QUANTITATIVE MASS SPECTROMETRY experiment annotation
3-30-2011
Annotations were compiled by Hannes Hahne
(not compliant to any standard).
Cell_biology
sample
1 -
Organism
10 - homo_sapiens
11 - mus_musculus
12 - rattus_norwegicus
13 - sus_scrota
14 - bos_taurus
2 -
human_cell_line
15 - not_applicable
16 - K562
17 - H292
3 -
mouse_cell_line
18 - not_applicable
Biochemistry
Separation
Separation_technique
4 -
Chromatography
19 - Strong_cation_exchange
20 - Strong_anion_exchange
21 - Isoelectric_focusing
22 - Weak_cation_exchange
23 - Weak
24 - Capillary_electrophoresis
Purification
Purification_method
5 -
Immunoprecipitation
25 - Protein
26 - Peptide
6 -
Tagged_protein
27 - GST
28 - FLAG
29 - Myc
30 - His
31 - TAP
Labeling
7 -
Labeling
32 - Dimethylation_of_Lys_residues_and_N-term
33 - tandem_mass_tags
34 - stable_isotope_labeling_with_amino_acids_in_cell_culture
35 - isobaric_tag_for_relative_and_absolute_quantitation
36 - O18_labeling
37 - metabolic_labeling
38 - isotope-coded_affinity_tag
39 - isotope-coded_protein_label
40 - absolute_quantification_of_proteins
Mass_spectrometry
LC_MS_instrumentation
8 -
LC_model
41 - Eksigent
42 - Proxeon_easy_nLC
43 - Dionex_U3000
9 -
MS_model
44 - Thermo_LTQ_Orbitrap_XL
45 - Bruker_Ultraflex
46 - Bruker_Amazon
10 -
LC_software_name
47 - Chromeleon
48 - Eksigent
49 - Proxeon
11 -
LC_software_version
50 - 1.0.0
12 -
MS_software_name
51 - XCalibur
52 - HyStar
13 -
LC_software_version
53 - 1.0.0
Liquid_chromatography
General_settings
14 -
column_setup
54 - no_trap
55 - vented_column
56 - conventional_setup
15 -
trap_colum
57 - not_applicable
58 - in_house-packed
59 - DrMaisch_3um_1cm_C18RP
60 - Kusters_BestTrapColumn
16 -
analytical_colum
61 - in_house_packed
62 - Kusters_BestSepColumn
17 -
loading_buffer
63 - 0.1%_formic_acid
64 - 0.5%_TFA
18 -
mobile_phase_A
65 - 0.1%_formic_acid
66 - 0.5%_TFA
19 -
mobile_phase_B
67 - 0.1%_formic_acid_90%_acetonitrile
68 - 0.5%_TFA_90%_acetonitrile
20 -
column_temperature
deg_C
21 -
injection_volume
microl/min
Gradient
22 -
loading_flow_rate
microl/min
23 -
loading_time
min
24 -
gradient_flow_rate
nl/min
25 -
gradient_length
min
26 -
gradient_step1
69 - applicable
70 - not_applicable
27 -
gradient_step1_time
min
28 -
gradient_step1_%B
%
29 -
gradient_step2
71 - applicable
72 - not_applicable
30 -
gradient_step2_time
min
31 -
gradient_step2_%B
%
32 -
gradient_step3
73 - applicable
74 - not_applicable
33 -
gradient_step3_time
min
34 -
gradient_step3_%B
%
35 -
gradient_step4
75 - applicable
76 - not_applicable
36 -
gradient_step4_time
min
37 -
gradient_step4_%B
%
38 -
gradient_step5
77 - applicable
78 - not_applicable
39 -
gradient_step5_time
min
40 -
gradient_step5_%B
%
41 -
gradient_step6
79 - applicable
80 - not_applicable
42 -
gradient_step6_time
min
43 -
gradient_step6_%B
%
44 -
gradient_step7
81 - applicable
