Proteomic Analysis of Human Neutrophil Granules

Proteomic Analysis of HumanNeutrophil Granules*□S

George Lominadze‡, David W. Powell§, Greg C. Luerman‡, Andrew J. Link§,Richard A. Ward¶, and Kenneth R. McLeish‡¶�**

Stimulated exocytosis of intracellular granules plays acritical role in conversion of inactive, circulating neutro-phils to fully activated cells capable of chemotaxis, phag-ocytosis, and bacterial killing. The functional changes in-duced by exocytosis of each of the granule subsets,gelatinase (tertiary) granules, specific (secondary) gran-ules, and azurophil (primary) granules, are poorly defined.To improve the understanding of the role of exocytosis ofthese granule subsets, a proteomic analysis of the azuro-phil, specific, and gelatinase granules from human neutro-phils was performed. Two different methods for granuleprotein identification were applied. First, two-dimensional(2D) gel electrophoresis followed by MALDI-TOF MS anal-ysis of peptides obtained by in-gel trypsin digestion ofproteins was performed. Second, peptides from trypticdigests of granule membrane proteins were separated bytwo-dimensional microcapillary chromatography usingstrong cation exchange and reverse phase microcapillaryhigh pressure liquid chromatography and analyzed withelectrospray ionization tandem mass spectrometry (2DHLPC ESI-MS/MS). Our analysis identified 286 proteins onthe three granule subsets, 87 of which were identified byMALDI MS and 247 were identified by 2D HPLC ESI-MS/MS. The increased sensitivity of 2D HPLC ESI-MS/MS,however, resulted in identification of over 500 proteinsfrom subcellular organelles contaminating isolated gran-ules. Defining the proteome of neutrophil granule subsetsprovides a basis for understanding the role of exocytosisin neutrophil biology. Additionally, the described methodsmay be applied to mobilizable compartments of othersecretory cells. Molecular & Cellular Proteomics 4:1503–1521, 2005.

Stimulated exocytosis of membrane-bound compartmentsplays a critical role in converting inactive, circulating neutro-phils to fully activated cells capable of directed migration,phagocytosis, and killing of microbes (1). Four subsets ofmembrane-bound compartments exist in neutrophils: secre-

tory vesicles, gelatinase (tertiary) granules, specific (second-ary) granules, and azurophil (primary) granules (1, 2). Secre-tory vesicles are generated by endocytosis, resulting inmembranes rich in receptors, signaling proteins, and adhe-sion molecules, whereas their lumen contains plasma (2).Azurophil, specific, and gelatinase granules contain variousenzymes and host defense proteins in their luminal spaces,whereas their membranes contain receptors, signaling pro-teins, adhesion molecules, and enzymes (2, 3). The targetingof proteins to individual granule compartments is determinedby the timing of protein synthesis during myeloid progenitorcell differentiation, not by granule-specific sorting (4). Thus,granule proteins that are synthesized at a given stage ofcellular differentiation will be localized to the same type ofgranule (5, 6). The overlap between the timing of synthesis ofdifferent granular proteins gives rise to some overlap of con-tents among different granule subsets (6, 7).

The extent of mobilization of the three types of granuledepends on the stimulus intensity, whereas the order of mo-bilization is fixed, a process termed graded exocytosis (8, 9).Gelatinase granules are most easily mobilized followed byspecific granules and then azurophil granules. Graded exocy-tosis results in stepwise addition of granule membrane pro-teins to the plasma membrane and stepwise release of gran-ule luminal contents into the extracellular space. Thecontrolled exocytosis of neutrophil granules allows sequentialacquisition of functional responses and targeted delivery oftoxic granule proteins, thereby reducing damage to normalhost tissue.

In addition to graded granule release, neutrophil exocytosisis distinguished by two other attributes. The first is a lack ofspatial organization of granules (10–12). The random distribu-tion of granules in the cytosol of circulating neutrophils sug-gests that graded exocytosis requires a mechanism to dis-criminate among granule subsets. The second attribute iscompound exocytosis, the fusion of two or more granulesprior to their fusion with the plasma membrane (13). Com-pound exocytosis requires recognition of granule subsets astarget membranes to allow for homotypic or heterotypic fu-sion. Homotypic fusion enhances the localized delivery ofgranule contents. Heterotypic fusion allows processing ofcertain granule constituents into active forms by proteolyticcleavage (14).

The molecular mechanisms that control exocytosis of neu-

From the Departments of ¶Medicine and ‡Biochemistry and Mo-lecular Biology, University of Louisville and the �Veterans Affairs Med-ical Center, Louisville, Kentucky 40202 and the §Department of Mi-crobiology and Immunology, Vanderbilt University School ofMedicine, Nashville, Tennessee 37232

Received, May 17, 2005Published, MCP Papers in Press, June 28, 2005, DOI 10.1074/

mcp.M500143-MCP200

Research

© 2005 by The American Society for Biochemistry and Molecular Biology, Inc. Molecular & Cellular Proteomics 4.10 1503This paper is available on line at http://www.mcponline.org

trophil granules are poorly defined. Additionally the full com-plement of functional changes resulting from exocytosis ofdifferent granule subsets remains to be identified. A majorreason for this limited understanding of neutrophil exocytosisis an incomplete identification of membrane and luminal pro-teins of each granule subset. To address this problem, weperformed proteomic profiling of the components of azuro-phil, specific, and gelatinase granules from human neutro-phils. Two different methods for granule protein identificationwere applied. One used two-dimensional gel electrophoresis(2DE)1 followed by MALDI-TOF MS analysis of peptides ob-tained by in-gel trypsin digestion of proteins. In the other,peptides from tryptic digests of granule membrane proteinswere separated by two-dimensional microcapillary chroma-tography using strong cation exchange and reverse phasemicrocapillary high pressure liquid chromatography and ana-lyzed with electrospray ionization tandem mass spectrometry(2D HLPC ESI-MS/MS). Our analysis identified 286 proteinson the three granule subsets. Additionally optimal methods forprotein identification differed among granule subsets basedon their physical properties and luminal components.

MATERIALS AND METHODS

Neutrophil Isolation

Neutrophils (8 � 108 cells) were isolated from healthy donors usingplasma-Percoll gradients as described by Haslett et al. (15). Trypanblue staining revealed that at least 97% of cells were neutrophils with�95% viability. After isolation neutrophils were suspended in Krebs-Ringer phosphate buffer (pH 7.2) at 4 � 107 cells/ml and treated with10 �M diisopropyl fluorophosphate for 10 min on ice to inhibit pro-teases (16). The Human Studies Committee of the University of Lou-isville approved the use of human donors.

Subcellular Fractionation for Granule Enrichment

Neutrophil granules were enriched by centrifugation on a three-layer Percoll density gradient as described by Kjeldsen et al. (17).Briefly isolated neutrophils (4 � 107/ml) were resuspended in disrup-tion buffer containing 100 mM KCl, 1 mM NaCl, 1 mM ATPNa2, 3.5 mM

MgCl2, 10 mM PIPES, and 0.5 mM PMSF and disrupted by nitrogencavitation at 380 p.s.i. and 4 °C. The cavitate was collected andsupplemented with 1.5 mM EGTA, and nuclei and intact cells wereremoved by centrifugation at 500 � g for 5 min. The postnuclearsupernatant was layered onto a discontinuous Percoll gradientformed from three 9-ml layers of Percoll prepared in a buffer contain-ing 100 mM KCl, 3 mM NaCl, 1 mM ATPNa2, 3.5 mM MgCl2, 1.25 mM

EGTA, 10 mM PIPES, and 0.5 mM PMSF to achieve final densities of

1.050, 1.090, and 1.120 g/ml. The gradient was centrifuged at37,000 � g for 30 min in an SS-34 fixed angle rotor in a Sorvall RC-5Bcentrifuge. The separated granule fractions were recovered from thegradient interfaces by aspiration, and Percoll was removed by ultra-centrifugation of each granule subset at 100,000 � g for 90 min.

Sample Preparation for 2DE

Preparation of Whole Granules—Whole granule fractions were re-suspended in 4 ml of disruption buffer and centrifuged at 100,000 �g for 20 min to obtain a solid pellet. Buffer was removed by aspiration,and the pellets were washed briefly with deionized water to removeresidual salt.

Fractionation of Granule Proteins—To separate granule proteinsinto membrane and luminal fractions, granules were resuspended in10 volumes of 0.1 M sodium carbonate, sonicated at high setting for5 s, and subjected to three freeze-thaw cycles each followed bysonication (18). Disrupted granules were incubated on ice for 30 min,and carbonate-washed membranes were pelleted at 100,000 � g.The supernatant from the carbonate wash was concentrated by ul-trafiltration through 1-kDa-cutoff centrifugal devices (MicrosepOmega, Pall, East Hills, NY), and the retentate proteins were precip-itated using chloroform-methanol desalting-precipitation (19). Theprecipitate was dried on room air and subjected to 2DE.

To separate granule proteins based on differential solubility inammonium sulfate solution, whole granules were solubilized in 3volumes of lysis buffer containing 50 mM Tris, pH 7.2, and 2% TritonX-100 and centrifuged at 20,000 � g to remove insoluble proteins.The Triton X-100-insoluble pellet was subjected to 4–12% acrylamidegradient SDS-PAGE and MALDI MS analysis, while the cleared lysatewas used for fractionation by ammonium sulfate precipitation ofproteins. One volume of 100% saturated ammonium sulfate solutionwas added to the lysate. The resulting precipitate was pelleted (sub-fraction one), and supernatant was removed. Solid ammonium sulfatewas added to the supernatant until saturation, and the protein pre-cipitate was pelleted (subfraction two). Precipitated protein pelletswere redissolved in the lysis buffer and subjected to chloroform-methanol desalting-precipitation (19).

