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Platform GPL6461 Query DataSets for GPL6461
Status Public on Aug 31, 2009
Title 2D-LC MS/MS Analyses of HLA Class I Peptides Isolated from B-cells Infected with Vaccinia Virus
Technology type MS
Distribution virtual
Organisms Homo sapiens; Bos taurus; Vaccinia virus
 
Description B-cell cultures were infected with live vaccinia virus (NYBOH strain). Cells were lysed, HLA/peptide complexes were enriched by immunoaffinity (W6/32 mAb), peptides were released with acid and separated from HLA proteins by 10 kDa ultrafilitration. HLA class I peptides were separated and identified by 2-dimensional liquid chromatography and tandem mass spectrometry to identify class I peptides derived from vaccinia proteins, that were being presented to the immune system.
 
Contributor(s) Johnson KL, Ovsyannikova IG
Submission date Feb 05, 2008
Last update date Aug 31, 2009
Contact name Kenneth L. Johnson
E-mail(s) johnson.kenneth@mayo.edu
Organization name Mayo Clinic
Lab Mayo Proteomics Research Center
Street address 200 First Street S.W.
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Samples (3) GSM266678, GSM266679, GSM266680
Series (1)
GSE10549 Identification of Vaccinia Virus HLA Class I Peptides Presented by the Immune System

Data table header descriptions
ID
Experiment name Scaffold: summary experiment/data set name (not used)
Biological sample name Scaffold: summary of sample (not used)
MS/MS sample name Scaffold: data field supplied by Scaffold program,
Protein name Scaffold: Protein name and description from SwissProt database
Protein accession numbers Scaffold: SwissProt protein entry name e.g. ACTH_HUMAN
Parsed name Protein abbreviation, as parsed from SwissProt entry name, e.g. ACTH
Parsed organism Organism, as parsed from SwissProt entry name, e.g. HUMAN
Decoy Test DECOY or TARGET; Tests whether peptide match result is from a Target or Decoy entry in database
Vacc label VACC or FALSE; Tests Parsed organism field for vaccinia peptides (all strains)
Protein molecular weight (Da) Scaffold: SwissProt calculated protein molecular weight from the protein sequence
Protein identification probability Scaffold: calculation of probability of correct protein identification (Protein Prophet algorithm)
Number of unique peptides Scaffold: number of unique peptide sequences identified from a protein
Number of unique spectra Scaffold: number of unique spectra identified from a protein
Number of total spectra Scaffold: total number of spectra identified from a protein
Percentage of total spectra Scaffold: spectra identified from a protein as a percentage of total # spectra
Percentage sequence coverage Scaffold: percentage of a protein sequence that was identified by MS/MS spectra
Manual validation Scaffold: field for manually validating identification: (not used)
Assigned Scaffold: field for manually assigning a spectrum to a protein (not used)
Passes 5% FPR Filter True or False: Whether search scores surpass the threshold for 5% false positive rate of peptide identification using rate of decoy database matches
Passes 1% FPR Filter True or False: Whether search scores surpass the threshold for 1% false positive rate of peptide identification using rate of decoy database matches
Spectrum name Scaffold: unique MS/MS spectrum name derived from datafile name (database search input)
Peptide sequence Scaffold: putative peptide sequence match from database search engines
C-Term AA The C-terminal amino acid from Peptide sequence field; used for estimating associated allele
Allele Estimated allele, based on comparing C-terminal amino acid to position 9 of HLA binding motifs
# Amino acids Peptide length in amino acids
Previous amino acid Scaffold: amino acid adjacent to the N-terminus of identified peptide
Next amino acid Scaffold: amino acid adjacent to the C-terminus of identified peptide
(Scaffold)Peptide identification probability Scaffold: calculation of probability of correct peptide identification (Peptide Prophet algorithm)
SEQUEST XCorr score Scaffold: Cross correlation score from Sequest search engine
SEQUEST DCn score Scaffold: Difference in cross correlation scores from Sequest search engine for the top 2 sequene matches to MS/MS spectrum
Mascot Ion score Scaffold: Mascot Ion Score from Mascot search engine
Mascot Identity score Scaffold: Mascot Identity Score from Mascot search engine
X! Tandem -log(e) score Scaffold: Match score from X!Tandem search engine
Number of enzymatic termini Scaffold: number of peptide termini consistent with specificity of specified protease (not used)
Variable modifications identified by spectrum Scaffold: whether peptide was identified with any modifications to amino acids; oxidized Methionine (+16) was the only modification allowed
Observed m/z Scaffold: experimental measurement of the peptide precursor mass-to-charge ratio
Actual peptide mass (AMU) Scaffold: neutral (uncharged) molecular weight of the peptide as calculated from the experimenatl m/z value
Calculated Peptide Mass (AMU) Scaffold: theoretical mass of peptide calculated from peptide sequence as [M+H]+
Spectrum charge Scaffold: charge state (z) of precursor ion
Actual minus calculated peptide mass (AMU) Scaffold: difference between experimental mass and theoretical mass calculated from putative peptide sequence
Actual minus calculated peptide mass (PPM) Scaffold: difference between experimental mass and theoretical mass expressed in parts-per-million (ppm)
Peptide start index Scaffold: location of peptide N-terminal amino acid within protein sequence
Peptide stop index Scaffold: location of peptide C-terminal amino acid within protein sequence

