Supplementary tables: Scaffold Results for MS data cases 1-6 and 8-13 with top 10

proteins identified by probability based algorithm per case.

Case 1

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
SPA706305.
mgf / Immunostains
SPA706306.
mgf
1 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 100% / 100%
2 / Ig lambda chain V-III region LOI / LV302_HUMAN / 12 / 100% / 100%
3 / Serum amyloid P-component precursor / SAMP_HUMAN / 25 / 100% / 100%
4 / Apolipoprotein A-IV precursor / APOA4_HUMAN / 45 / 94% / 100%
5 / Serum albumin precursor / ALBU-HUMAN / 69 / 100% / 100%
6 / Vitronectin precursor / VTNC_HUMAN / 54 / 100% / 94%
7 / Collagen alpha-1(I) chain precursor / CO1A1_HUMAN / 139 / 94% / 100%
8 / Multiple epidermal growth factor-ligand / MEGF8_HUMAN / 255 / 87 / 100
9 / Metallothionein-4 / MT4_HUMAN / 6 / 100 / 71
10 / Plasminogen precursor / PLMN_HUMAN / 91 / 100

Case 2

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD066s1.mgf / Immunostains
ISD066s2.mgf
1 / Ig gamma-2 chain C region / IGHG2_HUMAN / 36 / 100% / 99%
2 / Ig heavy chain V-III region BRO / HV305_HUMAN / 13 / 85% / 94%
3 / Fibrinogen beta chain precursor / FIBB_HUMAN / 56 / 100%
4 / Fibrinogen alpha chain precursor / FIBA_HUMAN / 95 / 100
5 / Vimentin / VIME_HUMAN / 54 / 100% / 94%
6 / Hemoglobin subunit beta / HBB_HUMAN / 16 / 100% / 100%
7 / Glial fibrillary acidic protein / GFAP_HUMAN / 50 / 100% / 100%
8 / Hemoglobin subunit alpha / HBA_HUMAN / 15 / 100% / 100%
9 / Pumilio homolog 2 / PUM2_HUMAN / 114 / 85% / 98%

Case 3

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
SPA706307.mgf / Immunostains
SPA706308.mgf
1 / Ig kappa chain C region / KAC_HUMAN / 12 / 100% / 100%
2 / Ig gamma-1 chain C region / IGHG1_HUMAN / 36 / 100% / 100%
3 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 100% / 100%
4 / Clusterin precursor / CLUS_HUMAN / 52 / 100% / 100%
5 / Glial fibrillary acidic protein / GFAP_HUMAN / 50 / 100% / 100%
6 / Collagen alpha-2(I) chain precursor / CO1A2_HUMAN / 129 / 100% / 100%
7 / Collagen alpha-1(I) chain precursor / CO1A1_HUMAN / 139 / 100% / 100%
8 / Serum albumin precursor / ALBU-HUMAN / 69 / 100% / 100%
9 / Hemoglobin subunit beta / HBB_HUMAN / 16 / 100% / 100%
10 / Vitronectin precursor / VTNC_HUMAN / 54 / 100% / 100%

Case 4

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD062s1.mgf / Immunostains
ISD062s2.mgf
1 / Ig gamma-1 chain C region / IGHG1_HUMAN / 36 / 100% / 100%
2 / Ig kappa chain C region / KAC_HUMAN / 12 / 100% / 100%
3 / Ig alpha-1 chain C region / IGHA1-HUMAN / 38 / 100% / 92%
4 / Ig gamma-3 chain C region / IGHG3_HUMAN / 32 / 92%
5 / Serum albumin precursor / ALBU-HUMAN / 69 / 100% / 100%
6 / Ryanodine receptor 3 / RYR3_HUMAN / 552 / 84% / 91%
7 / NFX1-type zinc finger-containing protein / ZNFX1_HUMAN / 220 / 94%
8 / Latent-transforming growth factor / LTBP3_HUMAN / 139 / 94% / 92%
9 / Mucin-16 / MUC16_HUMAN / 2353 / 94% / 92%
10 / Neurogenic locus notch homolog / NOTC4_HUMAN / 210 / 94% / 92%