Protein Separation by 2DE and Identification by MALDI-TOF MS

Whole granules and granule subfractions were dissolved in 160 �lof 7 M urea, 2 M thiourea rehydration buffer (Genomic Solutions, AnnArbor, MI). Proteins in all samples were separated by 2DE usingnon-linear pH 3–10 IPG strips for the first dimension and 4–12%gradient acrylamide gels for the second dimension (Invitrogen). Thegels were visualized by colloidal Coomassie staining. Proteins wereexcised and in-gel trypsin-digested, and the resulting peptides wereanalyzed by MALDI-TOF MS using the thin film sample preparationmethod as described previously (20, 21). Protein identification wascarried out by searching peptide spectra against the National Centerfor Biotechnology Information (NCBI) database using the Mascotweb-based search engine. The search parameters used were: taxon-omy, Homo sapiens; allowed error, 150 ppm; fixed modification,carbamidomethylation; variable modification, methionine oxidation;mass values, MH�; and maximum allowed missed cleavage, 1.

Protein Identification by 2D HPLC ESI-MS/MS

Granule membranes obtained following treatment with 0.1 M so-dium carbonate, as described above, were washed in 50 mM ammo-nium bicarbonate and then resuspended by sonication in 300 �l of 50mM ammonium bicarbonate. Trypsin digestion was performed byaddition of 20 ng/ml trypsin to the suspension, and samples wereincubated on a rotator overnight at 37 °C. Residual particulate mate-

1 The abbreviations used are: 2DE, two-dimensional gel electro-phoresis; TMA-DPH, 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene p-toluenesulfonate; CR1, complement component recep-tor 1; MEK1, extracellular signal-regulated kinase (ERK) activatorkinase 1; Hsp70, heat shock protein 70; MPO, myeloperoxidase;NGAL, neutrophil granule-associated lipocalin; PDI, protein-disulfideisomerase; 2D, two-dimensional; TX-100, Triton X-100; PIPES, 1,4-piperazinediethanesulfonic acid; MRP, myeloid-related protein;SCAMP, secretory carrier membrane protein; LAMP, lysosome-asso-ciated membrane protein; VAMP, vesicle-associated membraneprotein.

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1504 Molecular & Cellular Proteomics 4.10

rial was removed by centrifugation at 100,000 � g, and the trypsin-generated mixture was analyzed using an approach that combinedtwo-dimensional microcapillary HPLC with ESI-MS/MS (22). All tan-dem spectra were searched against H. sapiens open reading framedatabase (human.nci) using the SEQUEST algorithm (23). For singlycharged peptides, spectra with a cross-correlation score of greaterthan 1.5 were retained, whereas for multiply charged peptides, spec-tra with a cross-correlation score of greater than 2 were retained (24).The analysis was repeated three times for each granule subset, andonly proteins identified in at least two of three experiments wereassumed to be present on granules.

Quantitation of Granule Membranes and Western BlotAnalysis of Granules

Whole granule fractions were resuspended in 2 ml of disruptionbuffer and centrifuged at 100,000 � g for 20 min to obtain a solidpellet. Buffer was removed by aspiration, and the pellets were resus-pended in 100 �l of disruption buffer. Sample volume was brought upto 1 ml by water and preincubated at 37 °C. To quantitate phospho-lipid bilayers, TMA-DPH (Molecular Probes, Eugene, OR) was addedat a final concentration of 1 � 10�7 M, and fluorescence intensity wasmonitored continuously at excitation of 350 nm and emission of 430nm for 20 s on a Hitachi 4500 fluorescence spectrometer. Proteinsassociated with equal amounts of membrane from each granulesubset were loaded onto a gel for SDS-PAGE. Proteins were sepa-rated, transferred to nitrocellulose membrane, and probed with ananti-actin antibody.

RESULTS

Prior to subjecting granules to proteomic analysis, the pu-rity of each of the three granule subsets was determined.Granule subsets were analyzed by Western blotting forCD66b (specific granule marker) and by ELISA for gelatinaseand myeloperoxidase (MPO), markers for gelatinase andazurophil granules, respectively (Fig. 1). The Western blotshowed that CD66b was present in the specific granule frac-tion but essentially absent in gelatinase granule and azurophilgranule fractions. ELISA for gelatinase showed that 75% oftotal gelatinase was present in gelatinase granules, 20% wasin specific granules, and 5% was in azurophil granules,whereas 73% of MPO was in azurophil granules, 20% was inspecific granules, and 7% was in gelatinase granules. Thisdistribution of granule markers was similar to that reported byKjeldsen et al. (17, 25). Thus, optimal levels of granule subsetenrichment were obtained.

The initial analysis of granule subset proteomes was carriedout by subjecting whole granules to 2DE. Fig. 2A shows theseparation of gelatinase granule proteins. A total of 38 pro-teins were identified by peptide mass fingerprint analysis ofMALDI MS spectral data. Thirty of these proteins were cy-toskeletal and luminal proteins. The 2D gels of specific gran-ule proteins were dominated by large amounts of luminalproteins, such as lactoferrin and lipocalin (NGAL), which werepresent in such high abundance that proteins focused poorly(Fig. 2B). A total of 26 proteins were identified by peptidemass fingerprinting. The only cytoskeletal protein identifiedwas actin (Fig. 2B). Separation of azurophil granule proteinsby 2DE revealed large amounts of highly basic proteins, such

as myeloperoxidase, that focused poorly, leading to extensivesmearing on the basic end of the gel (Fig. 2C). Only eightproteins were identified from the azurophil granule gel.

To address the problem of overabundance of luminal pro-teins, granule proteins were fractionated by one of two meth-ods prior to their separation by 2DE. First, the luminal con-tents of granules were separated from membranes by lysingthe granules in 0.1 M sodium carbonate, pH 11. At high pHluminal cationic proteins lose their positive charge and disso-ciate from negatively charged matrix (18, 26, 27). Additionallyalkaline sodium carbonate treatment has been reported toremove the actin cytoskeleton from neutrophil membranes(28). To determine what proteins were removed from granulemembranes, carbonate-soluble proteins were also subjectedto 2DE. Second, differential solubility of proteins in ammo-nium sulfate solutions was applied to granule proteins prior to2DE. Whole granules were solubilized in a buffer containingTriton X-100, and proteins were separated based on precip-itation at different concentrations of ammonium sulfate. Thefirst subfraction contained proteins precipitated in a 20%ammonium sulfate solution, whereas the second subfractioncontained the proteins soluble in 20% ammonium sulfate butinsoluble in 100% ammonium sulfate.

Fractionation of gelatinase granules with sodium carbonateprior to 2DE resulted in identification of 26 proteins of whicheight proteins were not detected on whole granule gels (Fig. 3,A and B). On the other hand, 20 proteins identified by 2DE of

FIG. 1. Assessment of purity of granule fractions. Granule frac-tions separated by centrifugation on Percoll gradients were analyzedfor the content of CD66b (specific granule marker), gelatinase (gela-tinase granule marker), and myeloperoxidase (azurophil granulemarker). A, Western blotting analysis of CD66b content in granulefractions. B, ELISA for gelatinase. C, ELISA for myeloperoxidase.

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Molecular & Cellular Proteomics 4.10 1505

whole granules were not observed on either carbonate-washed membrane or carbonate-soluble protein gels. Most ofthese proteins were below 30 kDa, suggesting that low mo-lecular weight proteins were lost during fractionation. Fig. 3, Cand D, shows 2DE separation of ammonium sulfate-precipi-tated proteins from gelatinase granules. This fractionationallowed identification of 38 proteins, 22 of which were notpreviously identified. Use of ammonium sulfate precipitationalso identified all but three proteins detected following frac-tionation with sodium carbonate. Ten proteins seen in wholegelatinase granule gels were not detected after either frac-tionation method, indicating that protein fractionation is com-plementary to analysis of intact gelatinase granules. A total of62 proteins were identified from gelatinase granules by 2DEprotein separation and MALDI MS (Table I).

Fractionation of specific granule proteins with sodium car-bonate resulted in identification of more proteins than extrac-tion by ammonium sulfate precipitation. Sodium carbonatetreatment prior to 2DE resulted in identification of 51 proteinsfrom membranes and 27 proteins in the supernatant of which42 proteins were not detected on gels from whole specificgranules (Fig. 4, A and B). Ammonium sulfate precipitationallowed identification of 45 proteins, only 10 of which were notseen on gels from whole granules. Ammonium sulfate precip-itation did not lead to identification of any protein not identi-fied after fractionation with sodium carbonate (Fig. 4, C andD). Collagenase and cathepsin X were identified on the wholespecific granule gels but not after extraction by sodium car-bonate. A total of 70 proteins were identified from specificgranules (Table I).

Fractionation of azurophil granule proteins by sodium car-bonate or by ammonium sulfate precipitation failed to improvevisualization and identification of proteins. The 2D gels ofcarbonate-washed membranes were largely devoid of pro-teins (only four proteins were identified), whereas 2DE ofcarbonate-soluble proteins failed to reveal proteins notfound on gels of whole granule proteins (data not shown).Likewise fractionation of azurophil granule proteins by am-monium sulfate precipitation failed to improve the numberof proteins visualized by 2DE (data not shown). Thus, onlyeight proteins from azurophil granules were identified by2DE (Table I).

