Most differentially expressed peptides between US and S UM-CLL cells
| Spot no.* . | Fold change† . | Accession no.‡ . | Protein name§ . | Gene‖ . | t test¶ . | q value¶ . | Sequence cover, %# . | No. of peptides matched# . | No. of peptides matched# . | Theoretical (pI/MW**) . | Observed (pI/MW††) . | Function‡‡ . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 929 | −4.2§§ | P54727 | UV excision repair protein RAD23 homolog B | RAD23B | < .0002 | < .01 | 201 | 30 | 10 | 4.79/43 202 | 4.90/66 512 | DNA binding, regulation of nucleobase, nucleoside, and nucleic acid metabolism |
| 814 | −2.8§§ | Q03252 | Lamin-B2 | LMNB2 | < .00005 | < .01 | 189 | 39 | 26 | 5.29/67 762 | 5.51/72 102 | Structural molecule activity, cell growth, and/or maintenance |
| 884 | −2.5§§ | Q53EL6 | Programmed cell death protein 4 | PDCD4 | < .04 | < .01 | 424 | 28 | 11 | 5.07/52 088 | 4.97/67 848 | Apoptosis |
| 1292 | −1.8§§ | P36507 | Dual-specificity mitogen-activated protein kinase kinase 2 | MAP2K2 | < .002 | < .01 | 63 | 20 | 7 | 6.12/44 681 | 6.4/48 729 | Protein threonine-tyrosine kinase activity, cell communication, signal transduction |
| 557 | −1.7§§ | Q14005 | Pro-IL 16 | IL16 | < .007 | < .01 | 92 | 5 | 4 | 8.34/142976 | 5.82/84 930 | Cytokine activity, immune response |
| 1428 | −1.7§§ | P07910 | Heterogeneous nuclear ribonucleoproteins C1/C2 | HNRNPC | < .002 | < .01 | 185 | 23 | 13 | 4.95/33 707 | 5.07/43 198 | RNA binding, regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolism |
| 590 | −1.6§§ | P28331 | NADH-ubiquinone oxireductase 75-kDa subunit | NDUFS1 | < .05 | < .01 | 136 | 35 | 17 | 5.89/80 443 | 5.48/83 258 | Oxidoreductase activity, metabolism, energy pathways |
| 905 | −1.5§§ | Q9NYB0 | Telomeric repeat-binding factor 2-interacting protein 1 | TERF2IP | < .03 | < .02 | 62 | 31 | 9 | 4.64/44 404 | 4.75/67 059 | DNA binding, cell communication, signal transduction |
| 1559 | −1.5§§ | P37837 | Transaldolase | TALDO1 | < .05 | < .02 | 243 | 21 | 8 | 6.36/37 688 | 6.32/38 340 | Transferase activity, transferring aldehyde or ketonic groups, metabolism, energy pathways |
| 2099 | −1.4§§ | Q9Y5 × 3 | Sorting nexin-5 | SNX5 | < .006 | < .01 | 138 | 45 | 14 | 6.31/47 072 | 6.64/53 508 | Transporter activity |
| 620 | −1.4§§ | Q9Y5 × 1 | Sorting nexin-9 | SNX9 | < .05 | < .02 | 438 | 20 | 9 | 5.40/66 949 | 5.59/81 524 | Receptor signaling complex scaffold activity, cell communication, signal transduction |
| 568 | −1.4§§ | P42331 | Rho-GTPAse-activating protein 25 | ARHGAP25 | < .03 | < .05 | 308 | 16 | 10 | 5.83/72 955 | 5.46/75 000 | GTPAse activator activity |
| 433 | 1.4‖‖ | P14317 | Hematopoietic lineage cell-specific protein | HCLS1 | < .01 | < .01 | 48 | 4 | 2 | 4.74/54 079 | 4.85/90 151 | Cell communication, signal transduction |
| 1893 | 1.4‖‖ | P52566 | Rho-GDP-dissociation inhibitor 2 | ARHGDIB | < .006 | < .01 | 70 | 47 | 7 | 5.1/23 031 | 5.11/24 297 | Receptor signaling complex scaffold activity, cell communication, signal transduction |
| 773 | 1.5‖‖ | P13796 | Plastin-2 | LCP1 | < .02 | NA | 251 | 14 | 9 | 5.2/70 815 | 5.27/74 590 | Calcium ion binding, cell communication, signal transduction |
| 977 | 1.5‖‖ | P08670 | Vimentin | VIM | < .05 | < .03 | 155 | 36 | 14 | 5.06/53 676 | 5.0/64 219 | Structural constituent of cytoskeleton, cell growth and/or maintenance |
| 1920 | 1.6‖‖ | Q6IBC3 | Cathepsin H | CTSH | < .04 | < .01 | 155 | 12 | 6 | 8.38/37 980 | 6.02/23 763 | Cysteine-type peptidase activity, protein metabolism |
| 1366 | 1.6‖‖ | P11310 | Medium-chain specific acyl-coA des-hydrogenase, mitochondrial | ACADM | < .002 | < .01 | 76 | 26 | 10 | 8.61/47 015 | 6.62/45 546 | Catalytic activity, metabolism, energy pathways |
