Genome Biology 2007, 8:211
Maturation of the mammalian secretome
Jeremy C Simpson, Alvaro Mateos and Rainer Pepperkok
Address: Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse, 69117 Heidelberg, Germany.
Correspondence: Jeremy C Simpson. Email: firstname.lastname@example.org. Alvaro Mateos. Email: email@example.com
A recent use of quantitative proteomics to determine the constituents of the endoplasmic
reticulum and Golgi complex is discussed in the light of other available methodologies for
cataloging the proteins associated with the mammalian secretory pathway.
Published: 30 April 2007
Genome Biology 2007, 8:211 (doi:10.1186/gb-2007-8-4-211)
The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2007/8/4/211
© 2007 BioMed Central Ltd
The secretory pathway in mammalian cells consists of an
array of membrane-bounded organelles and transport carriers
through which secretory proteins move in a stepwise fashion
to reach their different cellular destinations. This arrange-
ment means that biochemical operations carried out by the
pathway, such as protein folding, protein glycosylation or
lipid biosynthesis, can be compartmentalized, which enables
efficient and specific reactions. Because of this link between
subcellular localization and function, a quantitative map of
the distribution of all the protein and lipid constituents of
the secretory pathway (the secretome) is an essential first
step to a comprehensive molecular understanding of how
the pathway functions. For the past 30 years, cell biologists
and biochemists have addressed this problem by imaging
immunolabeled components in intact cells and by the
biochemical analysis of subcellular fractions (reviewed in
[1,2]). Although these approaches have generated an
enormous amount of detailed knowledge on the composition
of the secretory pathway, the availability of the complete
sequences of several eukaryotic genomes has recently enabled
more systematic attempts to describe the secretory pathway
comprehensively at the molecular level. Landmark studies in
which a large, almost genome-wide, fraction of yeast open
reading frames (ORFs) were tagged with green fluorescent
protein (GFP) and their subcellular localizations determined
in living cells have generated comprehensive localization maps
for the Saccharomyces cerevisiae and Schizosaccharomyces
pombe proteomes and thus also the secretory pathways in
these organisms [3,4]. Related approaches in mammalian
cells have also been reported [5,6], although these are still far
less comprehensive than for yeast.
Subcellular fractionation followed by mass spectrometry
(MS)-based analysis has also proved highly successful in
mapping proteins to specific subcellular structures, such as
the Golgi complex [7-9] or clathrin-coated vesicles [10,11].
Remarkably, recent advances in MS-based proteomics
(reviewed in ) now even allow estimation of the relative
abundance of proteins in a specific biochemical fraction,
opening up new avenues for defining a genome-wide
localization map of a mammalian proteome. Taking
advantage of this technological progress, Gilchrist and
colleagues  have recently produced an MS-based
proteomic map of the major membrane-bounded entities of
the mammalian secretory pathway - the endoplasmic
reticulum (ER) and the Golgi complex. The significance of
this well controlled piece of work is that it both complements
and extends previous proteomic analyses of the mammalian
secretory pathway [7-11,14].
Gilchrist et al.  used classical biochemical procedures to
isolate rough ER, smooth ER and Golgi membranes from rat
liver, and then assessed fraction purity by electron micro-
scopy and enzyme activity analyses. Solubilized membranes
were subjected to gel electrophoresis and quantitative
tandem MS, which identified peptides that could be mapped
to more than 2,000 proteins. Assignment of these proteins
to 23 different functional categories allowed the in silico
removal of 470 proteins that were probably contaminants,
with almost two-thirds of these being residents of
mitochondria and the plasma membrane. Throughout this
study, independent samples were prepared and analyzed in
triplicate, with principal coordinate analysis confirming that
the ER and Golgi fractions were consistently distinct from
one another. Further clustering of the identified proteins
was facilitated by subfractionation using salt washing and
Triton X-114 phase separation, which finally yielded an
impressive list of 832 unique ER proteins, 193 proteins of
the Golgi complex and COPI transport vesicles, and a further
405 proteins that were found in both fractions.
This seems to be the most comprehensive effort so far to
elucidate the proteomes of the organelles of the mammalian
secretory pathway. An impressive number of controls were
incorporated at every step to give the highest degree of
confidence in the lists obtained. Closer analysis of these lists
reveals that the vast majority of well known residents of the
organelles have been identified, for example the components
of the protein folding and glycosylation machinery in the ER,
and the protein-modification enzymes in the Golgi complex,
in addition to more than 300 uncharacterized proteins. Of
particular note is the identification of many cytoplasmic
proteins that are only transiently associated with mem-
branes, including many components of the actin and micro-
tubule cytoskeletons. However, a significant number of likely
contaminants also seem to be present in the fractions,
highlighting the fact that, despite improvements in the
sensitivity of MS, the limitation of this type of approach
remains at the level of the organelle separation techniques.
