Science - USA (2022-01-28)

would uncover >50,000 additional proteoforms
in this size regime. We expect that larger pro-
teinsthatactashubsofcellulardecision-making
could have more proteoforms per protein [e.g.,

tumor suppressor protein p53 ( 21 )]. Further, to

estimate the number of human proteoforms,

we multiplied the theoretical number of pro-

teins by three times the standard deviation of

the mean number of proteoforms observed per

protein. From this, we estimated the number

of proteoforms to be ~1.1 million in a human

cell type, close to a previous estimation ( 22 ).

414 28 JANUARY 2022¥VOL 375 ISSUE 6579 science.orgSCIENCE

1%

3%

5%

7%

9%

11 %

13%

15%

17%

19%

0

4

8

12

16

20

24

28

32

1 2 3 4 5 6 7 8 9 10111213141516171819202122

Protein counts (x10)

Observed in # cell types

0%

0.1%

0.2%

0.3%

0.4%

0.5%

0.6%

0.7%

0.8%

0.9%

1.0%

0

50

100

150

200

250

300

8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

Proteoform counts (x1000)

Observed in # cell types

0%

10%

20%

30%

40%

50%

60%

0

2

4

6

8

10

12

14

16

18

1 2 3 4 5 6 7 8 9 10111213141516171819202122

Proteoform counts

ABProteins Proteoforms

-4

0

4

8

Monocytes (3)

CD14+

Monocytes (3)

CD14+CD16-

Neutrophils (5)

Pre-B-III (4)

Pre-B-I (4)Pre-B-II (4)

RBC (3)

Plasma (5)

PBMC (5)

Naïve B (5)

Memory B (5)

DC (3)

Macrophages (3)

T-cells (8)

T- cell

Help (3)

T- cell

Reg (6)

T-cell

Cyto (3)

Platelets (5)

Eosinophils (3)

NK (3)

B-cells (9)

HSC (3)

-4 0 4

T-SNE 1

T-SNE 2

Monocytes (3)

CD14+

Monocytes (3)

CD14+CD16-

Neutrophils (5)

Pre-B-III (4)

Pre-B-I (4)

RBC (3) Pre-B-II (4)

Plasma (5)

PBMC (5)

Naïve B (5)

Memory B (5)

DC (3)

Macrophages (3)

T-cells (8) T- cell

Help (3)

T- cell

Reg (6)

T- cell

Cyto (3)

Platelets (5)

Eosinophils (3)

NK (3)

B-cells (9)

HSC (3)

-5

0

5

-3 0 3

T-SNE 1

T-SNE 2

-6

CD

E

Fig. 2. Display of protein and proteoform analysis for entries in the Blood
Proteoform Atlas.t-SNE plots display cell types grouped by presence or
absence of (A) proteins and (B) proteoforms. T-cell Cyto, cytotoxic T cells;
T-cell Help, helper T cells; T-cell Reg, regulatory T cells; HSC, hematopoietic
stem cells; DC, dendritic cells; RBC, red blood cells. Histograms of (C) proteins
and (D) proteoforms shared by different cell types. (E) Heatmaps and cell

type hierarchical clustering of identified (yellow) or not-identified (black)

proteins (1690) and proteoforms (29,620) at 1% FDR, with proteoforms

exhibiting higher specificity for distinct cell types. NBC, naïve B cells; MBC,

memory B cells; PBI, pre-B-I cells; BC-BM, B cells from bone marrow; Eosino,

eosinophils; Macro, macrophages; Neutro, neutrophils; BC, B cells from

blood; Mono, monocytes; TC, T cells.

RESEARCH | RESEARCH ARTICLES