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