PDF《SUPPORTING INFORMATION》

265 144 sL/L 0.31796 0.40625 0.19572 0.24466 0.43586 0.23723 sL/uL 0.46618 0.68421 0.24335 0.32391 0.77259 0.31102 Amount (ug) 0.00697 0.01717 0.04341 0.11099 0.27504 0.69294 Amount (pmol) 0.1 0.25 0.63 1.6

4 10 Log2(Amount) -3.32193 -2 -0.66658 0.67807

2 3.32193 Supporting Table 1: Label-free features measured for albumin isoforms (1-100 dynamic range) digested with trypsin The three main yNXAF strategies are defined as: nNXAF, where label-free features (spectral counts, chromatographic peak areas, MS1 intensities or MS2 intensities) from peptides shared between mulitple proteins may be counted multiple times;

uNXAF, where label-free features derived from unique peptides are the only ones considered, and the shared spectral counts/peak areas/MS1 intensities/MS2 intensities are dismissed;

dNXAF, where label-free features from shared peptides are distributed amongst protein isoforms based on a distribution factor, d. MF: total MS2 intensities from peptides mapping to a protein SpC: total spectral counts from peptides mapping to a protein uSpC:spectral counts from peptides uniquely mapping to a protein sSpC: shared spectral counts from peptides mapping to more than one protein PA: total chromatographic peak areas from peptides mapping to a protein uPA: chromatographic peak areas from peptides uniquely mapping to a protein sPA: shared chromatographic peak areas from peptides mapping to more than one protein MI: total MS1 intensities from peptides mapping to a protein uMI: MS1 intensities from peptides uniquely mapping to a protein sMI: shared MS1 intensities from peptides mapping to more than one protein RSQ: square of the Pearson product moment correlation coefficients, obtained with the RSQ function in Microsoft Excel uMF: MS2 intensities from peptides uniquely mapping to a protein sMF: shared MS2 intensities from peptides mapping to more than one protein Abbreviations: pI: protein isoelectric point MW: molecular weight (Da) L: protein amino acid length uL: protein amino acid length mapping to unique peptides (defined theoritically based on multiple sequence alignments and enzyme digestion) sL: protein amino acid length mapping to shared peptides (defined theoritically based on multiple sequence alignments and enzyme digestion) SC: Sequence Coverage (%) P: Total peptide counts S-3

14 PRINTED PAGES Zhang_dNXAF_TableS1 Description Pig Mouse Rabbit Human Rat Bovine SC 26.19 50.66 62.34 59.44 65.63 67.22 P

15 29

29 37

38 45 SpC

197 368

235 304

565 645 sSpC

172 338

114 81

338 79 uSpC

25 30

121 223

227 566 dSpC 37.0426 68.2692 151.795 2........