For all granule subsets, the protein fraction precipitated by100% ammonium sulfate contained primarily luminal proteins.Only two proteins remained in solution after precipitation ofspecific and gelatinase granule proteins with 100% ammo-nium sulfate, MRP-14 and MRP-8, whereas the correspond-ing sample from azurophil granules was devoid of protein(data not shown). To identify any proteins that failed todissolve in the TX-100-containing buffer and thus could notbe detected in ammonium sulfate precipitated fractions,TX-100-insoluble pellets were also subjected to SDS-PAGE.Only actin, vimentin, CD11b, lactoferrin, and gelatinasewere detected in pellets from specific and gelatinase gran-

FIG. 2. 2D gels of whole granules. Neutrophil granules were sub-jected to 2DE, gels were stained with colloidal Coomassie Blue dye,the spots were excised and in-gel digested with trypsin, and theresultant peptides were analyzed by MALDI-TOF MS. A, gelatinasegranules. B, specific granules. C, azurophil granules.

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1506 Molecular & Cellular Proteomics 4.10

ules (data not shown), whereas myeloperoxidase, cathepsinG, and lysozyme were found in the TX-100-insoluble frac-tion of azurophil granules. A total of 87 proteins were iden-tified from granule subsets by the three 2DE approaches ofwhich 56 were cytoskeletal or luminal proteins. Membraneproteins, except for CD11b and CD18, were not visualizedby 2DE.

2DE-based approaches are biased against membrane pro-teins, low abundance proteins, and proteins at the extremesof isoelectric point and molecular mass. To address theseissues, we used an approach that couples 2D HPLC withESI-MS/MS analysis (22, 24). This high sensitivity mass spec-trometry-based approach that allows direct analysis of com-plex protein mixtures was applied to granule membranesfollowing removal of luminal and cytoskeletal proteins with

sodium carbonate. Only proteins present in at least two ofthree experiments or proteins also identified by 2DE-MALDIMS were considered as valid granule proteins. By this criteriaa total of 247 proteins were identified from all granule subsetsof which 48 were also identified by 2DE. Table II lists identifiedproteins by granule subset, method of identification, andfunctional classification of the protein. A total of 86 proteinswere identified only from gelatinase granules, 28 proteinswere identified from only specific granules, and 26 proteinswere identified from only azurophil granules. A number ofproteins were identified on multiple granule subsets, including79 proteins from gelatinase and specific granules, five pro-teins from specific and azurophil granules, and 62 proteinsfrom all three granule subsets. The peptide sequences de-tected by 2D HPLC ESI-MS/MS can be found in Supplemen-

FIG. 3. 2D gels of gelatinase granule proteins fractionated by carbonate lysis and by ammonium sulfate precipitation of TritonX-100-solubilized proteins. Shown is fractionation of gelatinase granule proteins by carbonate lysis (A and B) and by ammonium sulfateprecipitation (C and D). A, a 2D gel of proteins that remained on the membrane after granule lysis in 0.1 M sodium carbonate buffer. B, proteinsthat were solubilized in 0.1 M sodium carbonate. C, proteins precipitated in 20% ammonium sulfate solution. D, proteins that remained insolution in 20% ammonium sulfate but were precipitated in 100% ammonium sulfate solution.

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TABLE IProteins identified from 2D gels by MALDI-TOF MS

Eighty-seven proteins were identified from all 2D gels of neutrophil granules. The table lists the gene and protein designation, granule type,number of peptides matched, the percent protein coverage by these peptides, and the calculated molecular weight search (MOWSE) score foreach protein. SOD, superoxide dismutase; GE, gelatinase; SP, specific; AZ, azurophil; VDAC, voltage-dependent anion channel; ARP,actin-related protein; LSP1, lymphocyte-specific protein 1; BP, binding protein; TOLLIP, Toll-interacting protein; Arc, ARP-related complex;Grp, glucose regulated protein; Hsp, heat shock protein.

Entrez gene Entrez ID Protein name GranulePeptides

matched/totalCoverage

MOWSEscore

%

CA4 gi�409725 Carbonic anhydrase IV GE 10/30 36 101CFL1 gi�57099669 Cofilin 1 GE 16/53 70 1531F9PA gi�34810160 Connective tissue activating peptide GE 7/33 67 85ENO1 gi�4503571 Enolase GE 16/38 42 144GSN gi�38044288 Gelsolin GE 15/58 26 83ATP5A1 gi�50345982 H�-ATPase F0 subunit � GE 16/55 39 110IDH2 gi�28178832 Isocitrate dehydrogenase GE 12/47 27 74MMAA gi�26892295 Methylmalonic acid urea GE 7/14 16 69SOD2 gi�7546412 Mn-SOD chain b GE 8/52 57 72ARPC5 gi�56204524 p16 Arc GE 11/22 58 142ARPC3 gi�5031597 p21 Arc GE 6/20 40 68PPIA gi�31615559 Cyclophilin A GE 7/29 37 65RAB27A gi�34485711 Rab27A GE 9/33 37 93RAP1A gi�54696200 Rap1A GE 9/30 43 105TAGLN gi�55960374 Transgelin 2 GE 10/33 44 88VDAC2 gi�48146045 VDAC2 GE 7/31 32 65VIL2 gi�46249758 Villin 2 GE 28/58 41 170VIM gi�340234 Vimentin 35 kDa GE 9/34 30 73YWHAZ gi�49119653 14-3-3� GE, SG 9/21 36 106ACTB gi�14250401 Actin � GE, SG 9/26 30 88ACTG1 gi�178045 Actin � GE, SG 7/21 37 82ACTN1 gi�4501891 �-Actinin GE, SG 11/19 13 93ALB gi�28592 Albumin GE, SG 19/35 30 161ANXA3 gi�4826643 Annexin III GE, SG 8/12 28 104ACTR3 gi�27806335 ARP3 GE, SG 9/20 23 83B2M gi�1195503 �2-Microglobulin GE, SG 8/22 77 107CALR gi�30583735 Calreticulin GE, SG 8/21 19 79CAPZA1 gi�12652785 Cap Z GE, SG 11/26 56 134CAPZA2 gi�433308 Capping protein � GE, SG 8/27 36 83ITGAM gi�386975 CD11b GE, SG 10/16 10 85CLC gi�17942629 Charcot-Leyden protein GE, SG 9/35 43 81FTL gi�48145547 Ferritin light chain GE, SG 11/20 53 143FCN1 gi�8051584 Ficolin 1 precursor GE, SG 14/24 46 156MMP9 gi�22532481 Gelatinase GE, SG 11/21 18 103GCA gi�6912388 Grancalcin GE, SG 12/29 48 109PDIA3 gi�7437388 Grp58 GE, SG 22/43 44 181HP gi�47124562 Haptoglobin �2 GE, SG 14/26 39 151HBB gi�4504349 Hemoglobin GE, SG 12/26 93 184HSPA1A gi�5123454 Hsp70 1A GE, SG 15/23 32 168HSPA5 gi�1143492 Hsp70 5A GE, SG 20/50 37 149CST7 gi�9836652 Leukocystatin GE, SG 7/16 28 74LCP1 gi�4504965 L-plastin GE, SG 9/19 17 84LSP1 gi�12804709 LSP1 GE, SG 6/10 36 86S100A9 gi�4506773 MRP-14 GE, SG 15/34 92 150S100A8 gi�30583595 MRP-8 GE, SG 10/23 83 132MRCL3 gi�5453740 Myosin regulatory light chain GE, SG 10/36 65 90P4HB gi�20070125 PDI GE, SG 7/18 17 65PGLYRP1 gi�37182990 Peptidoglycan recognition protein GE, SG 8/38 48 70PHB gi�49456373 Prohibitin GE, SG 10/37 47 100SDCBP gi�55749523 Syntenin GE, SG 8/20 43 94TPM3 gi�55665783 Tropomyosin 3 GE, SG 9/19 29 100TUBA3 gi�18088719 Tubulins � GE, SG 9/17 27 104

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1508 Molecular & Cellular Proteomics 4.10

tal Tables 1 and 2. Supplemental Table 1 lists the proteinsidentified at least twice in three experiments and the se-quences of corresponding peptides. Proteins identified oncein a given granule subset by 2D HPLC ESI-MS/MS and iden-tified by either 2DE or at least twice by 2D HPLC ESI-MS/MSin another granule subset are listed in Supplemental Table 2.Sequences of corresponding peptides and the percent cov-erage of identified proteins are also shown.

To eliminate proteins present as contaminants of granulesubsets, proteins that were detected by only one of the three2D HPLC ESI-MS/MS experiments were classified as rejectedproteins. Supplemental Table 3 lists the rejected proteins foreach granule subset. A total of 344 proteins were rejectedfrom gelatinase granules, 211 were rejected from specificgranules, and 230 were rejected from azurophil granules.Most rejected proteins were of ribosomal, nuclear, and mito-chondrial origin or were hypothetical proteins, suggesting thatthe granule isolation method resulted in contamination with

small amounts of other subcellular organelles. That somecontamination did occur is supported by identification of sev-eral proteins listed in Table II. The benzodiazepine receptorwas described previously to be present on mitochondria (29).Lamin B receptor and Sad1 are of nuclear origin (30, 31),suggesting that membranes from these structures contami-nated granule preparations. The presence of signaling pro-teins (G protein-coupled receptor kinase 6; p21-activated ki-nase 5; small GTPases of the Ras, Rab, and Rho family; andheterotrimeric G protein subunits) and membrane traffickingproteins (syntaxin 2, syntaxin 3A, syntaxin 8, syntaxin 10, andsyntaxin 11) in the list of rejected proteins suggests the ex-clusion criteria eliminated some proteins that are likely com-ponents of the granule proteome. Functional classification ofproteins was performed by a literature search for each proteinin the PubMed database.