| 742 | 2‖‖ | P20700 | Lamin-B1 | LMNB1 | < .03 | < .01 | 432 | 25 | 14 | 5.11/66 653 | 5.1/76 355 | Structural molecule activity, cell growth, and/or maintenance |
| 1926 | 2.1‖‖ | O75489 | NADH dehydrogenase (ubiquinone) iron-sulfur protein 3 | NDUFS3 | < .03 | < .01 | 143 | 45 | 12 | 6.99/30 337 | 5.68/23 542 | Catalytic activity, metabolism, energy pathways |
| 1032 | 2.1‖‖ | P33241 | Lymphocyte-specific protein 1 | LSP1 | < .007 | < .01 | 174 | 18 | 4 | 4.69/37 397 | 4.56/61 787 | Calcium ion binding, cell communication, signal transduction |
| 1861 | 2.2‖‖ | Q06323 | Proteasome activator complex subunit 1 | PSME1 | < .01 | < .01 | 125 | 50 | 12 | 5.78/28 876 | 5.68/25 194 | Ubiquitin-specific protease activity, protein metabolism |
| 857 | 2.9‖‖ | P61978 | Heterogeneous nuclear ribonucleoprotein K | HNRNPK | < .0002 | < .01 | 127 | 32 | 11 | 5.39/51 230 | 5.47/70 107 | Ribonucleoprotein, regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolism |
| 1851 | 3.4‖‖ | P21964 | Catechol O-methyltransferase | COMT | < .004 | < .01 | 186 | 19 | 3 | 5.26/30 037 | 5.34/25 550 | Metabolism, energy pathways |
| 541 | 4.1‖‖ | Q13409 | Cytoplasmic dynein 1 intermediate chain 2 | DYNC1I2 | < .02 | < .01 | 235 | 9 | 5 | 5.08/71 811 | 5.26/85 329 | Motor activity, cell growth, and/or maintenance |
| Spot no.* . | Fold change† . | Accession no.‡ . | Protein name§ . | Gene‖ . | t test¶ . | q value¶ . | Sequence cover, %# . | No. of peptides matched# . | No. of peptides matched# . | Theoretical (pI/MW**) . | Observed (pI/MW††) . | Function‡‡ . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 929 | −4.2§§ | P54727 | UV excision repair protein RAD23 homolog B | RAD23B | < .0002 | < .01 | 201 | 30 | 10 | 4.79/43 202 | 4.90/66 512 | DNA binding, regulation of nucleobase, nucleoside, and nucleic acid metabolism |
| 814 | −2.8§§ | Q03252 | Lamin-B2 | LMNB2 | < .00005 | < .01 | 189 | 39 | 26 | 5.29/67 762 | 5.51/72 102 | Structural molecule activity, cell growth, and/or maintenance |
| 884 | −2.5§§ | Q53EL6 | Programmed cell death protein 4 | PDCD4 | < .04 | < .01 | 424 | 28 | 11 | 5.07/52 088 | 4.97/67 848 | Apoptosis |
| 1292 | −1.8§§ | P36507 | Dual-specificity mitogen-activated protein kinase kinase 2 | MAP2K2 | < .002 | < .01 | 63 | 20 | 7 | 6.12/44 681 | 6.4/48 729 | Protein threonine-tyrosine kinase activity, cell communication, signal transduction |
| 557 | −1.7§§ | Q14005 | Pro-IL 16 | IL16 | < .007 | < .01 | 92 | 5 | 4 | 8.34/142976 | 5.82/84 930 | Cytokine activity, immune response |
| 1428 | −1.7§§ | P07910 | Heterogeneous nuclear ribonucleoproteins C1/C2 | HNRNPC | < .002 | < .01 | 185 | 23 | 13 | 4.95/33 707 | 5.07/43 198 | RNA binding, regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolism |
| 590 | −1.6§§ | P28331 | NADH-ubiquinone oxireductase 75-kDa subunit | NDUFS1 | < .05 | < .01 | 136 | 35 | 17 | 5.89/80 443 | 5.48/83 258 | Oxidoreductase activity, metabolism, energy pathways |
| 905 | −1.5§§ | Q9NYB0 | Telomeric repeat-binding factor 2-interacting protein 1 | TERF2IP | < .03 | < .02 | 62 | 31 | 9 | 4.64/44 404 | 4.75/67 059 | DNA binding, cell communication, signal transduction |
| 1559 | −1.5§§ | P37837 | Transaldolase | TALDO1 | < .05 | < .02 | 243 | 21 | 8 | 6.36/37 688 | 6.32/38 340 | Transferase activity, transferring aldehyde or ketonic groups, metabolism, energy pathways |
| 2099 | −1.4§§ | Q9Y5 × 3 | Sorting nexin-5 | SNX5 | < .006 | < .01 | 138 | 45 | 14 | 6.31/47 072 | 6.64/53 508 | Transporter activity |
| 620 | −1.4§§ | Q9Y5 × 1 | Sorting nexin-9 | SNX9 | < .05 | < .02 | 438 | 20 | 9 | 5.40/66 949 | 5.59/81 524 | Receptor signaling complex scaffold activity, cell communication, signal transduction |