Data table
ID Experiment name Biological sample name MS/MS sample name Protein name Protein accession numbers Parsed name Parsed organism Decoy Test Vacc label Protein molecular weight (Da) Protein identification probability Number of unique peptides Number of unique spectra Number of total spectra Percentage of total spectra Percentage sequence coverage Manual validation Assigned Passes 5% FPR Filter Passes 1% FPR Filter Spectrum name Peptide sequence C-Term AA Allele # Amino acids Previous amino acid Next amino acid (Scaffold)Peptide identification probability SEQUEST XCorr score SEQUEST DCn score Mascot Ion score Mascot Identity score X! Tandem -log(e) score Number of enzymatic termini Variable modifications identified by spectrum Observed m/z Actual peptide mass (AMU) Calculated Peptide Mass (AMU) Spectrum charge Actual minus calculated peptide mass (AMU) Actual minus calculated peptide mass (PPM) Peptide start index Peptide stop index
VHLA_00001 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct FALSE TRUE FALSE ./kjo261_07apr05_10_vvscx_frxn4z23.3172.3172.2.dta TLYDISPGHVYA A U 12 H K 0.95 1.76 0.329 24.3 44.1 2.37 0 668.3314 1334.6472 1335.6586 2 -0.0035358 -2.65 137 148
VHLA_00002 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct FALSE TRUE FALSE ./kjo261_07apr05_16_vvscx_frxn4z23.3868.3868.2.dta TLYDISPGHVYA A U 12 H K 0.95 2.11 0.3 25.5 44.1 0 0 668.3324 1334.6492 1335.6586 2 -0.0015855 -1.188 137 148
VHLA_00003 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07apr05_10_vvscx_frxn4z23.2397.2397.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.43 0.359 39.9 44.3 2.12 0 720.3609 1438.7062 1439.7172 2 -0.0031752 -2.205 233 245
VHLA_00004 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07apr05_11_vvscx_frxn5z23.2916.2916.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.59 0.403 42.3 44.4 3.02 0 720.3614 1438.7071 1439.7172 2 -0.0021955 -1.526 233 245
VHLA_00005 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE FALSE ./kjo261_07mar21_04_vv_unfracz2.2150.2150.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.15 0.298 26.9 43.8 1.43 0 720.3624 1438.7092 1439.7172 2 -0.0001221 -0.084757 233 245
VHLA_00006 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07mar22_09_vvscx_frxn5z2.2000.2000.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.87 0.325 39.9 44.1 1.96 0 720.3634 1438.7112 1439.7172 2 0.001831 1.272 233 245
VHLA_00007 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07mar22_20_vvscx_frxn4z23.2081.2081.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.91 0.361 49.4 44.1 3.29 0 720.3634 1438.7112 1439.7172 2 0.001831 1.272 233 245
VHLA_00008 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07mar22_08_vvscx_frxn4z2.1817.1817.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.77 0.3 41.1 44 2.54 0 720.3639 1438.7122 1439.7172 2 0.0028056 1.95 233 245
VHLA_00009 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE FALSE ./kjo261_07mar22_09_vvscx_frxn5z2.1878.1878.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.36 0.272 20.9 44.1 1.77 0 720.3644 1438.7131 1439.7172 2 0.003784 2.628 233 245
VHLA_00010 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE FALSE ./kjo261_07mar22_20_vvscx_frxn4z23.2202.2202.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.4 0.226 24.7 44.1 1.36 0 720.3644 1438.7131 1439.7172 2 0.003784 2.628 233 245