82 - not_applicable
45 -
gradient_step7_time
min
46 -
gradient_step7_%B
%
47 -
gradient_step8
83 - applicable
84 - not_applicable
48 -
gradient_step8_time
min
49 -
gradient_step8_%B
%
50 -
gradient_step9
85 - applicable
86 - not_applicable
51 -
gradient_step9_time
min
52 -
gradient_step9_%B
%
53 -
gradient_step10
87 - applicable
88 - not_applicable
54 -
gradient_step10_time
min
55 -
gradient_step10_%B
%
MALDI_spotting
56 -
Spotting_roboter
89 - not_applicable
90 - Dionex_Probot
91 - Bruker_Proteineer_fc
57 -
Matrix
92 - not_applicable
93 - CHCA
94 - Sinapic_acid
58 -
Matrix_concentration
mg/ml
59 -
Spotting_solution
95 - not_applicable
97 - 0.5%TFA_50%acetonitrile
60 -
MALDI_target
98 - not_applicable
99 - stainless_steel
100 - Bruker_Prespotted_AnchorChip_PAC384
61 -
Number_of_spotted_columns
62 -
Number_of_spotted_rows
63 -
Matrix_addition
nl/min
64 -
Collection_time_per_spot
sec
65 -
Spot_volume
nl
Mass_spectrometer
Thermo_LTQ_Orbitrap_ETD_XL
ESI_source
66 -
Ion_source
101 - not_applicable
102 - source1
103 - source2
104 - source3
67 -
Sprayer_type
105 - not_applicable
106 - qwertz
68 -
Sprayer_tip_diameter
microm
69 -
Sprayer_inner_diameter
microm
70 -
Voltage_supply
107 - not_applicable
108 - liquid_junction
109 - coated_tip
71 -
Spray_voltage
110 - not_applicable
Tune_settings
72 -
LTQ_tune_file_name
111 - not_applicable
112 - Tune_nano_default
73 -
Target_settings_LTQ_MS
74 -
Target_settings_FT_MS
75 -
Target_settings_LTQ_MSn
76 -
Target_settings_FT_MSn
77 -
Target_settings_LTQ_MS_time
ms
78 -
Target_settings_FT_MS_time
ms
79 -
Target_settings_LTQ_MSn_time
ms
80 -
Target_settings_FT_MSn_time
ms
81 -
Microscans_LTQ_MS
82 -
Microscans_FT_MS
83 -
Microscans_LTQ_MSn
84 -
Microscans_FT_MSn
MS1
85 -
Acquistion_time
min
86 -
Analyzer
114 - not_applicable
115 - LTQ
116 - Orbitrap
117 - Iontrap
87 -
Orbitrap_Resolution
118 - not_applicable
119 - 7.5k
120 - 15k
121 - 30k
122 - 60k
123 - 100k
88 -
Polarity
124 - Positive
125 - Negative
89 -
Scan_range_first_mass
m/z
90 -
Scan_range_last_mass
m/z
91 -
Scan_type
126 - Full
127 - SIM
92 -
Data_type
128 - Profile
129 - Centroid
MS2
93 -
MS2_selection
[Top
94 -
Analyzer
130 - not_applicable
131 - LTQ
132 - Orbitrap
133 - Iontrap
95 -
Orbitrap_Resolution
134 - not_applicable
135 - 7.5k
136 - 15k
137 - 30k
138 - 60k
139 - 100k
96 -
LTQ_Scan_rate
140 - not_applicable
141 - Normal
142 - Enhanced
143 - Turbo
144 - Zoom
145 - UltraZoom
97 -
Wideband_activation
146 - not_applicable
147 - enabled
148 - disabled
98 -
Inclusion_list
149 - not_applicable
150 - enabled
151 - disabled
99 -
Inclusion_list_width
100 -
inclusion_list_width_unit
152 - Da
153 - ppm
154 - mmu
101 -
Number_of_inclusion_list_entries
102 -
Neutral_loss_list
155 - not_applicable
156 - enabled
157 - disabled
103 -
Neutral_loss_width
104 -
Neutral_loss_width_unit
158 - Da
159 - ppm
160 - mmu