Receptors and Cytoskeletal Membrane Anchors—Thisgroup included transmembrane proteins involved in adhesion,

TABLE I—continued

Entrez gene Entrez ID Protein name GranulePeptides

matched/totalCoverage

MOWSEscore

%

TUBB1 gi�57013276 Tubulins � GE, SG 10/15 31 129VIM gi�4507895 Vimentin 50 kDa GE, SG 14/19 36 168ANXA1 gi�54696696 Annexin I SG 9/18 34 101S100A12 gi�5032059 Calgranulin C SG 4/11 40 65CTSZ gi�7546546 Cathepsin X SG 6/16 24 73ITGB2 gi�46255730 CD18 SG 7/14 12 64CHI3L1 gi�4557018 gp39 chitinase SG 20/37 55 195CHSY1 gi�37182181 Chondroitin sulfate synthase SG 13/33 20 87MMP8 gi�4505221 Collagenase SG 10/23 25 83DEFA1 gi�4758146 Defensin �1 SG 5/22 28 68QPCT gi�525241 Glutaminyl cyclase SG 9/17 41 123GNB2 gi�29789261 GTP-binding protein �2 SG 7/23 20 67OLFM4 gi�29126831 GW112 SG 7/15 20 78STXBP2 gi�1944130 Hunc-18b SG 8/19 22 74SLPI gi�13489087 Leukocyte anti-elastase SG 7/15 25 72LTA4H gi�4505029 Leukotriene A4 hydrolase SG 7/12 14 76PPFIBP1 gi�28278230 Liprin-like SG 7/19 40 71MAP2K1IP1 gi�11496277 MEK1 BP SG 5/16 62 75MYH9 gi�189036 Myosin heavy chain SG 12/21 14 78PTX3 gi�4506333 Pentaxin 3 SG 11/25 34 107PFC gi�3183860 Properdin P factor SG 14/30 33 134SEMG1 gi�1147569 Semenogelin I SG 16/38 38 146SEMG2 gi�4506885 Semenogelin II SG 12/38 25 84ST6GALNAC3 gi�37182203 Sialyltransferase 3 SG 7/25 45 75EHD1 gi�30240932 Testilin SG 15/26 25 138TOLLIP gi�21361619 TOLLIP SG 8/33 36 65CRISP3 gi�2136189 SGP-28 SG, AG 7/25 23 74CTSG gi�2392230 Cathepsin G GE, SG, AG 7/24 24 70CHIT1 gi�47480958 Chitotriosidase GE, SG, AG 12/26 30 113RETN gi�37183250 FIZZ-3 (Resistin) GE, SG, AG 8/24 76 85CAMP gi�39753970 hCAP-18 GE, SG, AG 9/22 45 109LTF gi�640200 Lactoferrin GE, SG, AG 10/22 16 83LCN2 gi�38455402 Lipocalin (NGAL) GE, SG, AG 12/27 64 163LYZ gi�442591 Lysozyme GE, SG, AG 8/24 53 102MPO gi�494396 MPO chain B, D GE, SG, AG 6/29 69 78

gi�494397 26/52 53 191

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transmigration, cellular activation, and cytoskeletal anchoringto the membrane, including components of lipid rafts. Of the40 proteins, 12 were identified only from gelatinase granules,19 were found on both specific and gelatinase granules, sixwere found on all three granule types, and three were foundonly on azurophil granules. Proteins unique to specific gran-ules were not found in this group. Formyl peptide receptors,complement component receptor 1 (CR1), CD11b, CD18,SCAMPs, Stomatin, CD63, and LAMPs have been identifiedpreviously as components of neutrophil granules (1, 2, 32).

Channels and Transporters—Proteins that function in facil-itating the movement of solutes across lipid bilayers wereincluded in this category. Thirteen proteins were identifiedonly on gelatinase granules, 10 were from gelatinase and spe-cific granules, two were from all three granule subtypes, and

two were only from azurophil granules. These proteins includedproton pumps and transporters for metal ions, glucose, adeninenucleotides, amines, and steroids. Eleven of these proteinswere described previously to be of mitochondrial origin.

GTPases—This group included both monomeric and het-erotrimeric GTPases and two GTPase-activating proteins. Ofthe total of 21 identified proteins, 10 were found on gelatinasegranules only, one was only from specific granules, twowere from specific and gelatinase granules, and eight werefrom all three granule subsets. Monomeric GTPases of theRab family and Cdc42 have been shown to be involved ingranule exocytosis in other cell types (33–35). Of note,Rab27A was shown previously to associate with many typesof granules and play a crucial role in exocytosis by modu-lating granule binding with cytoskeleton and with proteins

FIG. 4. 2D gels of specific granule proteins fractionated by carbonate lysis and by ammonium sulfate precipitation of TX-100-solubilized proteins. Shown is fractionation of specific granule proteins by carbonate lysis (A and B) and by ammonium sulfate precipitation(C and D). A, a 2D gel of proteins that remained on the membrane after granule lysis in 0.1 M sodium carbonate buffer. B, proteins that weresolubilized in 0.1 M sodium carbonate. C, proteins precipitated in 20% ammonium sulfate solution. D, proteins that remained in solution in 20%ammonium sulfate but were precipitated in 100% ammonium sulfate solution.

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1510 Molecular & Cellular Proteomics 4.10

that control membrane fusion (36). Rab27A was a compo-nent of all three granule types. To our knowledge this is thefirst report of the presence of Rab27A in neutrophils. Cdc42was also found on all three granule subsets. This Rho familyGTPase stimulates exocytosis by activating the inositol1,4,5-trisphosphate and calcium second messenger signal-ing pathway (35).

Structural Proteins and Adaptors—We included cytoskel-etal proteins and actin-binding proteins in this group. Elevenproteins were identified only on gelatinase granules, 13 werefrom gelatinase and specific granules, four were from specificgranules only, 10 were from all three granule types, and twowere from only azurophil granules. The presence of actin,tubulin, and vimentin on all three granule subtypes is consist-ent with a role for these cytoskeletal structures in neutrophilexocytosis (1, 2, 37, 38). Visual inspection of 2D gels sug-gested that greater amounts of cytoskeletal proteins wereassociated with gelatinase granules than specific granules,which in turn had more than azurophil granules. To confirmthis observation, Western blotting of whole granules for actinwas performed following normalization for membrane contentusing a membrane-binding fluorescent dye (Fig. 5). Theamount of actin associated with gelatinase granules was dra-matically greater than that associated with specific granules.A minimal amount of actin was associated with azurophilgranules.

Kinases and Phosphatases—This group included tyrosinekinases, tyrosine phosphatases, and one kinase scaffoldingprotein, MEK1-binding protein. Tyrosine kinases were identi-fied previously on neutrophil granules, and inhibition of tyro-sine kinase activity prevents neutrophil degranulation (39–42).To our knowledge, this is the first report of a tyrosine phospha-tase association with neutrophil granules. Tyrosine phosphata-ses are localized to granules in other cells, and they have beenshown to participate in signaling leading to exocytosis (43–46).

Luminal and Host Defense Proteins—This group includedproteins localized to granule lumens and luminal and mem-brane proteins that participate in host defense, such as themembrane proteases neprilysin and leukolysin. Four proteinswere identified on gelatinase granules only, 13 proteins werefrom gelatinase and specific granules, 11 were proteins onlyfrom specific granules, 18 were from all three granule subsets,three were from specific and azurophil granules, and 13 werefrom azurophil granules only. All of the luminal proteins in thislist are annotated on the NCBI database as proteins destinedeither to lysosomal or to secretory compartments. Proteins oflysosomal origin were found previously in azurophil granulesin agreement with the hypothesis that azurophil granules arelysosome-related organelles (1, 2). Among the identified pro-teins in this group was calreticulin, a component of the endo-plasmic reticulum (47). Calreticulin may also be a bona fidegranule protein, however, as it acts as a chaperone for neu-trophil granule luminal proteins (48) and is present on theextracellular surface of the neutrophil plasma membrane (49).

Calreticulin was identified as a cytolytic component of T lym-phocyte granules (50).

Membrane Traffic and Fusion—In this group four proteinswere found on gelatinase granules only, one was from gela-tinase and specific granules, two were from specific granulesalone, four were from all three granule types, and two werefrom azurophil granules only. Hunc18b (Munc18-2) andUnc-13 homolog 3 (Munc-13) have not been previously iden-tified in neutrophils. These proteins are members of a family ofproteins that bind to and modulate the activity of membranefusion proteins (51, 52). A hypothetical protein with a C2domain, which is known to be involved in membrane fusionevents (53), was identified on gelatinase granules. Syntaxin 7and VAMP 8 were expressed on all three granule subsets.These two membrane fusion proteins have not been previ-ously identified from neutrophil granules.

Redox Proteins—Proteins involved in redox reactions, in-cluding a transmembrane protein related to thioredoxin andthe components of the neutrophil NADPH oxidase, p22-phoxand gp91-phox, were included in this group. Ten proteinswere found only on gelatinase granules, one was from gela-tinase and specific granules, two were from specific granulesalone, and three were from all three granules. Components ofthe NADPH oxidase were found on all three granule subsets.

Miscellaneous Proteins—This group included proteins notclassified into the other groups or for which no function hasbeen described. Twenty-one proteins were identified on gel-atinase granules, 16 were from gelatinase and specific gran-ules, six were from specific granules only, 10 were from allthree granule types, two were from specific and azurophilgranules, and four were from azurophil granules only. Amongthe proteins found were chaperones such as PDI and Hsp70and 11 hypothetical proteins. Hemoglobin was also found ongelatinase and specific granules, suggesting that hemoglobinfrom lysed red blood cells binds to phospholipid membranes.Hemoglobin was completely removed from granule mem-branes by sodium carbonate treatment.

