelA = second in-gel digestion of Gel A (100 μg); 2nd_In-gel_digestion_50 μgGelA = second in-gel digestion of Gel A (50 μg); 2nd_In-gel_digestion_50 μgGelB = second in-gel digestion of Gel B (50 μg); 2nd_In-gel_digestion_100μgGelB = second in-gel digestion of Gel B (100 μg); 2nd_In-gel_digestion_50μgGelB = second in-gel digestion of Gel B (50 μg); All_2nd_In-gel_digestion_IDs = composite of all second in-gel digestion samples; 3rd_In-gel_digestion_200μg = crude serum protein of the third in-gel digestion (200 μg); 3rd_In-gel_digestion_100μg = crude serum protein of the third in-gel digestion (100 μg); 3rd_In-gel_digest_100μgx2CrudeI = crude serum protein with a protease inhibitor (Roche) of the third in-gel digestion (100 μg × 2); 3rd_In-gel_digest_100μgx2AcePPT = acetone precipitated serum protein without a protease inhibitor of the third in-gel digestion (100 μg × 2); 3rd_In-gel_digest_100μgx2No_I = crude serum protein without a protease inhibitor of the third in-gel digestion (100 μg × 2); All_3rd_In-gel_Digestion_IDs = composite of all third in-gel digestion samples; All_In-gel_digestion_IDs = all in-gel digestion workflow; 1st_In-solution_digestion_10 μg = acetone precipitated serum protein from the first in-solution digestion (10 μg); 2nd_In-solution_digestion_20 μg = crude serum protein from the second in-solution digestion (20 μg); 3rd_In-solution_digestion_100μg = crude serum protein from the third in-solution digestion (100 μg); All_In-solution_digestion_IDs = all in-solution workflow samples; All_Proteins + Peptide_Sequences = 274 protein IDs and peptide sequences of the entire in-gel and in-solution digestion experiments. (XLSX 423 kb)