105 -
Within_top_N
106 -
Static_exclusion_list
161 - not_applicable
162 - enabled
163 - disabled
107 -
Static_exclusion_list_width
108 -
Static_exclusion_width_unit
164 - Da
165 - ppm
166 - mmu
109 -
Number_of_exclusion_list_entries
110 -
Dynamic_exclusion
167 - not_applicable
168 - enabled
169 - disabled
111 -
Dynamic_exclusion_width
ppm
112 -
Dynamic_exclusion_width_unit
170 - Da
171 - ppm
172 - mmu
113 -
Dynamic_exclusion_duration
s
114 -
Dynamic_exclusion_list_length
115 -
Dynamic_exclusion_early_expiration
173 - not_applicable
174 - enabled
175 - disabled
116 -
Early_expiration_threshold
S/N
117 -
Early_expiration_counts_below_threshold
counts
118 -
Automatic_charge_state_recognition
177 - not_applicable
178 - enabled
179 - disabled
119 -
Rejection_of_singly_charged_species
180 - not_applicable
181 - enabled
182 - disabled
120 -
Minimum_signal_threshold
counts
121 -
Activation_type
183 - not_applicable
184 - CID
185 - ETD
186 - HCD
187 - PQD
122 -
Isolation_width_for_MS2
m/z
123 -
Normalized_collision_energy
%
124 -
Activation_Q
125 -
Activation_time
ms
126 -
Multistage_acivation
188 - not_applicable
189 - enabled
190 - disabled
127 -
Data_Dependent_Decision_Tree
191 - not_applicable
192 - enabled
193 - disabled
128 -
Charge_state_3_mass
m/z
129 -
Charge_state_4_mass
m/z
130 -
Charge_state_5_mass
m/z
131 -
ETD_reaction_time
ms
132 -
Enable_supplemental_activation
198 - not_applicable
199 - enabled
200 - disabled
MS3
133 -
MS3_selection
201 - not_applicable
202 - disabled
203 - neutral_loss
204 - most_intense
205 - repeat_previous_scan_with_different_activation_type
206 - selected_mass
134 -
Analyzer
207 - not_applicable
208 - LTQ
209 - Orbitrap
210 - Iontrap
135 -
Orbitrap_Resolution
211 - not_applicable
212 - 7.5k
213 - 15k
214 - 30k
215 - 60k
216 - 100k
136 -
LTQ_Scan_rate
217 - not_applicable
218 - Normal
219 - Enhanced
220 - Turbo
221 - Zoom
222 - UltraZoom
137 -
Wideband_activation
223 - not_applicable
224 - enabled
225 - disabled
138 -
Minimum_signal_threshold
counts
139 -
Activation_type
227 - not_applicable
228 - CID
229 - ETD
230 - HCD
231 - PQD
140 -
Isolation_width_for_MS2
m/z
141 -
Normalized_collision_energy
%
142 -
Activation_Q
143 -
Activation_time
ms
144 -
Multistage_acivation
232 - not_applicable
233 - enabled
234 - disabled
Peak_list_generation
Mascot_Distiller
MS_processing
145 -
Un-centroiding_Peak_half_width
Da
146 -
Un-centroiding_Data_points_per_Da
147 -
Un-centroiding_Always_uncentroid
235 - not_applicable
236 - enabled
237 - disabled
148 -
Re-gridding_Data_points_per_Da
149 -
Multi-Format_Spectrum_Preferred_type
238 - not_applicable
239 - Profile
240 - Centroided
150 -
Peaks_Minimum_number
151 -
Peaks_Maximum_charge
152 -
Aggregation_Scan_group_aggregation_method
241 - not_applicable
242 - Sum
243 - none
MSMS_processing
153 -
Un-centroiding_Peak_half_width
Da
