MaxQuant Run

Summary
The summary file contains summary information for all the raw files processed with a single MaxQuant run.
The summary information consists of some MaxQuant parameters, information of the raw file contents, and
statistics on the peak detection. Based on this file a quick overview can be gathered on the quality of the data
in the raw file.
The last row in this file contains the summary information for each column on each of the processed files.
Name
Raw file
Experiment
Enzyme
Enzyme mode
Enzyme first search
Enzyme mode first search
Use enzyme first search
Variable modifications
Variable modifications first search
Use variable modifications first
search
Multiplicity
Max. missed cleavages
Labels0
LC-MS run type
Time-dependent recalibration
MS
MS/MS
MS/MS Submitted
MS/MS Submitted (SIL)
MS/MS Submitted (ISO)

MS/MS Submitted (PEAK)
MS/MS Identified
MS/MS Identified (SIL)
MS/MS Identified (ISO)
MS/MS Identified (PEAK)
MS/MS Identified [%]
MS/MS Identified (SIL) [%]
MS/MS Identified (ISO) [%]
MS/MS Identified (PEAK) [%]
Peptide Sequences Identified
Peaks
Peaks Sequenced
Peaks Sequenced [%]
Peaks Repeatedly Sequenced
Peaks Repeatedly Sequenced [%]
Isotope Patterns
Separator
Description
The raw file processed.
Experiment name assigned to this LC-MS run in the
experimental design.
The protease used to digest the protein sample.
The protease used to digest the protein sample.
The protease used for the first search.
The protease used for the first search.
Marked with '+' when a different protease setup was used for
the first search.
The variable modification(s) used during the identification of
peptides.
The variable modification(s) used during the first search.
Marked with '+' when different variable modifications were used
for the first search.
The number of labels used.
The maximum allowed number of missed cleavages.
The labels used in the labeling experiment. Allowed values for
X: 0=light; 1=medium; 2=heavy label partner.
The type of LC-MS run. Usually it will be 'Standard' which
refers to a conventional shotgun proteomics run with datadependent MS/MS.
When marked with '+', time-dependent recalibration was
applied to improve the data quality.
The number of MS spectra recorded in this raw file.
The number of tandem MS spectra recorded in this raw file.
The number of tandem MS spectra submitted for analysis.
The number of tandem MS spectra submitted for analysis,
where the precursor ion was detected as part of a labeling
cluster.
where the precursor ion was detected as an isotopic pattern.
where the precursor ion was detected as a single peak.
The total number of identified tandem MS spectra.
The total number of identified tandem MS spectra, where the
precursor ion was detected as part of a labeling cluster.
precursor ion was detected as an isotopic pattern.
precursor ion was detected as a single peak.
The percentage of identified tandem MS spectra.
The percentage of identified tandem MS spectra, where the
precursor ion was detected as part of a labeling cluster.
precursor ion was detected as an isotopic pattern.
precursor ion was detected as a single peak.
The total number of unique peptide amino acid sequences
identified from the recorded tandem mass spectra.
The total number of peaks detected in the full scans.
The total number of peaks sequenced by tandem MS.
The percentage of peaks sequenced by tandem MS.
The total number of peaks repeatedly sequenced (i.e. 1 or
more times) by tandem MS.
The percentage of peaks repeatedly sequenced (i.e. 1 or more
times) by tandem MS.
The total number of detected isotope patterns.
Isotope Patterns Sequenced

Isotope Patterns Sequenced (z>1)
Isotope Patterns Sequenced [%]
Isotope Patterns Sequenced (z>1)
[%]
Isotope Patterns Repeatedly
Sequenced
Isotope Patterns Repeatedly
Sequenced [%]
Recalibrated
Av. Absolute Mass Deviation [ppm]
Mass Standard Deviation [ppm]
Av. Absolute Mass Deviation [mDa]
Mass Standard Deviation [mDa]
Label free norm param
The total number of isotope patterns sequenced by tandem

