Agilent Spectrum Mill MS Proteomics Workbench

Index


A B C D E F G H I J K L M N O P Q R S T U V W X Y Z


A

adding
amino acid choices for VML score
amino acid modifications
contaminant mass list files
cyclic modifications
enzymatic digest rules
fixed modifications
instrument types
new taxonomy codes for IPI databases
protein categories
required/disallowed amino acids
species filter
variable modifications
aligning sequences
within Multiple Sequence Aligner (utility)
within Protein/Peptide Summary
amino acids
adding custom modifications
adding amino acid choices to VML score
adding required/disallowed to Protein/Peptide Summary
composition ions
filtering
modifications
user-specified
archive data
automatic validation
automation
see workflow automation
averagine
Protein/Peptide Summary
MS Isotope
Autovalidation
defaults
overview
using form
workflows

B

batch size
browser windows, multiple

C

cautions
categories, protein
Choose button
cICAT quantitation
cleavages, missed
charge assignment
client PC
configuring
shortcut on desktop
Clustal W
within Multiple Sequence Aligner (utility)
within Protein/Peptide Summary
color-coded quantitation results
combining two databases
comparing two databases
Completion Log Viewer
configuration
default cysteine modification
default database location
default instrument
disable match filtering
disable quality filtering
protein categories
configuring client PCs
contaminant mass list files, adding
convert spectra
CPU count
custom modifications
cyclic modifications, adding
cysteine modifications
configuring default
more than one

D

data file placeholder script
de novo Sequencing, using form
de novo Summary, using form
data directories, selecting
Data Extractor
defaults
generic files
how it works
instruments supported
Maximize CPUs
*.mgf files
MS/MS data files
MS/MS spectral quality filtering
peak detection
peak list files
precursor charge assignment
settings in instrument.txt
spectral extraction
spectral features
timeouts
using form
data file selection, troubleshooting
data recalibration, PMF Search
data review, MS/MS data
database format, background
database list, updating
database search times
database search
reversed
saving hits
stopping
timeouts
database summary report
databases
combining two databases
comparing two
configuring default database location
file naming for proprietary databases
file naming for public databases
making subset FASTA file from accession numbers
updating via command line
used with Spectrum Mill workbench
defaults
Autovalidation
Data Extractor
MS/MS Search
PMF Search
PMF Summary
Protein/Peptide Summary
Sherenga de novo Sequencing
Sherenga de novo Summary
Spectrum Summary
deisotoping
differential expression quantitation
ICAT and most isotopic labels
iTRAQ and TMT
labels with small mass differences
nitrogen isotopes
SILAC
disallowed amino acids, customizing
discriminant scoring
discriminant scoring coefficients
digestion, theoretical
directory structure for Spectrum Mill workbench
disable match filtering
disable quality filtering
DNA databases, frame translation

E

Easy MS/MS Search
what happened to it?
Edit Workflow form
enzymatic digest rules, adding
enzyme cleavages
error messages
page not found
proteins not same length
timeouts
Excel
exporting data
to Excel
to HTML files
to LIMS
to PepXML
to PowerPoint files

F

FAQs
false discovery rate
reporting false discovery rate (FDR) and quality metrics
overview
use in Autovalidation
FAQs
FASTA format, background
FASTA header format change
FASTA file, making subset from accession numbers
features, new in this version
File Collector
file naming
proprietary databases
public databases
file permission scripts
general
msdataSM
file placeholder script
file system for Spectrum Mill workbench
filtering
amino acid
protein molecular weight
protein pI
fixed modifications, adding
folders for Spectrum Mill workbench
fragment ion tag
fragment ion types, MS Product
fragment ions, for different instruments
frame translation in DNA databases
frequently asked questions

G

generic files, Data Extractor

H

hits, maximum reported
homology mode
overview
HTML links (changing)
accession number
elemental composition
MS Digest index number
peptide sequence
HTML links (enabling) to BLAST search
HTML links in results
accession number
elemental composition
general features
MS Digest index number
peptide sequence

I

ICAT quantitation
icon for Spectrum Mill workbench
IIS
scripts to set configuration
immonium ions
indices
creating for a new database
for databases
instrument types
adding
PMF Search
instrument_charges_certain in instrument.txt
instruments
configuring default
fragment ion types
selecting Thermo Fisher Scientific models
interactive automation
iTRAQ
applying correction factors
creating/storing iTRAQ correction factors
quantitation

J

K

L

LC-ESI-TOF data extraction
library spectra (File Collector)
LIMS
links (changing)
accession number
elemental composition
MS Digest index number
peptide sequence
Links (enabling) to BLAST search
links in results
accession number
elemental composition
general features
MS Digest index number
peptide sequence

M

Manual PMF Search, using
marker ions
mass tolerances
mass type
masses, inputing (m/z)
match filtering, disabling
maximize CPUs
Data Extractor
MS/MS Search
*.mgf file support
minimum scored peak intensity
missed cleavages
modifications
adding
choosing
listing details
types supported
molecular weight filtering
MRM Selector
transferring results to MassHunter Acquisition
using form
MS Comp
combination type
double bond equivalent
nitrogen rule
using form
MS Digest
database entry retrieval method
using form
overview
MS Edman
mismatched AA's
overview
regular expressions
search mode
using form
MS Isotope, using form
MS Product
fragment ion types
using form
MS/MS autovalidation and workflows
MS/MS data, spectral preprocessing
MS/MS Search
batch size
creating summary file
defaults
equivalent search modes across versions
fragment ion types for various instruments
homology mode
introduction
mass tolerances
minimum scored peak intensity
multiply-charged ions
overview
precursor mass shift
ranking results
results review
results
scoring based on marker ions
scoring
search modes
timeouts
using form
view identification statistics
MS/MS spectral quality filtering
MS-only data files, Data Extractor
multiple browser windows
multiply-charged ions
multiple sequence alignment tool
aligning sequences within Multiple Sequence Aligner (utility)
aligning sequences within Protein/Peptide Summary
introduction
peptide table
report description