154 -
Un-centroiding_Data_points_per_Da
155 -
Un-centroiding_Always_uncentroid
244 - not_applicable
245 - enabled
246 - disabled
156 -
Re-gridding_Data_points_per_Da
157 -
Multi-Format_Spectrum_Preferred_type
247 - not_applicable
248 - Profile
249 - Centroided
158 -
Peaks_Minimum_number
159 -
Peaks_Maximum_charge
160 -
Peaks_Use_precursor_charge_as_maximum
250 - not_applicable
251 - enabled
252 - disabled
161 -
Precursor_charge_1st_choice
253 - not_applicable
254 - Try_to_re-determine_charge_from_parent_scan
255 - If_available_take_charge_from_file
256 - Use_default_charges
162 -
Precursor_charge_2nd_choice
257 - not_applicable
258 - Try_to_re-determine_charge_from_parent_scan
259 - If_available_take_charge_from_file
260 - Use_default_charges
163 -
Precursor_charge_3rd_choice
261 - not_applicable
262 - Try_to_re-determine_charge_from_parent_scan
263 - If_available_take_charge_from_file
264 - Use_default_charges
164 -
Precursor_charge_Default_charge_range_min
165 -
Precursor_charge_Default_charge_range_max
166 -
Precursor_charge_Ignore_singly_charged_precursors
265 - not_applicable
266 - enabled
267 - disabled
167 -
Precursor_selection_Search_within
m/z
168 -
Precursor_selection_Re-determine_precursor_m/z_value_when_possible
268 - not_applicable
269 - enabled
270 - disabled
169 -
Aggregation_Scan_group_aggregation_method
271 - not_applicable
272 - none
273 - Time_Domain
Time_domain
170 -
Group_assignment_Minimum_precursor_Mr
Da
171 -
Group_assignment_Maximum_precursor_Mr
Da
172 -
Group_assignment_Precursor_m/z_tolerance
m/z
173 -
Group_assignment_Maximum_intermediate_time
s
174 -
Group_assignment_Maximum_intermediate_scan_count
scan_counts
175 -
Group_assignment_Use_intermediate_scan_count_where_possible
274 - not_applicable
275 - enabled
276 - disabled
176 -
Group_assignment_Collapse_MSn_into_precursor
277 - not_applicable
278 - enabled
279 - disabled
177 -
Group_filtering_Minimum_number_of_scans
scan_counts
MS_peak_picking
178 -
Filtering_Correlation_threshold_Rho
179 -
Filtering_Minimum_signal-to-noise
S/N
180 -
Filtering_Minimum_peak
m/z
181 -
Filtering_Maximum_peak
m/z
182 -
Peak_profile_Minimum_peak_width
Da
183 -
Peak_profile_Expected_peak_width
Da
184 -
Peak_profile_Maximum_peak_width
Da
185 -
Peak_profile_Reject_outliers
280 - not_applicable
281 - enabled
282 - disabled
186 -
General_Apply_baseline_correction
283 - not_applicable
284 - enabled
285 - disabled
187 -
General_Fit_method
286 - not_applicable
287 - Isotope_distribution
288 - Single_peak
188 -
General_Maximum_iterations_per_scan
189 -
Single_peak_window_Pick_single_peaks_in_this_range_(eg._Reporter_ions)
289 - not_applicable
290 - enabled
291 - disabled
190 -
Single_peak_window_Minimum_peak
m/z
191 -
Single_peak_window_Maximum_peak
m/z
MSMS_peak_picking
192 -
Filtering_Correlation_threshold_Rho
193 -
Filtering_Minimum_signal-to-noise
