Table I

Partial list of human proteins identified and characterized using top down MS

No.Protein accession no.Fragmentation methodProtein sizeΔmassaPscorebFunctionGene familycSNPcAlternative splicePTMNotesd
1P39019CAD15.90.31.E-0340 S ribosomal protein S19XE44G
2P56378CAD6.70.124.E-076.8-kDa mitochondrial proteolipid PRO1574XI9V
3P18124CAD29.20.201.E-0260 S ribosomal protein L7XE47K
4P23411ECD8.10.032.E-0560 S ribosomal protein L38XK52E,F34L
5O75964CAD11.30.201.E-10ATP synthase, e.g. chain, mitochondrial EC subunit GXXK47R,A56V
6P56381ECD5.60.128.E-26ATP synthase ϵ chain, mitochondrialXE30K
7O75531ECD10.280.052.E-10Barrier-to-autointegration factorXPhosphorylated near N terminus, N-term Ac
8P61769CAD11.80.03.E-10β2-microglobulin precursor HDCMA22PXXSignal peptide; 20 N-term residues cleaved; K61R,D73N,E56K,F42L,P34S, R32C,P92H
10P31949ECD, CAD11.60.11.E-12Calgizzarin S100C protein MLN 70XE36K
11P02593ECD16.80.13.E-24CalmodulinXTrimethylated on Lys-115
12P15954CAD5.40.021.E-07Cytochrome c oxidase polypeptide VIIc, mitochondrial precursor; EC of N-term 16 residues to mature form
13P63241CAD170.16.E-17Eukaryotic translation initiation factorXHypusine residue at position 50, N-term Ac
14P49773ECD13.70.01.E-30Histidine triad nucleotide-binding protein 1 (adenosine 5′-monophosphoramidase) (protein kinase C inhibitor 1)XG105R,E100A
15P10412ECD21.70.22.E-17Histone H1.4 member H1bXXN-terminal Ac
16P20670ECD14.00.02.E-18Histone H2A member OXXXAcetylations, H124Y
17P02278IRMPD13.8 e 7.E-14Histone H2BXXMultiple family members possible
18P16106CAD15.5 e 1.E-02Histone H3XXMultiple methylations/acetylations
19P02304IRMPD11.30.19.E-18Histone H4XMultiple acetylated forms, dimethylation
20P14174ECD, CAD12.30.01.E-04Macrophage migration-inhibitory factor, phenylpyruvate tautomerase, glycosylation-inhibitory factorXXDisulfide; N106S,I68T,P44L
21O95167CAD9.20.147.E-07NADH-ubiquinone oxidoreductase B9 subunitXXConsistent w/N-term Ac,L81V
22O00483CAD9.41.001.E-22NADH-ubiquinone oxidoreductase MLRQ subunit ECXD80G
23P26447ECD11.90.12.E-28Placental calcium-binding protein, calvasculin S100, calcium-binding protein A4 MTS1XE9V
24P06454ECD12.00.09.E-15Prothymosin αXXXAlternatively spliced, N-term Ac
25P06454IRMPD12.10.01.E-09Prothymosin αXXXAlternatively spliced, N-term Ac
26Q99584IRMPD11.40.17.E-06S100 calcium-binding protein A13XXConsistent with N-term Ac at Ala-2, E14D
27P25815ECD10.50.12.E-14S-100P proteinXE32D
28P08578ECD10.70.55.E-07Small nuclear ribonuclear protein E, snRNP-E, Sm protein E, Sm-E, SmEXG5C
29Q9UEA3CAD6.50.12.E-21Ubiquinol-cytochrome c reductase complex, 6.4-kDa proteinXL24W
30P02248ECD8.40.00UbiquitinXLoss of C-term GG to mature form
31Q15843IRMPD8.60.105.E-15Ubiquitin-like protein NEDD8XLoss of C-term GGLRQ to mature form
  • a Mass errors are from comparison of intact mass values; fragment ion mass errors are typically 1–20 ppm.

  • b E-x represents ×10x.

  • c All cSNPs were verified using dbSNP; the major allele (in boldface type) was observed for cases where allelic frequencies were provided.

  • d N-term, N-terminal; Ac, acetylation; C-term, C-terminal.

  • e Multiple isobaric forms observed with identical Pscore values.