DISCUSSION

Using two approaches, 2DE followed by MALDI MS and 2DHPLC ESI-MS/MS, 286 granule and granule-associated pro-teins from human neutrophils were identified. Only 87 proteinswere identified by 2DE and MALDI MS of which 56 wereabundant structural or luminal proteins. The only transmem-brane-spanning proteins identified after 2DE were the inte-grins CD11b and CD18, both of which have a single trans-membrane domain. The limited protein identification usingintact granules was marginally enhanced by fractionation ofgranule proteins using sodium carbonate treatment or ammo-nium sulfate precipitation. These results emphasize the rec-ognized limitations to 2DE-based proteomics, namely, thebias against low abundance proteins, transmembrane pro-teins, and proteins at the extremes of isoelectric point andmolecular mass (54, 55). Despite these limitations, 39 proteins

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Molecular & Cellular Proteomics 4.10 1511

TABLE IIAll proteins identified on neutrophil granules by 2DE MALDI-TOF MS and SCX-RP ESI-MS/MS

A total of 286 proteins were identified, and proteins were catalogued by function based on a literature search for each protein in the PubMeddatabase. The gene and protein designation, method of identification, and granule subset on which the protein was found are listed. To belisted as a component of the granule subset, a protein was either identified from a granule subset by MALDI-MS analysis of 2D gels, detectedby at least two of three 2D HPLC ESI-MS/MS experiments, or detected by 2D HPLC ESI-MS/MS experiment once in one granule subset andadditionally detected by 2DE MALDI-MS or at least twice by 2D HPLC ESI-MS/MS in a different granule subset (indicated by an asterisk nearthe method designation in “Granule typeMETHOD” column). In the method designation, LCMS is an abbreviation for 2D HPLC ESI-MS/MS, and2D is an abbreviation for 2DE MALDI-TOF MS. SOD, superoxide dismutase; hnRNP, heterogeneous nuclear ribonucleoprotein; GE, gelatinase;SG, specific granule; AG, azurophil granule; ICAM, intracellular adhesion molecule; CEACAM, carcinoembryonic antigen-related cell adhesionmolecule; ADAM, a disintegrin and metalloprotease; LSP1, lymphocyte-specific protein 1; SNAP, synaptosomal-associated protein; ARP,actin-related protein; VAMP, vesicle associated membrane protein; Grp, glucose-regulated protein; Hsp, heat shock protein.

Entrez gene Entrez protein Protein name Granule typeMETHOD

Receptors and transmembranecytoskeletal anchors

BZRP NP_000705 Benzodiazepine receptor GELCMS

FCGR3B NP_000561 CD16, Fc�RIIIb GELCMS

CR1 NP_000564 CD35, CR1 GELCMS

NP_000642SPN NP_003114 CD43, sialophorin GELCMS

CD9 NP_001760 CD9, motility-related protein GELCMS

FLOT2 NP_004466 Flotillin 2 GELCMS

LBR NP_919424 Lamin B receptor GELCMS

NP_002287GP9 NP_000165 Platelet glycoprotein IX GELCMS

SELPLG NP_002997 P-selectin glycoprotein ligand-1 GELCMS

UNC84B NP_056189 Sad1 GELCMS

SCAMP1 NP_004857 SCAMP1 GELCMS

SCAMP2 NP_005688 SCAMP2 GELCMS

CEACAM1 NP_001703 CEACAM-1 GELCMS, SPLCMS

ITGAM NP_000623 CD11b, complement component receptor 3 (CR3) GE2D LCMS, SP2D LCMS

ADAM8 NP_001100 CD156, ADAM-8 GELCMS, SPLCMS

ITGB2 NP_000202 CD18, macrophage antigen 1 (mac-1) � subunit GELCMS, SP2D LCMS

ITGA2B NP_000410 CD41, platelet fibrinogen receptor, � subunit GELCMS, SPLCMS

ITGB3 NP_000203 CD61, platelet glycoprotein IIIa GELCMS, SPLCMS

C5R1 NP_001727 CD88, C5aR1 GELCMS, SPLCMS

DSG1 NP_001933 Desmoglein preproprotein GELCMS, SPLCMS*

FPR1 NP_002020 Formyl peptide receptor GELCMS, SPLCMS

GP1BB NP_000398 Glycoprotein Ib � precursor GELCMS, SPLCMS

HLA-A NP_002107 HLA-A1 GELCMS, SPLCMS*

ICAM3 NP_002153 ICAM-3 precursor GELCMS, SPLCMS*

LAIR1 NP_002278 Leukocyte-associated Ig-like receptor 1 GELCMS, SPLCMS*

NP_068352NP_068354

LILRB2 NP_005865 Leukocyte Ig-like receptor 2 GELCMS, SPLCMS

CLEC12A NP_612210 Myeloid inhibitory C-type lectin-like receptor GELCMS, SPLCMS

NP_963917SIGLEC5 NP_003821 Sialic acid-binding Ig-like lectin 5 GELCMS, SPLCMS

SDCBP NP_005616 Syntenin GE2D, SP2D

VNN1 NP_004657 Vanin 1 precursor GELCMS, SPLCMS*

VNN2 NP_004656 Vanin 2 GELCMS, SPLCMS*

NP_511043CANX NP_001737 Calnexin GELCMS, SPLCMS, AZLCMS*

FLOT1 NP_005794 Flotillin 1 GELCMS, SPLCMS*, AZLCMS*

FCER1G NP_004097 Fc receptor for IgE, high affinity I, � polypeptide GELCMS, SPLCMS, AZLCMS*

ITGB5 NP_002204 Integrin, �5 GELCMS*, SPLCMS*, AZLCMS

LAMP2 NP_002285 LAMP2 GELCMS, SPLCMS*, AZLCMS*

NP_054701STOM NP_004090 Stomatin GELCMS, SPLCMS, AZLCMS

CD63 NP_001771 CD63, LAMP3 AZLCMS

TM7SF3 NP_057635 Seven-transmembrane receptor AZLCMS

STOML3 NP_660329 Stomatin-like 3 AZLCMS

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TABLE II—continued

Entrez gene Entrez protein Protein name Granule typeMETHOD

Channels and transportersSLC25A5 NP_001143 Adenine nucleotide translocator 2 GELCMS

SLC25A6 NP_001627 Adenine nucleotide translocator 3 GELCMS

SLC4A1 NP_000333 Anion exchanger, member 1 GELCMS

ATP5A1 NP_004037 ATP synthase, H�-transporting, mitochondrial F1

complex, � subunitGE2D LCMS

ATP6V1C2 NP_653184 ATPase, H�-transporting, lysosomal 42-kDa, V1subunit C isoform 2

GELCMS

ATP6V0A1 NP_005168 ATPase, H�-transporting, lysosomal V0 subunit aisoform 1

GELCMS

ATP6V0A2 NP_036595 ATPase, H� transporting, lysosomal V0 subunit aisoform 2

GELCMS

SLC2A3 NP_008862 Glucose transporter type 3 GELCMS

TMED9 NP_059980 gp25L2 protein, protein transporter GELCMS

MTCH2 NP_055157 Mitochondrial carrier homolog 2 GELCMS

SFXN1 NP_073591 Sideroflexin 1 GELCMS

SLCO4C1 NP_851322 Solute carrier organic anion transporter family,member 4C1

GELCMS

VDAC2 NP_003366 Voltage-dependent anion channel 2 GE2D LCMS

SLC25A4 NP_001142 Adenine nucleotide translocator 1 GELCMS, SPLCMS

ATP5F1 NP_001679 ATP synthase, H�-transporting, mitochondrial F0

complex, subunit bGELCMS, SPLCMC*

ATP5H NP_006347 ATP synthase, H�-transporting, mitochondrial F0

complex, subunit dGELCMS, SPLCMS*

SLC25A24 NP_037518 Calcium-binding transporter GELCMS, SPLCMS*

MVP NP_059447 Major vault protein GELCMS*, SPLCMC

NP_005106SLC25A3 NP_005879 Mitochondrial phosphate carrier precursor isoform 1 GELCMS, SPLCMS*

NP_002626PLSCR1 NP_066928 Phospholipid scramblase 1 GELCMS, SPLCMS*

ATP2A3 NP_005164 Sarco/endoplasmic reticulum Ca2�-ATPase GELCMS, SPLCMS

NP_777613NP_777614NP_777615NP_777617NP_777618

VDAC1 NP_003365 Voltage-dependent anion channel 1 GELCMS, SPLCMC*

VDAC3 NP_005653 Voltage-dependent anion channel 3 GELCMS, SPLCMC*

ATP6V0D1 NP_004682 ATPase, H�-transporting, lysosomal, V0 subunit Disoform 1

GELCMS, SPLCMS*, AZLCMS

TCIRG1 NP_006010 ATPase, H�-transporting, 116 kDa, vacuolar, T cellimmune regulator