Case 5

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
SPA706309.mgf / Immunostains
SPA706310.mgf
1 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 100% / 100%
2 / Serum amyloid P-component precursor / SAMP_HUMAN / 25 / 100% / 100%
3 / Ig alpha-1 chain C region / IGHA1-HUMAN / 38 / 100% / 100%
4 / Apolipoprotein A-IV precursor / APOA4_HUMAN / 45 / 100% / 100%
5 / Ig lambda chain C regions / LAC_HUMAN / 11 / 100%
6 / Glial fibrillary acidic protein / GFAP_HUMAN / 50 / 100% / 100%
7 / Vimentin / VIME_HUMAN / 54 / 100% / 100%
8 / Vitronectin precursor / VTNC_HUMAN / 54 / 100% / 100%
9 / Serum albumin precursor / ALBU-HUMAN / 69 / 100% / 100%
10 / Clusterin precursor / CLUS_HUMAN / 52 / 100% / 100%

Case 6

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD157s1.mgf / Immunostains
ISD157s2.mgf / Postimmunostains
ISD157s2.mgf
1 / Ig gamma-1 chain C region / IGHG1_HUMAN / 36 / 100% / 100%
2 / Ig kappa chain C region / KAC_HUMAN / 12 / 100% / 90%
3 / Serum albumin precursor / ALBU-HUMAN / 69 / 100% / 100%
4 / Vimentin / VIME_HUMAN / 54 / 100% / 100%
5 / Actin, cytoplasmic 1 / ACTB_HUMAN / 42 / 100% / 100%
6 / Hemoglobin subunit alpha / HBA_HUMAN / 15 / 100% / 93%
7 / Ryanodine receptor 3 / RYR3_HUMAN / 552 / 84% / 91%
8 / NF-X1-type zinc finger protein / NFXL1_HUMAN / 101 / 98% / 87%
9 / Vacuolar protein sorting-associated / VP13B_HUMAN / 449 / 91% / 93%
10 / Metallothionein-4 / MT4_HUMAN / 6 / 74% / 93%

Case 8

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD160s1.mgf / Immunostains
ISD160s2.mgf
1 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 100% / 100%
2 / Apolipoprotein A-IV precursor / APOA4_HUMAN / 45 / 100% / 100%
3 / Ig lambda chain V-IV region / LV4A_HUMAN / 11 / 94% / 94%
4 / Serum amyloid P-component precursor / SAMP_HUMAN / 25 / 100% / 100%
5 / Apolipoprotein A-I precursor / APOA1_HUMAN / 31 / 94% / 100%
6 / Hemoglobin subunit beta / HBB_HUMAN / 16 / 100% / 100%
7 / Vitronectin precursor / VTNC_HUMAN / 54 / 100% / 100%
8 / Glial fibrillary acidic protein / GFAP_HUMAN / 50 / 100% / 100%
9 / Clusterin precursor / CLUS_HUMAN / 52 / 100% / 100%
10 / Low density lipoprotein / LRP1B_HUMAN / 515 / 99% / 98%

Case 9

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD160s1.mgf / Immunostains
ISD160s2.mgf
1 / Ig mu chain C-region / MUC_HUMAN / 50 / 100% / 100%
2 / Ig kappa chain V-III region HAH / KV312_HUMAN / 14 / 100% / 100%
3 / Apolipoprotein A-I precursor / APOA1_HUMAN / 31 / 90% / 100%
4 / Ig kappa chain C region / KAC_HUMAN / 12 / 90% / 100%
5 / Immunoglobulin J chain / IgJ_HUMAN / 16 / 100% / 100%
6 / Ig kappa chain V-III region WOL / KV305_HUMAN / 12 / 90% / 89%
7 / Ig heavy chain V-I region V35 / HV103_HUMAN / 13 / 89%
8 / Serum albumin precursor / ALBU-HUMAN / 69 / 100% / 100%
9 / Hemoglobin subunit beta / HBB_HUMAN / 16 / 100% / 93%
10 / Hemoglobin subunit alpha / HBA_HUMAN / 15 / 100% / 93%