MS.
The total number of isotope patterns sequenced by tandem MS
with a charge state of 2 or more.
The percentage of isotope patterns sequenced by tandem MS.
The percentage of isotope patterns sequenced by tandem MS
with a charge state of 2 or more.
The total number of isotope patterns repeatedly sequenced
(i.e. 1 or more times) by tandem MS.
The percentage of isotope patterns repeatedly sequenced (i.e.
1 or more times) by tandem MS.
When marked with '+', the masses taken from the raw file were
recalibrated.
The average absolute mass deviation found comparing to the
identification mass in parts per million.
The standard deviation of the mass deviation found comparing
to the identification mass in parts per million.
The average absolute mass deviation found comparing to the
identification mass in milli-Dalton.
The standard deviation of the mass deviation found comparing
to the identification mass in milli-Dalton.
The normalization factor used to scale the intensity values in a
label-free experiment.
Evidence
The evidence file combines all the information about the identified peptides and normally is the only file
required for processing the results. Additional information about the peptides, modifications, proteins, etc. can
be found in the other files by unique identifier linkage.
Name
Sequence
Length
Modifications
Modified sequence
Oxidation (M) Probabilities
Oxidation (M) Score Diffs
Acetyl (Protein N-term)

Oxidation (M)
Missed cleavages
Proteins
Leading Proteins
Leading Razor Protein

Type
Raw file
Experiment
MS/MS m/z
Charge
m/z
Mass
Resolution
Uncalibrated - Calibrated m/z [ppm]
Uncalibrated - Calibrated m/z [Da]
Mass Error [ppm]
Mass Error [Da]
Uncalibrated Mass Error [ppm]
Separator
Description
The identified AA sequence of the peptide.
The length of the sequence stored in the column 'Sequence'.
Post-translational modifications contained within the identified
peptide sequence.
Sequence representation including the post-translational
modifications (abbreviation of the modification in brackets
before the modified AA). The sequence is always surrounded
by underscore characters ('_').
Sequence representation of the peptide including PTM
positioning probabilities ([0..1], where 1 is best match) for
'Oxidation (M)'.
Sequence representation for each of the possible PTM
positions in each possible configuration, the difference is
calculated between the identification score with the PTM added
to that position and the best scoring identification where no
PTM is added to that position. When this value is negative, it is
unlikely that the particular modification is located at this
position.
The number of occurrences of the modification 'Acetyl (Protein
N-term)'.
The number of occurrences of the modification 'Oxidation (M)'.
Number of missed enzymatic cleavages.
The identifiers of the proteins this particular peptide is
associated with.
The identifiers of the proteins in the proteinGroups file, with this
protein as best match, this particular peptide is associated with.
When multiple matches are found here, the best scoring
protein can be found in the 'Leading Razor Protein' column.
The identifier of the best scoring protein, from the
proteinGroups file this, this peptide is associated to.
The type of MS/MS spectrum this sequence is derived from.
MSMS MS/MS for an unidentified peak.
ISO-MSMS MS/MS from an identified isotope cluster.
MULTI-MSMS MS/MS from an identified labeling cluster.
The name of the RAW-file the mass spectral data was derived
from.
The m/z used for fragmentation (not necessarily the monoisotopic m/z).
The charge-state of the precursor ion.
The recalibrated mass-over-charge value of the precursor ion.
The predicted monoisotopic mass of the identified peptide
sequence.
The resolution of precursor ion measured in Full Width at Half
Maximum (FWHM).
The difference between the uncalibrated and recalibrated
mass-over-charge value of the precursor ion measured in
parts-per-million. This gives an indication of the mass drift in
the original data, which was automatically corrected by
MaxQuant.
The difference between the uncalibrated and recalibrated
mass-over-charge value of the precursor ion measured in
parts-per-million. This gives an indication of the mass drift in
the original data, which was automatically corrected by
MaxQuant.
Mass error of the recalibrated mass-over-charge value of the
precursor ion in comparison to the predicted monoisotopic
mass of the identified peptide sequence in parts per million.
mass of the identified peptide sequence in milli-Dalton.
Mass error of the uncalibrated mass-over-charge value of the
mass of the identified peptide sequence.
Note: This column can contain missing values (denoted as
NaN).
Uncalibrated Mass Error [Da]
Max intensity m/z 0
Retention time
Retention length
Calibrated retention time
Calibrated retention time start
Calibrated retention time finish
Retention time calibration
Match time difference
Match m/z difference
Match q-value
Match score
Number of data points
Number of scans
Number of isotopic peaks
PIF
Fraction of total spectrum
Base peak fraction
PEP
MS/MS Count
MS/MS Scan Number
Score
Delta score
Combinatorics
Intensity
Reverse
Potential contaminant
id
Mass error of the uncalibrated mass-over-charge value of the