For example, the identification of proteins of the plasma
membrane/endocytic machinery (such as the clathrin
adaptor 2 alpha subunit (CALM) and the GTPase dynamin)
in the ER fraction indicates the difficulty of separating these
How near are we to a complete secretome?
The work by Gilchrist et al. , together with the infor-
mation available in the literature, raises the question of
whether we are now able to define a mammalian secretome.
Considering the care taken to exclude likely contaminants in
this study, and comparing it with earlier proteomic analyses
(Table 1), the indication is that subcellular fractionation
combined with MS-based proteomics is unlikely to reveal
many more new proteins that map to the organelles of the
secretory pathway. Nevertheless, extrapolation of the
genome-wide localization data from S. cerevisiae [3,15] and
S. pombe  to the 30,000 ORFs of the human genome
suggests that the number of human proteins associated with
the ER and Golgi complex could be between 2,850 and 4,110
. This is more than twice the number proposed by
Gilchrist et al. , and may indicate an intrinsic lack of
completeness in subcellular fractionation and MS-based
approaches. One reason for this may be that during
subcellular fractionation, a significant number of proteins
transiently associated with the organelles under
investigation may be lost to the extent that they fall below
the current detection level of MS. Future improvements in
MS sensitivity may help to overcome this problem. Also,
211.2 Genome Biology 2007,Volume 8, Issue 4, Article 211 Simpson et al. http://genomebiology.com/2007/8/4/211
Genome Biology 2007, 8:211
Notable experimental studies in the determination of the secretome
YearApproachOrganelle Number of proteinsCommentReference
1980Mutagenesis Cell-wide23 First attempt to systematically identify secretory
machinery (S. cerevisiae)
2000 ProteomicsGolgi93 (588)* First concerted effort to analyze the Golgi proteome.
Cycloheximide treatment used to enrich for Golgi residents
2003 GFP-tagging ER
Subcellular localization of more than 75% of the yeast
proteome was determined using GFP fusions (S. cerevisiae)
2004Proteomics Golgi 151 (421)†
Improved proteomics technologies allowed more
comprehensive identification of proteins
2006 Functional assayCell-wide130First genome-wide RNAi screen to search for proteins
with a functional involvement in secretion (Drosophila S2 cells)
Proteomics and protein correlation profiling of multiple
organelles separated by gradient centrifugation
Subcellular localization of 90% of the yeast proteome
was determined using GFP fusions (S. pombe)
Most quantitative proteomic characterization of the ER,
Golgi and COPI vesicles reported to date
*Mass spectrometry was used to identify only 93 of the 588 unique spots observed on two-dimensional gels. †From 421 identified proteins, only 151
were annotated as being either unknown or bona fide Golgi residents. ‡An additional 68 proteins localized to the ER and Golgi. §An additional 405
proteins were identified in both ER and Golgi fractions.
most fractionation/MS-based studies focus on a single type
of tissue (predominantly brain and liver) as the material for
analysis. The number of proteins associated with the ER and
Golgi complex should, therefore, increase when the variety
of tissues in the human body is considered.
The problem of transient protein-organelle interactions
within the secretory pathway can be addressed by GFP-
tagging and subcellular localization in living cells. Light-
microscopy of cells expressing GFP-tagged markers provides
excellent resolution and sensitivity, and can, in principle,
monitor even very transient localizations lasting only
seconds. Many examples of functionally significant transient
interactions in the secretory pathway are known (see, for
example, [17-19]). Indeed, proteins shown to interact with
components of the secretory pathway in those experiments
(p150glued, γ-BAR , and the PICTAIRE kinases )
were not found by Gilchrist et al.  to be associated with
any of their fractions. This shows that approaches that can
also reveal transient interactions with membranes of the
secretory pathway are essential if the secretome is to be
Having defined the essential secretome components, the
next step will be to go beyond basic localization studies and
map these proteins to the organelles in which they function.
Live-cell imaging of GFP-tagged proteins can provide
sufficient spatial and temporal resolution but is, unfortu-
nately, still limited in throughput (reviewed in ).
Although simple cellular morphological changes can be
monitored by time-lapse microscopy in a high-throughput
manner , and sophisticated image-analysis technologies
have become available to accurately determine subcellular
localization (reviewed in ), large-scale quantitative
mapping of the GFP-tagged proteins to specific organelles is
still not possible, as it requires the acquisition of image data
in three dimensions, which is a slow process.
Combining localization and functional studies
Functional studies may help here as they not only support
the localization information but can also begin to provide
information about the networks in which each protein
operates. In cultured mammalian cells, protein over-
expression and downregulation are the most immediate
ways of studying a protein’s function [23,24]. Vast and easily
accessible collections of cDNAs and ORFs make over-
expression possible , while RNA interference (RNAi)
makes large-scale knockdown experiments feasible .