GELCMS, SPLCMS*, AZLCMS

ATP8A1 NP_006086 Aminophospholipid transporter ATPase AZLCMS

VAT1 NP_006364 Vesicle amine transport protein 1 AZLCMS

GTPasesHSPC121 NP_057479 Butyrate-induced transcript 1, GTPase-activating

proteinGELCMS

IQGAP1 NP_003861 IQ motif-containing GTPase-activating protein 1 GELCMS

RAB7 NP_004628 RAB7 GELCMS

RAB10 NP_057215 RAB10 GELCMS

RAB11A NP_004654 RAB11A GELCMS

RAB11B NP_004209 RAB11B GELCMS

RAB14 NP_057406 Rab14 GELCMS

RAB21 NP_055814 RAB21 GELCMS

RAB32 NP_006825 RAB32 GELCMS

RAP2A NP_066361 RAP2 GELCMS

RAP2B NP_002877RAP2C NP_067006RAB31 NP_006859 RAB31 SPLCMS

RAB2 NP_002856 RAB2 GELCMS, SPLCMS*

RAB5C NP_958842 RAB5C GELCMS, SPLCMS

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TABLE II—continued

Entrez gene Entrez protein Protein name Granule typeMETHOD

NP_004574CDC42 NP_001782 Cdc42 GELCMS, SPLCMS*, AZLCMS

GNAI2 NP_002061 Gi �2 GELCMS, SPLCMS, AZLCMS

GNB1 NP_002065 G �1,2 GELCMS*, SP2D LCMS*, AZLCMS

GNB2 NP_005264RAB1A NP_004152 RAB1 GELCMS, SPLCMS*, AZLCMS

RAB1B NP_112243RAB3A NP_002857 RAB3 GELCMS, SPLCMS, AZLCMS

RAB3B NP_002858RAB3C NP_612462RAB3D NP_004274 RAB3D GELCMS, SPLCMS, AZLCMS*

RAB27A NP_004571 Rab27A GE2D LCMS, SPLCMS, AZLCMS

NP_899057NP_899058NP_899059

RAP1A NP_002875 RAP1 GE2D, SPLCMS, AZLCMS

RAP1B NP_056461Structural proteins and

adaptorsAP2A1 NP_055018 Adaptin GELCMS

NP_570603CFL1 NP_005498 Cofilin 1 GE2D LCMS*

NP_068733NP_619579

CORO7 NP_078811 Coronin 7 GELCMS

ARPC5 NP_005708 p16 Arc GE2D

ARPC3 NP_005710 p21 Arc GE2D

MYL6 NP_066299 Myosin alkali light chain GELCMS

NP_524147NP_524149NP_524148

TAGLN NP_003177 Transgelin GE2D

TUBB1 NP_110400 Tubulin �1 GELCMS

URP2 NP_848537 UNC-112-related protein 2 GELCMS

NP_113659VIL2 NP_003370 Villin 2 GE2D

RP2 NP_008846 XRP2 GELCMS

YWHAZ NP_003397 14-3-3� GE2D, SP2D

NP_663723ACTN1 NP_001093 Actinin, � 1 GE2D LCMS, SP2D LCMS

ANXA3 NP_005130 Annexin III GE2D, SP2D

ACTR3 NP_005712 ARP3 GE2D, SP2D

CAPZA1 NP_006126 Cap Z GE2D, SP2D

CAPZA2 NP_006127 Capping protein a GE2D, SP2D

CORO1A NP_009005 Coronin 1A GELCMS, SPLCMS

GSN NP_000168 Gelsolin GE2D LCMS, SPLCMS

NP_937895TLN1 NP_006280 Talin 1 GELCMS, SPLCMS

TPM3 NP_689476 Tropomyosin 3 GE2D, SP2D

TUBA2 NP_005992 Tubulin � 2, 3 GELCMS, SPLCMS

TUBA3 NP_524575NP_006000

MRCL3 NP_006462 Myosin regulatory light chain GE2D, SP2D

LSP1 NP_002330 LSP1 GE2D, SP2D

CALD1 NP_149129 Caldesmon 1 SPLCMS

NP_004333NP_149347NP_149130NP_149131

CYLC2 NP_001331 Cylicin 2 SPLCMS

MSN NP_002435 Moesin SPLCMS

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1514 Molecular & Cellular Proteomics 4.10

TABLE II—continued

Entrez gene Entrez protein Protein name Granule typeMETHOD

TUBA4 NP_079295 Tubulin � 4 SPLCMS

ACTA1 NP_001091 Actin, � GELCMS, SPLCMS, AZLCMS

ACTA2 NP_001604ACTB NP_001092 Actin, � or � GE2D LCMS, SP2D LCMS, AZLCMS

ACTG1 NP_001605ANXA1 NP_000691 Annexin I (lipocortin I) GELCMS, SP2D, AZLCMS*

FLNA NP_001447 Filamin 1 GELCMS, SPLCMS, AZLCMS*

LCP1 NP_002289 L-plastin GE2D LCMS, SP2D LCMS, AZLCMS*

MYH9 NP_002464 Myosin heavy chain GELCMS, SP2D LCMS, AZLCMS

PFN1 NP_005013 Profilin 1 GELCMS, SPLCMS*, AZLCMS*

TUBA1 NP_005991 Tubulin � 1 GE2D LCMS, SP2D LCMS, AZLCMS*

TUBB2 NP_001060 Tubulin � 3 GE2D LCMS, SP2D LCMS, AZLCMS

VIM NP_003371 Vimentin GE2D LCMS, SP2D LCMS*, AZLCMS

HCLS1 NP_005326 Hematopoietic lineage cell-specific protein 1 AZLCMS

ZYX NP_003452 Zyxin AZLCMS

Kinases and phosphatasesHCK NP_002101 Hck tyrosine kinase GELCMS

FGR NP_005239 Fgr tyrosine kinase GELCMS, SPLCMS

PTPRJ NP_002834 Protein tyrosine phosphatase, receptor type J GELCMS, SPLCMS

PTPN7 NP_002823 Protein tyrosine phosphatase, non-receptortype 7

GELCMS, SPLCMS*

NP_542155PTPNS1 NP_542970 Protein tyrosine phosphatase, non-receptor

type substrate 1GELCMS, SPLCMS

TTBK2 NP_775771 Tau tubulin kinase SPLCMS

MAP2K1IP1 NP_068805 MEK1-binding protein, MP1 SP2D

PTPRC NP_002829 Protein tyrosine phosphatase, receptor type C GELCMS, SPLCMS, AZLCMS

NP_563578NP_563579

Luminal and host defenseproteinsC10orf42 NP_612366 Chromosome 10 ORF 42 GELCMS

SPCS2 NP_055567 KIAA0102 gene product (signal peptidase) GELCMS

MME NP_000893 Neprilysin GELCMS

NP_009218NP_009219NP_009220

1F9PA NP_002695 Connective tissue activating peptide GE2D

CLC NP_001819 Charcot-Leyden crystal protein GE2D, SP2D

DEFA1 NP_004075 Defensin �1 GE2D, SP2D

DCD NP_444513 Dermcidin precursor GELCMS, SPLCMS

FCN1 NP_001994 Ficolin 1 precursor GE2D LCMS*, SP2D LCMS

HP NP_005134 Haptoglobin �2 GE2D, SP2D

PGLYRP1 NP_005082 Peptidoglycan recognition protein 1 GE2D, SP2D

PADI4 NP_036519 Peptidyl arginine deiminase, type IV GELCMS, SPLCMS*

B2M NP_004039 �2-Microglobulin GE2D, SP2D

MGAM NP_004659 Maltase-glucoamylase GELCMS, SPLCMS

MMP25 NP_071913 Matrix metalloprotease 25 (leukolysin) GELCMS, SPLCMS*

NP_073209ANPEP NP_001141 Membrane alanine aminopeptidase GELCMS, SPLCMS*

SIGLEC5 NP_003821 Sialic acid-binding Ig-like lectin GELCMS, SPLCMS

THBS1 NP_003237 Thrombospondin 1 precursor GELCMS, SPLCMS*

CAT NP_001743 Catalase SPLCMS

CHI3L1 NP_001267 gp-39 chitinase SP2D

CHSY1 NP_055733 Chondroitin sulfate synthase SP2D

CHGA NP_001266 Chromogranin A SPLCMS

QPCT NP_036545 Glutaminyl cyclase SP2D

SLPI NP_003055 Leukocyte anti-elastase SP2D

LTA4H NP_000886 Leukotriene A4 hydrolase SP2D

MMP8 NP_002415 Neutrophil collagenase SP2D LCMS

PTX3 NP_002843 Pentraxin-3 SP2D LCMS

PFC NP_002612 Properdin P factor SP2D

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Molecular & Cellular Proteomics 4.10 1515

TABLE II—continued

Entrez gene Entrez protein Protein name Granule typeMETHOD

T6GALNAC3 NP_694541 Sialyltransferase 3 SP2D

AZU1 NP_001691 Azurocidin 1 preproprotein GELCMS*, SPLCMS, AZLCMS

BPI NP_001716 Bactericidal/permeability-increasing protein GELCMS, SPLCMS, AZLCMS

CALR NP_004334 Calreticulin precursor GE2D, SP2D LCMS*, AZLCMS*

CAMP NP_004336 hCAP-18 GE2D, SP2D LCMS, AZ2D LCMS

CTSG NP_001902 Cathepsin G preproprotein GE2D LCMS, SP2D LCMS, AZ2D LCMS

CHIT1 NP_003456 Chitotriosidase GE2D, SP2D LCMS*, AZLCMS*

EPX NP_000493 Eosinophil peroxidase GELCMS, SPLCMS, AZLCMS

FTL NP_000137 Ferritin, light polypeptide GE2D, SP2D, AZLCMS

RETN NP_065148 FIZZ-3, resistin GE2D, SP2D, AZ2D

OLFM4 NP_006409 GW112 GELCMS*, SP2D LCMS, AZLCMS*

LTF NP_002334 Lactoferrin GE2D LCMS, SP2D LCMS, AZ2D LCMS

CST7 NP_003641 Leukocystatin; Cystatin GE2D, SP2D, AZLCMS

LCN2 NP_005555 Lipocalin 2; NGAL GE2D LCMS, SP2D LCMS, AZLCMS

LYZ NP_000230 Lysozyme precursor GE2D, SP2D LCMS, AZ2D LCMS

MMP9 NP_004985 Gelatinase GE2D LCMS, SP2D LCMS, AZLCMS

MPO NP_000241 Myeloperoxidase GE2D LCMS, SP2D LCMS, AZ2D LCMS

PRTN3 NP_002768 Proteinase 3 GELCMS, SPLCMS, AZLCMS

PRG2 NP_002719 Proteoglycan 2 GELCMS, SPLCMS, AZLCMS

CTSZ NP_001327 Cathepsin Z (X) SP2D, AZLCMS*

ELA2 NP_001963 Elastase 2 SPLCMS*, AZLCMS

CRISP3 NP_006052 SGP-28 SP2D, AZ2D LCMS*

PPGB NP_000299 Cathepsin A AZLCMS

CTSC NP_001805 Cathepsin C AZLCMS

TPP1 NP_000382 Tripeptidyl-peptidase I AZLCMS

DPP7 NP_037511 Dipeptidyl peptidase 7 preproprotein AZLCMS

GGH NP_003869 �-Glutamyl hydrolase precursor AZLCMS

GUSB NP_000172 Glucuronidase, � AZLCMS

HEXA NP_000511 Hexosaminidase A preproprotein AZLCMS

HEXB NP_000512 Hexosaminidase B preproprotein AZLCMS

HYAL3 NP_003540 Hyaluronidase 3 AZLCMS

ACP6 NP_057445 Lysophosphatidic acid phosphatase AZLCMS

ACP2 NP_001601 Lysosomal acid phosphatase 2 AZLCMS

GAA NP_000143 Lysosomal �-glucosidase AZLCMS

MAN2B1 NP_000519 Mannosidase, � B, lysosomal AZLCMS

Membrane traffic andfusion proteins

MBC2 NP_056107 KIAA0747 protein (membrane-bound C2domain-containing)