VHLA_00011 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07mar22_20_vvscx_frxn4z23.1964.1964.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.61 0.348 36.3 44.1 2.75 0 720.3644 1438.7131 1439.7172 2 0.003784 2.628 233 245
VHLA_00012 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE TRUE ./kjo261_07mar22_22_vvscx_frxn5z23.2288.2288.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.71 0.332 39.9 44.1 1.57 0 720.3644 1438.7131 1439.7172 2 0.003784 2.628 233 245
VHLA_00013 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct TRUE TRUE FALSE ./kjo261_07mar22_08_vvscx_frxn4z2.1707.1707.2.dta IQYPGSEIKGNAY Y B15 13 Y F 0.95 2.94 0.175 21.3 44.1 1.59 0 720.3654 1438.7152 1439.7172 2 0.005859 4.07 233 245
VHLA_00014 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct FALSE TRUE TRUE ./kjo261_07mar22_20_vvscx_frxn4z23.4069.4069.2.dta LLISADDVQEIRV V A2 13 K I 0.95 2.51 0.345 56.4 42.4 3.01 1 735.9109 1469.8061 1470.8169 2 -0.00293 -1.992 20 32
VHLA_00015 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct FALSE TRUE TRUE ./kjo261_07apr05_10_vvscx_frxn4z23.4240.4240.2.dta LLISADDVQEIRV V A2 13 K I 0.95 2.75 0.369 64.3 42.4 2.68 1 735.9119 1469.8082 1470.8169 2 -0.0008545 -0.581 20 32
VHLA_00016 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCA 3BHS VACCA TARGET VACC 39380.6 0.932 1 2 12 0.0000279 0.136 possibly correct FALSE TRUE FALSE ./kjo261_07apr05_12_vvscx_frxn6z23.2577.2577.2.dta KISNTTFEV V A2 9 L R 0.95 1.74 0.168 35.1 42.8 0 0 519.7774 1037.5392 1038.5474 2 -0.0003662 -0.3526 306 314
VHLA_00017 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCC 3BHS VACCC TARGET VACC 39349.7 1 6 7 15 0.00003457 0.139 possibly correct TRUE TRUE FALSE ./kjo261_07_apr05_26_vvscx_frxn15z23.3975.3975.3.dta IQYPGSKIKGNAYF F B15 14 Y C 0.917 2.6 0.163 16.7 44.2 0 0 529.2842 1584.8292 1585.8378 3 -0.0007324 -0.4619 233 246
VHLA_00018 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCC 3BHS VACCC TARGET VACC 39349.7 1 6 7 15 0.00003457 0.139 possibly correct TRUE TRUE FALSE ./kjo261_07apr05_10_vvscx_frxn4z23.3172.3172.2.dta TLYDISPGHVYA A U 12 H K 0.95 1.76 0.329 24.3 44.1 2.37 2 668.3314 1334.6472 1335.6586 2 -0.0035358 -2.65 137 148
VHLA_00019 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCC 3BHS VACCC TARGET VACC 39349.7 1 6 7 15 0.00003457 0.139 possibly correct TRUE TRUE FALSE ./kjo261_07apr05_16_vvscx_frxn4z23.3868.3868.2.dta TLYDISPGHVYA A U 12 H K 0.95 2.11 0.3 25.5 44.1 0 2 668.3324 1334.6492 1335.6586 2 -0.0015855 -1.188 137 148
VHLA_00020 kjo261_marapr07_vaccinia_random_07jun25 Class_I_peptides_from_vaccinia-infected_cells Mudpit_kjo261_07_apr05_20_vvscx_frxn9z23.tar.gz ############################################################################################################################################################################################################################################################### 3BHS_VACCC 3BHS VACCC TARGET VACC 39349.7 1 6 7 15 0.00003457 0.139 possibly correct TRUE TRUE FALSE ./kjo261_07_apr05_25_vvscx_frxn14z23.2730.2730.2.dta IQYPGSKIKGNAY Y B15 13 Y F 0.95 1.81 0.0967 24.8 43.6 1.92 0 719.8874 1437.7592 1438.7694 2 -0.002441 -1.697 233 245

Total number of rows: 23797

Table truncated, full table size 12193 Kbytes.




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