Understanding the molecular basis of the secretory pathway
using overexpression and downregulation techniques has
effectively been ‘work in progress’ for more than 25 years.
The pioneering experiments were carried out in yeast ,
largely because of its genetic tractability and the fact that its
genome does not have the complexity of higher eukaryotes,
which have tissue-specific variation in gene expression and
extensive splice variants, for example. These first lists of
candidate secretome proteins have stood the test of time,
and represent much of the core secretion machinery found
in all eukaryotes.
More recently, a complete genome-wide downregulation
screen in Drosophila S2 cells was reported , highlighting
the advent of functional screening as a means of determining
the secretome in more complex organisms. Combining the
information from such approaches with proteomics-based
localization strategies is a potentially enormously powerful
approach, as the two methods are methodologically indepen-
dent yet aspire to the same goal. Indeed, of the 77 mamma-
lian orthologs identified in the Drosophila screen as affect-
ing secretion (from 130 fly candidates), a third were also
identified by Gilchrist et al. . This correspondence allows
preliminary mapping of the functional effects of these
proteins to a particular subcellular compartment, but the
question remains as to why there is not greater overlap
between these lists. Incorrect identification of orthologs
across species may be one explanation, but this discrepancy
is more likely to reflect the fact that functional approaches
alone cannot provide comprehensive lists of the constituents
of the organelles involved. Similarly, determination of
localization does not directly infer function, but rather
should be considered as another essential piece of infor-
mation towards the goal of identifying the secretome.
The approaches outlined above are complementary to other
methods that are now being applied to studying cellular
composition and function on a genome-wide scale - for
example, comparative proteomics and mRNA expression
profiling . The power of these approaches is that in silico
data can be readily incorporated to extrapolate and predict
discrete functional networks. An excellent example of this
strategy is the recent definition of the ‘membrome’, a
comprehensive listing of the key interacting components that
define the membrane architecture of a specific cell type .
The complete secretome may still not have been identified,
but the tools and technologies that will achieve this are now
established and in use. As well as its intrinsic interest, the
secretome is of great medical importance, because dysfunc-
tional membrane trafficking pathways have many clinical
implications . Drug-discovery programs will surely
become more efficient if we have already mapped all the
relevant proteins to their organelle and functional inter-
We thank Monica Campillos for advice on data mining. A.M. is supported
by a fellowship of the program of Becas de Especializacion en Organismos
Internacionales of the Spanish Ministry of Education and Science (MEC).
The R.P. lab is funded by the German Ministry of Education and Research
(BMBF) in the framework of the National Genome Research Network
(NGFN-2, SMP-Cell, SMP-RNAi) and by a grant of the Landesstiftung
Baden Wuerttemberg research program (RNS/RNAi).
Genome Biology 2007,Volume 8, Issue 4, Article 211 Simpson et al. 211.3
Genome Biology 2007, 8:211
1. Presley JF: Imaging the secretory pathway: the past and
future impact of live cell optical techniques. Biochim Biophys
Acta 2005, 1744:259-272.
2.Bonifacino JS, Glick BS: The mechanisms of vesicle budding and
fusion. Cell 2004, 116:153-166.
3.Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman
JS, O’Shea EK: Global analysis of protein localization in
budding yeast. Nature 2003, 425:686-691.
4.Matsuyama A, Arai R, Yashiroda Y, Shirai A, Kamata A, Sekido S,
Kobayashi Y, Hashimoto A, Hamamoto M, Hiraoka Y, et al.:
ORFeome cloning and global analysis of protein localization
in the fission yeast Schizosaccharomyces pombe. Nat Biotech
5.Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S:
Systematic subcellular localization of novel proteins identi-
fied by large-scale cDNA sequencing. EMBO Rep 2000, 1:287-
6.Uhlen M, Bjorling E, Agaton C, Szigyarto CA, Amini B, Andersen E,
Andersson AC, Angelidou P, Asplund A, Asplund C, et al.: A human
protein atlas for normal and cancer tissues based on anti-
body proteomics. Mol Cell Proteomics 2005, 4:1920-1932.
7.Taylor RS, Wu CC, Hays LG, Eng JK, Yates III JR, Howell KE: Pro-
teomics of rat liver Golgi complex: minor proteins are iden-
tified through sequential fractionation. Electrophoresis 2000, 21:
8. Bell AW, Ward MA, Blackstock WP, Freeman HNM, Choudhary JS,
Lewis AP, Chotai D, Fazel A, Gushue JN, Paiement J, et al.: Pro-
teomics characterization of abundant Golgi membrane pro-
teins. J Biol Chem 2001, 276:5152-5165.
9. Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates
III JR, Howell KE: Organellar proteomics reveals Golgi argi-
nine dimethylation. Mol Biol Cell 2004, 15:2907-2919.
10.Blondeau F, Ritter B, Allaire PD, Wasiak S, Girard M, Hussain NK,
Angers A, Legendre-Guillemin V, Roy L, Boismenu D, et al.:
Tandem MS analysis of brain clathrin-coated vesicles
reveals their critical involvement in synaptic vesicle recy-
cling. Proc Natl Acad Sci USA 2004, 101:3833-3838.
11.Borner GHH, Harbour M, Hester S, Lilley KS, Robinson MS: Com-
parative proteomics of clathrin-coated vesicles. J Cell Biol
12. Andersen JS, Mann M: Organellar proteomics: turning invento-
ries into insights. EMBO Rep 2006, 7:874-879.
13. Gilchrist A, Au CE, Hiding J, Bell AW, Fernandez-Rodriguez J, Lesim-
ple S, Nagaya H, Roy L, Gosline SJC, Hallett M, et al.: Quantitative
proteomics analysis of the secretory pathway. Cell 2006, 127:
14. Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, Mann
M: A mammalian organelle map by protein correlation pro-
filing. Cell 2006, 125:187-199.
15.Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S,
Umansky L, Drawid A, Jansen R, Liu Y, et al.: Subcellular localiza-
tion of the yeast proteome. Genes Dev 2002, 16:707-719.
16.Simpson JC, Pepperkok R: Localizing the proteome. Genome Biol
17.Watson P, Forster R, Palmer KJ, Pepperkok R, Stephens DJ: Cou-
pling of ER exit to microtubules through direct interaction
of COPII with dynactin. Nat Cell Biol 2005, 7:48-55.
18.Neubrand VE, Will RD, Mobius W, Poustka A, Wiemann S, Schu P,
Dotti CG, Pepperkok R, Simpson JC: Gamma-BAR, a novel AP-
1-interacting protein involved in post-Golgi trafficking.
EMBO J 2005, 24:1122-1133.
19. Palmer KJ, Konkel JE, Stephens DJ: PCTAIRE protein kinases
interact directly with the COPII complex and modulate
secretory cargo transport. J Cell Sci 2005, 118:3839-3847.
20.Pepperkok R, Ellenberg J: High-throughput fluorescence
microscopy for systems biology. Nat Rev Mol Cell Biol 2006, 7:
21. Neumann B, Held M, Liebel U, Erfle H, Rogers P, Pepperkok R, Ellen-
berg J: High-throughput RNAi screening by time-lapse
imaging of live human cells. Nat Methods 2006, 3:385-390.
22. Glory E, Murphy RF: Automated subcellular location determi-
nation and high-throughput microscopy. Dev Cell 2007, 12:7-16.
23.Starkuviene V, Liebel U, Simpson JC, Erfle H, Poustka A, Wiemann S,
Pepperkok R: High-content screening microscopy identifies
novel proteins with a putative role in secretory membrane
traffic. Genome Res 2004, 14:1948-1956.
24. Simpson JC, Cetin C, Erfle H, Joggerst B, Liebel U, Ellenberg J, Pep-
perkok R: An RNAi screening platform to identify secretion
machinery in mammalian cells. J Biotech, in press.
Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD,
Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, et al.:
Generation and initial analysis of more than 15,000 full-
length human and mouse cDNA sequences. Proc Natl Acad Sci
USA 2002, 99:16899-16903.
Bard F, Casano L, Mallabiabarrena A, Wallace E, Saito K, Kitayama H,
Guizzunti G, Hu Y, Wendler F, DasGupta R, et al.: Functional
genomics reveals genes involved in protein secretion and
Golgi organization. Nature 2006, 439:604-607.
Novick P, Field C, Schekman R: Identification of 23 complemen-
tation groups required for post-translational events in the
yeast secretory pathway. Cell 1980, 21:205-215.
Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott
MS, Gramolini AO, Morris Q, Hallett MT, et al.: Global survey of
organ and organelle protein expression in mouse: combined
proteomic and transcriptomic profiling. Cell 2006, 125:173-
Gurkan C, Lapp H, Alory C, Su AI, Hogenesch JB, Balch WE: Large-
scale profiling of Rab GTPase trafficking networks: the
membrome. Mol Biol Cell 2005, 16:3847-3864.
Aridor M, Hannan LA: Traffic jams II: an update of diseases of
intracellular transport. Traffic 2002, 3:781-790.
211.4 Genome Biology 2007,Volume 8, Issue 4, Article 211 Simpson et al.http://genomebiology.com/2007/8/4/211
Genome Biology 2007, 8:211