| 568 | −1.4§§ | P42331 | Rho-GTPAse-activating protein 25 | ARHGAP25 | < .03 | < .05 | 308 | 16 | 10 | 5.83/72 955 | 5.46/75 000 | GTPAse activator activity |
| 433 | 1.4‖‖ | P14317 | Hematopoietic lineage cell-specific protein | HCLS1 | < .01 | < .01 | 48 | 4 | 2 | 4.74/54 079 | 4.85/90 151 | Cell communication, signal transduction |
| 1893 | 1.4‖‖ | P52566 | Rho-GDP-dissociation inhibitor 2 | ARHGDIB | < .006 | < .01 | 70 | 47 | 7 | 5.1/23 031 | 5.11/24 297 | Receptor signaling complex scaffold activity, cell communication, signal transduction |
| 773 | 1.5‖‖ | P13796 | Plastin-2 | LCP1 | < .02 | NA | 251 | 14 | 9 | 5.2/70 815 | 5.27/74 590 | Calcium ion binding, cell communication, signal transduction |
| 977 | 1.5‖‖ | P08670 | Vimentin | VIM | < .05 | < .03 | 155 | 36 | 14 | 5.06/53 676 | 5.0/64 219 | Structural constituent of cytoskeleton, cell growth and/or maintenance |
| 1920 | 1.6‖‖ | Q6IBC3 | Cathepsin H | CTSH | < .04 | < .01 | 155 | 12 | 6 | 8.38/37 980 | 6.02/23 763 | Cysteine-type peptidase activity, protein metabolism |
| 1366 | 1.6‖‖ | P11310 | Medium-chain specific acyl-coA des-hydrogenase, mitochondrial | ACADM | < .002 | < .01 | 76 | 26 | 10 | 8.61/47 015 | 6.62/45 546 | Catalytic activity, metabolism, energy pathways |
| 742 | 2‖‖ | P20700 | Lamin-B1 | LMNB1 | < .03 | < .01 | 432 | 25 | 14 | 5.11/66 653 | 5.1/76 355 | Structural molecule activity, cell growth, and/or maintenance |
| 1926 | 2.1‖‖ | O75489 | NADH dehydrogenase (ubiquinone) iron-sulfur protein 3 | NDUFS3 | < .03 | < .01 | 143 | 45 | 12 | 6.99/30 337 | 5.68/23 542 | Catalytic activity, metabolism, energy pathways |
| 1032 | 2.1‖‖ | P33241 | Lymphocyte-specific protein 1 | LSP1 | < .007 | < .01 | 174 | 18 | 4 | 4.69/37 397 | 4.56/61 787 | Calcium ion binding, cell communication, signal transduction |
| 1861 | 2.2‖‖ | Q06323 | Proteasome activator complex subunit 1 | PSME1 | < .01 | < .01 | 125 | 50 | 12 | 5.78/28 876 | 5.68/25 194 | Ubiquitin-specific protease activity, protein metabolism |
| 857 | 2.9‖‖ | P61978 | Heterogeneous nuclear ribonucleoprotein K | HNRNPK | < .0002 | < .01 | 127 | 32 | 11 | 5.39/51 230 | 5.47/70 107 | Ribonucleoprotein, regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolism |
| 1851 | 3.4‖‖ | P21964 | Catechol O-methyltransferase | COMT | < .004 | < .01 | 186 | 19 | 3 | 5.26/30 037 | 5.34/25 550 | Metabolism, energy pathways |
| 541 | 4.1‖‖ | Q13409 | Cytoplasmic dynein 1 intermediate chain 2 | DYNC1I2 | < .02 | < .01 | 235 | 9 | 5 | 5.08/71 811 | 5.26/85 329 | Motor activity, cell growth, and/or maintenance |
Spot numbers refer to Master gel spots.
FC was calculated using DeCyder Version 6.5 software: negative FC indicates that the polypeptide spot is underexpressed in S samples compared with US; and positive FC, the spot is overexpressed in S UM-CLL cells.
Accession number in UniProt database (www.uniprot.org).
Full protein name recommended by UniProt consortium.
Gene names according to HUGO gene nomenclature.
P value from t test was calculated using DeCyder Version 6.5 software; q-value was calculated using SAM.
Mascot score indicates the confidence of protein identification using the Mascot search engine (www.matrixscience.com), depending on amino acid sequence coverage (in %) and on the number of matched peptides used for identification in the Swiss-Prot database (www.expasy.org/sprot).
Theoretic isoelectric point (pI) and molecular weight obtained from the Mascot database.
Observed molecular weight and pI calculated by DeCyder Version 6.5 software, according to location in the gel.
Protein function and biologic process were assigned in accordance with the Human Protein Reference Database (www.hprd.org).
Protein isoforms down-regulated in S UM-CLL cells.
Protein isoforms up-regulated in S UM-CLL cells.