GELCMS

SNAP23 NP_003816 SNAP-23A GELCMS

SACM1L NP_054735 Synaptojanin GELCMS

UNC13D XP_113950 Unc-13 homolog D GELCMS

NP_954712DYSF NP_003485 Dysferlin GELCMS, SPLCMS

CLTC NP_004850 Clathrin heavy chain 1 SPLCMS

STXBP2 NP_008880 Hunc18b SP2D

DNAJC5 NP_079495 DnaJ (Hsp40) homolog, subfamily C, member 5 GELCMS, SPLCMS*, AZLCMS*

STX7 NP_003560 Syntaxin 7 GELCMS, SPLCMS*, AZLCMS

VAMP2 NP_004772 VAMP 2 GELCMS, SPLCMS*, AZLCMS*

NP_055047VAMP8 NP_003752 VAMP 8 GELCMS, SPLCMS, AZLCMS

SYTL1 NP_116261 Synaptotagmin-like 1 AZLCMS

C20orf178 NP_789782 Snf7 homologue associated with Alix 1 AZLCMS

Redox proteinsDIA1 NP_000389 Cytochrome b5 reductase GELCMS

NP_015565NQO3A2 NP_057327 Cytochrome b5 reductase 1 (B5R.1) GELCMS

GSTK1 NP_057001 Glutathione transferase Kappa 1 GELCMS

SOD2 NP_000627 Mn-SOD chain b GE2D

NDUFB8 NP_004995 NADH dehydrogenase 1 � subcomplex, 8 GELCMS

ND5 NP_536853 NADH dehydrogenase subunit 5 GELCMS

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1516 Molecular & Cellular Proteomics 4.10

TABLE II—continued

Entrez gene Entrez protein Protein name Granule typeMETHOD

NP_776061NDUFB11 NP_061929 Neuronal protein 17.3 GELCMS

HSD17B12 NP_057226 Steroid dehydrogenase homolog GELCMS

SQRDL NP_067022 Sulfide dehydrogenase GELCMS

TXNDC NP_110382 Thioredoxin-related transmembrane protein GELCMS

DHRS8 NP_057329 Dehydrogenase/reductase member 8 GELCMS, SPLCMS

GAPD NP_002037 Glyceraldehyde-3-phosphate dehydrogenase SPLCMS

PRDX5 NP_036226 Peroxiredoxin 5 precursor SPLCMS

NP_857634CYBA NP_000092 p22-phox GELCMS, SPLCMS, AZLCMS*

PDIA3 NP_005304 Grp58 GE2D LCMS, SP2D LCMS*, AZLCMS

CYBB NP_000388 gp91-phox GELCMS, SPLCMS, AZLCMS

Miscellaneous proteinsCA4 NP_000708 Carbonic anhydrase IV GE2D

CGI-51 NP_056195 CGI-51 protein GELCMS

ENO1 NP_001419 Enolase GE2D

FGG NP_000500 Fibrinogen � chain precursor GELCMS

NP_068656GPI NP_000166 Glucose phosphate isomerase GELCMS

E2IG5 NP_055182 Growth and transformation-dependent protein GELCMS

HNRPU NP_004492 hnRNP U protein GELCMS

NP_114032ATAD3A NP_060658 Hypothetical protein FLJ10709 GELCMS

TNFAIP9 NP_078912 Hypothetical protein FLJ23153 GELCMS

EFHA1 NP_689939 Hypothetical protein FLJ34588 GELCMS

TMEM43 NP_077310 Hypothetical protein MGC3222 GELCMS

LOC255809 XP_172995 Hypothetical protein XP_172995 GELCMS

IDH2 NP_002159 Isocitrate dehydrogenase GE2D

KIAA0792 XP_375848 KIAA0792 gene product GELCMS

LAP1B NP_056417 Lamina-associated polypeptide 1B GELCMS

LST1 NP_995309 Leukocyte-specific transcript 1 GELCMS

NP_995310NP_995311NP_995312

MMAA NP_758454 Methylmalonic acid urea GE2D

PHB2 NP_009204 Prohibitin-like GELCMS

RPN1 NP_002941 Ribophorin I GELCMS

RPN2 NP_002942 Ribophorin II precursor GELCMS

TMEM16F XP_113743 Similar to RIKEN cDNA F730003B03 GELCMS

ALB NP_000468 Albumin GE2D LCMS*, SP2D LCMS*

C20orf3 NP_065392 C20 ORF 3; adipocyte plasma membrane-associated

GELCMS, SPLCMS

DSP NP_004406 Desmoplakin GELCMS, SPLCMS*

FGB NP_005132 Fibrinogen � chain preproprotein GELCMS, SPLCMS*

GCA NP_036330 Grancalcin GE2D LCMS, SP2D LCMS

HBB NP_000509 Hemoglobin GE2D, SP2D

HSPA1A NP_005336 Hsp70 1A GE2D LCMS*, SP2D

LOC199675 NP_777578 Hypothetical protein LOC199675 GELCMS, SPLCMS

PHB NP_002625 Prohibitin GE2D LCMS, SP2D LCMS

P4HB NP_000909 PDI GE2D LCMS, SP2D

PKM2 NP_002645 Pyruvate kinase 3 isoform GELCMS, SPLCMS

NP_872270NP_872271

RTN4 NP_065393 Reticulon 4 GELCMS, SPLCMS*

NP_722550NP_008939NP_997403NP_997404

LOC388015 XP_370776 Similar to RTI1 GELCMS, SPLCMS

HRNR XP_373868 Similar to hornerin GELCMS, SPLCMS*

NP_001009931

Proteomic Analysis of Human Neutrophil Granules

Molecular & Cellular Proteomics 4.10 1517

were identified only by the 2DE-based approach.The 2DE analysis of whole granules revealed that the quality

of protein separation paralleled the density of the lumen ma-trix for each granule subset (1, 2, 17, 25). This is likely due tothe presence of large amounts of basic proteins in the granulelumens that interfere with IEF and render the less abundantmembrane-associated proteins unable to focus. This obser-vation led to attempts to fractionate granule proteins withalkaline sodium carbonate or precipitation with various con-centrations of ammonium sulfate. The sodium carbonatemethod fractionated granule proteins largely into luminal andmembrane fractions. This method resulted in effective 2DEseparation of specific granule proteins possibly becausethese granules contain large amounts of moderately cationic

luminal proteins that can be dissociated from the luminalmatrix and granule membranes. The less dense granule ma-trix of gelatinase granules was associated with adequate pro-tein resolution by 2D gels, resulting in minimal improvementafter sodium carbonate extraction of luminal proteins. Sodiumcarbonate extraction did not improve separation and identifi-cation of proteins from azurophil granules, which contain ahighly packed matrix of acid mucopolysaccharide and highlycationic myeloperoxidase (56). Sodium carbonate treatmentof gelatinase, but not specific granules, also resulted in thesignificant loss of low molecular weight proteins comparedwith 2DE of whole granules (compare Fig. 2A with Fig. 3, Aand B).

The failure of sodium carbonate extraction to improve pro-tein identification of gelatinase or azurophil granulesprompted us to seek an alternative method of protein frac-tionation based on a different physical characteristic. Ammo-nium sulfate precipitation fractionates proteins according totheir solubility in concentrated ammonium sulfate solutions.For neutrophil granules, this method separated cytoskeletaland cytoskeleton-binding proteins from more hydrophilic lu-minal proteins. This fractionation method enhanced proteinseparation and identification of gelatinase granule proteins(Fig. 3, C and D). Fractionation of specific and azurophil

FIG. 5. Assessment of actin content on neutrophil granules byWestern blotting. Membrane lipid content was quantitated in neu-trophil granules by TMA-DPH lipophilic dye, and granule proteinswere loaded such that amounts of granule membranes loaded wereequal among different granule subsets. Proteins were transferred tonitrocellulose and probed for actin with an anti-actin antibody.