Case 10

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD159_B1_S1.
mgf / Immunostains
ISD159_B1_S3.mgf / Immunostains
ISD159_B1_S3.mgf
1 / Apolipoprotein A-IV precursor / APOA4_HUMAN / 45 / 100% / 100%
2 / Ig lambda chain C regions / LAC_HUMAN / 11 / 86% / 100% / 100%
3 / Apolipoprotein A-I precursor / APOA1_HUMAN / 31 / 100% / 94%
4 / Serum amyloid P-component precursor / SAMP_HUMAN / 25 / 100% / 94%
5 / Ig alpha-1 chain C region / IGHA1-HUMAN / 38 / 100% / 94%
6 / Ig gamma-1 chain C region / IGHG1_HUMAN / 36 / 94% / 94%
7 / Vimentin / VIME_HUMAN / 54 / 100% / 100%
8 / Glial fibrillary acidic protein / GFAP_HUMAN / 50 / 100% / 100%
9 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 100% / 100%
10 / Actin, cytoplasmic 1 / ACTB_HUMAN / 42 / 100% / 100%

Case 11

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD161 combined
1 / Ig alpha-1 chain C region / IGHA1-HUMAN / 38 / 100%
2 / Ig kappa chain V-III region / KV3B_HUMAN / 12 / 100%
3 / Ig kappa chain C region / KAC_HUMAN / 12 / 100%
4 / Apolipoprotein A-I precursor / APOA1_HUMAN / 31 / 100%
5 / Immunoglobulin J chain / IgJ_HUMAN / 16 / 100%
6 / Fibrinogen alpha chain precursor / FIBA_HUMAN / 95 / 100%
7 / Ig gamma-1 chain C region / IGHG1_HUMAN / 36 / 100%
8 / Amyloid beta A4 precursor / APBB2_HUMAN / 83 / 92%
9 / Apolipoprotein A-II precursor / APOA2_HUMAN / 11 / 92%
10 / Fibrinogen beta chain precursor / FIBB_HUMAN / 56 / 92%

Case 12

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD155s1.mgf / Immunostains
ISD155s2.mgf / Immunostains
ISD155s3.mgf
1 / Apolipoprotein A-IV precursor / APOA4_HUMAN / 45 / 100% / 100%
2 / Serum amyloid P-component precursor / SAMP_HUMAN / 25 / 92% / 100%
3 / Apolipoprotein A-I precursor / APOA1_HUMAN / 31 / 100% / 100%
4 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 93% / 98%
5 / Ig lambda chain V-VI region SUT / LV603_HUMAN / 12 / 93% / 91%
6 / Ig lambda chain C regions / LAC_HUMAN / 11 / 93%
7 / Serum amyloid A-4 protein precursor / SAA4_HUMAN / 15 / 91%
8 / Hemoglobin subunit beta / HBB_HUMAN / 16 / 100% / 100% / 100%
9 / Serum albumin precursor / ALBU_HUMAN / 69 / 100% / 100% / 100%
10 / Collagen alpha 2(I) chain precursor / CO1A2_HUMAN / 129 / 100% / 100% / 100%

Case 13

Identified Proteins / Accession number / Molecular weight (kDa) / Immunostains
ISD170s1 / Immunostains
ISD170s2
1 / Apolipoprotein E precursor / APOE_HUMAN / 36 / 100% / 94%
2 / Ig mu chain C-region / MUC_HUMAN / 50 / 100%
3 / Ig gamma-1 chain C region / IGHG1_HUMAN / 36 / 100%
4 / Complement component C9 precursor / CO9_HUMAN / 63 / 93% / 94%
5 / Ig kappa chain C region / KAC_HUMAN / 12 / 100%
6 / Ig lambda chain C regions / LAC_HUMAN / 11 / 100%
7 / Apolipoprotein A-I precursor / APOA1_HUMAN / 31 / 99%
8 / Ig heavy chain V-III region GA / HV308_HUMAN / 13 / 94%
9 / Ig gamma-2 chain C region / IGHG2_HUMAN / 36 / 93%
10 / Ig gamma-3 chain C region / IGHG3_HUMAN / 32 / 93%