N

naming
proprietary databases
public databases
New Folder dialog box
 

O

Open Workflow dialog box
overview
MS Edman
MS Search
MS/MS Autovalidation
MS/MS Search
workflow automation

P

parameter files
parameter table
patches for software
peak detection
peak list files, Data Extractor
Peptide List to Masses
peptide mass fingerpinting
automated
manual
Peptide Selector
transferring results to MassHunter Acquisition
troubleshooting
using form
peptide validation
PepXML
PMF Search
data recalibration
defaults
instrument types
mass tolerance
overview
scoring
using
PMF Summary
defaults
using
precursor charge assignment
precursor mass shift
process automation
see workflow automation
processes, stopping
Protein Databases
command line version
combining two databases
comparing two databases
creating indices for a new database
creating or appending to a custom database
creating subset databases (saved hits)
creating subset databases (species and molecular weight)
database summary report
FASTA header format change
introduction
output files (the indices)
re-indexing an updated database
subset FASTA file from accession numbers
updating the database list
user database
using browser version
protein categories, configuring
protein grouping
protein molecular weight filtering
protein pI filtering
Protein/Peptide Summary
color-coded quantitation results
comparing results of individual samples from separate directories
customizing amino acid filtering
comparing results of individual samples from separate directories
defaults
overview
peptide validation
protein grouping
review fields
sequence alignment
setting summary modes
setting validation and sorting
summarizing results
summary modes
troubleshooting
using form

Q

quality filtering, disabling
quantitation
approximate
ICAT and most isotopic labels
iTRAQ
labels with small mass differences
nitrogen isotopes
SILAC
TMT
questions, frequently asked

R

recalibration, PMF Search
Request Queue Viewer
required amino acids, customizing
results validation, automatic
reversed database search
review fields, for Protein/Peptide Summary
review fields, for Spectrum Summary

S

sample ID
saved results file
Save Workflow dialog box
saving hits for later search
scoring
MS/MS Search and marker ions
MS/MS Search
PMF Search
scripts, for server administration
search engines, other
search modes for MS/MS Search
comparison
definitions
translator across Spectrum Mill versions
search results, saving
search statistics
search times
search, stopping
Select button
sequence alignment
within Multiple Sequence Aligner (utility)
within Protein/Peptide Summary
sequence coverage, increasing
server administration
adding amino acid modifications
adding VML score amino acid choices
adding contaminant mass list files
adding cyclic modifications
adding digest rules
adding fixed modifications
adding instrument types
adding new taxonomy codes for IPI databases
adding species filter
adding variable modifications
changing links from accession number
changing links from elemental composition
changing links from MS Digest index number
changing links from peptide sequence
configuring default cysteine modification
configuring default database location
configuring default instrument
configuring protein categories
disable match filtering
disable quality filtering
enabling links to BLAST search
guidelines for modifying files (read first)
limiting the number of parallel workflow processes
resolving timeout problems
scripts
starting and stopping SRM
Shared Resource Manager
starting
stopping
Sherenga de novo Sequencing
defaults
using form
Sherenga de novo Summary
defaults
using form
shortcut, PC desktop
signal-to-noise filtering
SILAC quantitation
software
defects
patches
updates, troubleshooting
Software Status Bulletin
sorting results
species
definitions for Spectrum Mill workbench
species filtering
including in subset database
spectra
library (File Collector)
segregating good
spectral extraction
spectral features
spectral preprocessing for MS/MS data
spectral quality filtering
MS/MS Search
Spectrum Matcher
Spectrum Summary
Spectrum Summary
defaults
review fields
setting validation and sorting
spectral quality filtering
summarizing results
troubleshooting
using form
Spectrum Viewer
troubleshooting
using
starting SRM
stopping
processes
SRM
subset databases
creating for saved hits
creating for species and molecular weight
ensuring that species are represented
summarizing results, PMF
summary modes, Protein/Peptide Summary

T

Thermo Fisher Scientific instruments
timeouts
tips
TMT
applying correction factors
creating/storing TMT correction factors
quantitation
TOF data
acquisition
extraction
TOF-TOF support
Tool Belt
applying iTRAQ correction factors
calculating discriminant scoring coefficients
converting spectra - mzXML files
creating a saved results file
creating iTRAQ correction factors
creating MS/MS Search summary file
exporting PepXML file
listing modifications details
overview
stopping processes
using the File Collector
viewing a parameter table
tools, server administration
troubleshooting
connection to server times out
list of database names does not update
warning about need for additional license
page not found
peptides appear twice in the summary report
Peptide Selector seems to ignore settings
premature "Search Done" message
Protein/Peptide Summary
results different between versions
selecting data files
software updates
some programs do not work
Spectrum Summary
Spectrum Viewer
timeouts
unusual or blank selection values
workflow stuck

U

updating databases
uploading data to LIMS
user database, creating or appending
user-specified amino acid
utilities
Archive Data
MRM Selector
MS Comp
MS Digest
MS Edman
MS Isotope
MS Product
Multiple Sequence Aligner
Peptide List to Masses
Peptide Selector

V

validation, automatic

W

workflow automation
Completion Log Viewer
Edit Workflow form
interactive automation
introduction
limiting the number of parallel processes
New Folder dialog box
Open Workflow dialog box
parameter files
Request Queue Viewer
Save Workflow dialog box
Spectrum Mill Workflow Manager Service
troubleshooting
Workflows form
Workflows for autovalidation
 

X

Y

Z