S/N
194 -
Filtering_Minimum_peak
m/z
195 -
Filtering_Maximum_peak
m/z
196 -
Peak_profile_Minimum_peak_width
Da
197 -
Peak_profile_Expected_peak_width
Da
198 -
Peak_profile_Maximum_peak_width
Da
199 -
Peak_profile_Reject_outliers
292 - not_applicable
293 - enabled
294 - disabled
200 -
General_Same_as_MS_peak_picking
295 - not_applicable
296 - enabled
297 - disabled
201 -
General_Apply_baseline_correction
298 - not_applicable
299 - enabled
300 - disabled
202 -
General_Fit_method
301 - not_applicable
302 - Isotope_distribution
303 - Single_peak
203 -
General_Maximum_iterations_per_scan
204 -
Single_peak_window_Pick_single_peaks_in_this_range_(eg._Reporter_ions)
304 - not_applicable
305 - enabled
306 - disabled
205 -
Single_peak_window_Minimum_peak
m/z
206 -
Single_peak_window_Maximum_peak
m/z
Search engine
Mascot
207 -
Search_engine
307 - Mascot
308 - XTandem
208 -
Database
309 - IPI_human
310 - IPI_mouse
311 - MSDB
312 - NCBInr
313 - SwissProt
314 - Tremble
315 - NCBInrPlus
209 -
Create_decoy_database_on_the_fly
316 - enabled
317 - disabled
210 -
Taxonomy
318 - not_applicable
319 - Archaea
320 - Eukaryota
321 - Metazoa
322 - C_elegans
323 - D_melanogaster
324 - Mammalia
325 - Homo_sapiens
326 - Mus_musculus
327 - Rattus
328 - Other_mammalia
329 - Xenopus_laevis
330 - Fungi
331 - S_cerevisiae
332 - Viridiplantae
333 - Bacteria
334 - Actinobacteria
335 - Firmicutes
336 - Proteobacteria
337 - Viruses
211 -
Fixed_modifications
338 - Carbamidomethyl_C
339 - Carboxymethyl_C
340 - iTRAQ4Plex_Nterm
341 - iTRAQ4Plex_K
342 - iTRAQ8Plex_Nterm
343 - iTRAQ8Plex_K
344 - 18O_1_label_Cterm
345 - 18O_2_label_Cterm
346 - TMT6plex_K
347 - TMT6plex_Nterm
212 -
Variable_modifications
348 - pyro-Glu_Nterm_Q
349 - pyro-Glu_Nterm_E
350 - HexNac_ST
351 - Oxidation_M
352 - Phospho_ST
353 - Phospho_Y
213 -
Enzyme
354 - ArgC
355 - AspN
356 - AspN_ambic
357 - Chymotrypsin
358 - CNBr
359 - CNBr+Trypsin
360 - Formic_acid
361 - LysC
362 - LysC/P
363 - LysN
364 - PepsinA
365 - Trypsin+Chymotrypsin
366 - Trypsin
367 - Trypsin/P
368 - V8-DE
369 - V8-E
370 - semiTrypsin
371 - LysC+AspN
372 - none
214 -
Max_missed_cleavages
215 -
Peptide_charge
373 - 2+_3+
216 -
Number_of_allowed_C13
217 -
Mass
374 - Monoisotopic
375 - Average
218 -
Peptide_tolerance
219 -
Peptide_tolerance_unit
376 - ppm
377 - Da
378 - mmu
220 -
Fragment_tolerance
Da
221 -
Error_tolerant_search
379 - enabled
380 - disabled
222 -
Quantitation
381 - none
382 - iTRAQ_4plex
383 - iTRAQ_8plex
384 - 18O_corrected_multiplex
385 - SILAC_K+6_R+6_multiplex
386 - SILAC_K+6_R+10
387 - TMT_6plex
388 - 18O_corrected
389 - 15N_metabolic
223 -
Instrument
390 - Default
391 - ESI-QUAD-TOF
392 - MALDI-TOF-PSD
393 - ESI-TRAP
394 - ESI-QUAD
395 - ESI-FTICR
396 - MALDI-TOF-TOF
397 - ESI-4SECTOR
398 - FTMS-ECD
399 - ETD-TRAP
400 - MALDI-QUAD-TOF
401 - MALDI-QIT-TOF