TABLE II—continued

Entrez gene Entrez protein Protein name Granule typeMETHOD

SEMG1 NP_002998 Semenogelin I GELCMS*, SP2D

NP_937782SEMG2 NP_002999 Semenogelin II GELCMS*, SP2D

B3GTL NP_919299 � 3-glycosyltransferase-like SPLCMS

S100A12 NP_005612 Calgranulin C SP2D

EP300 NP_001420 E1A-binding protein p300 SPLCMS

GALIG NP_919308 Galectin-3 internal gene SPLCMS

PPFIBP1 NP_003613 Liprin-like SP2D

NP_803193EHD1 NP_006786 Testilin SP2D LCMS*

PPIA NP_066953 Cyclophilin A GE2D, SPLCMS*, AZLCMS*

NP_982254NP_982255

HCLS1 NP_005326 Hematopoietic cell-specific Lyn substrate 1 GELCMS*, SPLCMS*, AZLCMS

HIST1H1C NP_005310 Histone H1 family GELCMS, SPLCMS*, AZLCMS

HIST1H2BG NP_003509 Histone H2B GELCMS, SPLCMS*, AZLCMS

HIST1H4I NP_003486 Histone H4 GELCMS, SPLCMS, AZLCMS

HSPA5 NP_005338 Hsp70 5A GE2D, SP2D LCMS, AZLCMS*

S100A8 NP_002955 MRP-8 GE2D LCMS, SP2D LCMS, AZLCMS*

S100A9 NP_002956 MRP-14 GE2D LCMS, SP2D LCMS, AZLCMS*

TOLLIP NP_061882 Toll-interacting protein GELCMS*, SP2D, AZLCMS

RPS27A NP_002945 Ubiquitin precursor GELCMS, SPLCMS, AZLCMS

UBB NP_061828UBA52 NP_003324UBC NP_066289C9orf19 NP_071738 C9orf19, GAPR-1 SPLCMS, AZLCMS

TMEM30A NP_060717 Hypothetical protein FLJ10856 SPLCMS, AZLCMS

DDX4 NP_061912 DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 AZLCMS

ARL10B NP_620150 Hypothetical protein BC015408 AZLCMS

FLJ22662 NP_079105 Hypothetical protein FLJ22662 AZLCMS

SQSTM1 NP_003891 Sequestosome 1 AZLCMS

Proteomic Analysis of Human Neutrophil Granules

1518 Molecular & Cellular Proteomics 4.10

granule proteins by ammonium sulfate precipitation did notimprove protein separation or identification. This was likelydue to the fact that most of the protein content in thesegranules was of luminal origin and, therefore, hydrophilic.Such proteins precipitate at high concentrations of ammo-nium sulfate, and therefore they precipitated in the 100%ammonium sulfate solution. More hydrophobic proteins,which were mostly cytoskeletal and were less abundant, pre-cipitated in the 20% ammonium sulfate solution. The use ofother concentrations of ammonium sulfate did not result inimproved fractionation of granule proteins (data not shown).Thus, sodium carbonate treatment was more effective foridentification of specific granule proteins, whereas ammoniumsulfate precipitation was more effective for identification ofgelatinase granule proteins. Neither approach improved pro-tein identification from azurophil granules. These results indi-cate that optimal protein extraction and separation of granuleproteins by 2DE is highly dependent on the properties of thegranule matrix and luminal proteins.

To overcome the limitations of 2DE-based protein identifi-cation, granule proteins were also identified by strong cationexchange reverse phase two-dimensional chromatographycombined with ESI-MS/MS, commonly referred to as directanalysis of large protein complexes (DALPC) or multidimen-sional protein identification technology -spanning and mem-brane-associated proteins, sodium carbonate extraction wasused to remove luminal and cytoskeletal proteins (18, 26–28,58). As shown by the comparison of Fig. 2 with Figs. 3 and 4,the use of sodium carbonate significantly reduced high abun-dance luminal proteins, whereas the reduction in cytoskeletonwas modest. 2D HPLC ESI-MS/MS identified 247 proteinsfrom the three granule subsets.

The distribution of proteins among the granule subsetsindicates that approximately half were present on more thanone granule subset. The presence of proteins in more thanone granule subset could be due to neutrophil granule bio-genesis or to cross-contamination among the granule subsetsfollowing separation by Percoll gradient centrifugation. Gran-ule biogenesis occurs during myeloid cell maturation withdifferent granules forming at different stages of differentiation.The protein content of these granules is determined by thetiming of protein synthesis relative to formation of differentgranule subsets, not by selective targeting of proteins todifferent granules (1–7). The relative purity of granule subsetpreparations was addressed to determine the quality of theproteome for each granule. The distribution of markers foreach granule subset showed granule separation similar to thatreported by other groups (17, 25). Western blot analysis forCD66b, a marker for specific granules, showed that gelatinaseand azurophil granules were not contaminated by specificgranules. The presence of gelatinase in the specific granulepreparation is consistent with a previous study showing that60% of myeloperoxidase-negative granules contain gelatin-ase in addition to a marker of specific granules, lactoferrin (1,

2). The presence of myeloperoxidase in specific and gelatin-ase granules may be due to the extremely basic nature of thisprotein, which allows myeloperoxidase released from azuro-phil granules to bind to phospholipid membranes of othergranules. Based on current separation techniques and knowngranule markers, however, minimal cross-contaminationamong the granule subsets cannot be excluded.

We attempted to establish a valid list of proteins for eachgranule type by rejecting proteins that were identified in onlyone of three 2D HPLC ESI-MS/MS experiments. A total ofover 500 proteins, including nuclear, mitochondrial, riboso-mal, and cytosolic proteins, were rejected using this exclusioncriterion. A few contaminating proteins may have still beenpresent in granule proteomes as several mitochondrial mem-brane transporters were identified in more than one granulepreparation, especially in the lighter gelatinase granule frac-tion. This is likely due to the fact that gelatinase granulessediment at a density of 1.08 g/ml in Percoll (17, 25), whereasmitochondria sediment at a density of 1.05 g/ml (59). Histoneswere also identified in all three granule subsets. Their pres-ence may reflect nuclear contamination from the reportedbreakage of 16% of nuclei during nitrogen cavitation of neu-trophils (17, 25) and subsequent nonspecific binding to gran-ule membranes. Histones recently were described to co-lo-calize with granule enzymes in neutrophil extracellular traps(60). Subcellular fractionation showed that murine macro-phage granules contained histones (61). Histones were alsosecreted by amnion cells (62). Thus, histones may be com-ponents of neutrophil granules. The list of rejected proteinscontained several proteins, including syntaxins and synapto-brevin-like proteins, that regulate granule membrane fusion.Although none of these proteins have been identified previ-ously on neutrophil granules, these results suggest the pos-sibility that some granule proteins may have been excluded bythe criteria used in this study. The presence of false positiveand false negative results indicates that defining subcellularorganelle proteomes using highly sensitive mass spectrome-try-based techniques is limited by the ability to purify theseorganelles. Ultimately confirmation that a specific protein ispresent in an organelle will require histologic studies.

Analysis of the distribution of proteins among the granulesubsets revealed differences among the subsets that suggestfunctional heterogeneity. The total number of proteins and thenumber of proteins in each functional classification, except forluminal proteins, increased from azurophil to specific to gel-atinase granules. The number of luminal proteins identifiedwas greatest in specific granules (45 proteins), whereasazurophil (34) and gelatinase (35) granules contained similarnumber of proteins. Gelatinase granules are the most easilymobilized granules in neutrophils, and, therefore, these gran-ules will undergo exocytosis at an earlier stage of neutrophilactivation than specific or azurophil granules. Gelatinasegranule membranes contain a large number of membranereceptors and adhesion molecules and are associated with

Proteomic Analysis of Human Neutrophil Granules

Molecular & Cellular Proteomics 4.10 1519

the largest amount of actin cytoskeleton and cytoskeletalregulatory proteins. These results support a role for gelatinasegranules in enhancing the plasma membrane expression ofmolecules necessary for neutrophil adherence to and migra-tion through inflamed vascular endothelium and for subse-quent chemotaxis. On the other hand, azurophil granulesprimarily fuse with phagosomes, while exocytosis is negligi-ble. These granules contain the largest number of luminalbactericidal proteins, while there is a paucity of membrane,cytoskeletal, and GTP-binding proteins. The greater complex-ity of the specific granule lumen and the presence of a signif-icant number of transmembrane and membrane-associatedproteins suggest that these granules represent a transitionalphase that can contribute to neutrophil activation throughexocytosis or provide bactericidal proteins to phagosomes.Our results also suggest a differential role of the actin cy-toskeleton in regulation of granule exocytosis. Gelatinasegranules, the most easily mobilizable granule subset, are as-sociated with the largest amount of actin cytoskeleton. On theother hand, azurophil granules are associated with very littleactin, and they fail to exhibit exocytosis unless the subplasmamembrane actin cytoskeleton is disrupted (1, 2). Once again,specific granules represent a transition between these twoextremes. Previous reports have emphasized the role of thesubplasma membrane actin cytoskeleton as a barrier to gran-ule exocytosis (63). The present study suggests that the actincytoskeleton associated with granules also plays an activerole in mediating exocytosis.

To our knowledge, this is the first proteomic study of neu-trophil granules. The importance of regulated exocytosis indetermining the activation state of neutrophils and the use ofregulated exocytosis by a large number of other cells indicatethe value of defining granule proteomes. The methodologydescribed herein provides an approach to defining granuleproteomes. In our experience, 2DE identified and revealedrelative distribution of more abundant proteins in granules,whereas 2D HPLC ESI-MS/MS identified less abundant pro-teins and hydrophobic proteins not amenable to detection by2DE. The sensitivity of this latter approach demands thatgranules be isolated to a high degree of purity and/or exper-imental approaches be used to eliminate false positive proteinidentification. Our data show that neutrophil granules arecomplex organelles. Analysis of the more than 200 proteinsassociated with neutrophil granules will allow a better under-standing of the contribution of each of the granule subsets toneutrophil biology.

* The costs of publication of this article were defrayed in part by thepayment of page charges. This article must therefore be herebymarked “advertisement” in accordance with 18 U.S.C. Section 1734solely to indicate this fact.

□S The on-line version of this article (available at http://www.mcponline.org) contains supplemental material.

** To whom correspondence should be addressed: Molecular Sig-naling Group, Kidney Disease Program, Donald E. Baxter Research

Bldg., 570 S. Preston St., University of Louisville, Louisville, KY40202. Tel.: 502-852-0014; Fax: 502-852-4384; E-mail: [email protected].

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