Note: This column can contain missing values (denoted as
NaN).
Summed up eXtracted Ion Current (XIC) of all isotopic clusters
associated with the identified AA sequence. In case of a
labeled experiment this is the total intensity of all the isotopic
patterns in the label cluster.
The uncalibrated retention time in minutes in the elution profile
of the precursor ion.
The total retention time of the peak (last timepoint first
timepoint).
The recalibrated retention time in minutes in the elution profile
The recalibrated retention start in minutes in the elution profile
The recalibrated retention finish in minutes in the elution profile
The difference in minutes between the uncalibrated and
recalibrated retention time. This gives an indication of the
retention time drift in the original data, which was automatically
corrected by MaxQuant.
Note: This column can contain missing values (NaN).
When the option match between runs is used in MaxQuant,
this value indicates the time difference between the feature
from the raw file it was taken from and the feature from the raw
file it was matched to.
When the option match between runs is used in MaxQuant,
this value indicates the m/z difference between the feature
from the raw file it was taken from and the feature from the raw
file it was matched to.
This is the q-value for features that have been identified by
'matching between runs'.
The andromeda score of the MS/MS identification that is the
source of this identification by 'matching between runs'.
The number of data points (peak centroids) collected for this
peptide feature.
The number of MS scans that the 3d peaks of this peptide
feature are overlapping with.
The number of isotopic peaks contained in this peptide feature.
Short for Parent Ion Fraction; indicates the fraction the target
peak makes up of the total intensity in the inclusion window.
The percentage the ion intensity makes up of the total intensity
of the whole spectrum.
The percentage the parent ion intensity in comparison to the
highest peak in the MS spectrum.
Posterior Error Probability of the identification. This value
essentially operates as a p-value, where smaller is more
significant.
The number of sequencing events for this sequence, which
matches the number of identifiers stored in the column MS/MS
IDs. This number is independent of the times the AA sequence
has been identified through (other) modifications (e.g. heavy
label, oxidation, etc.), about which information can be found in
the columns 'Labeling State' and 'Modification'.
The RAW-file derived scan number of the MS/MS with the
highest peptide identification score (the highest score is stored
in the column 'Score').
Andromeda score for the best associated MS/MS spectrum.
Score difference to the second best identified peptide.
Number of possible distributions of the modifications over the
peptide sequence.
When marked with '+', this particular peptide was found to be
part of a protein derived from the reversed part of the decoy
database. These should be removed for further data analysis.
part of a commonly occurring contaminant. These should be
removed for further data analysis.
A unique (consecutive) identifier for each row in the evidence
table, which is used to cross-link the information in this file with
the information stored in the other files.
Protein group IDs
Peptide ID
Mod. peptide ID
MS/MS IDs
Best MS/MS
AIF MS/MS IDs
Oxidation (M) site IDs
The identifier of the protein-group this redundant peptide

sequence is associated with, which can be used to look up the
extended protein information in the file 'proteinGroups.txt'.
As a single peptide can be linked to multiple proteins (e.g. in
the case of razor-proteins), multiple ids can be stored here
separated by a semicolon.
As a protein can be identified by multiple peptides, the same id
can be found in different rows.
The identifier of the non-redundant peptide sequence.
Identifier of the associated modification summary stored in the
file 'modificationSpecificPeptides.txt'.
Identifier(s) of the associated MS/MS summary(s) stored in the
file 'msms.txt'.
Identifier(s) of the best MS/MS associated spectrum stored in
the file 'msms.txt'.
Identifier(s) of the associated All Ion Fragmentation MS/MS
summary(s) stored in the file 'aifMsms.txt'.
Identifier(s) of the modification summary stored in the file
'Oxidation (M)Sites.txt'.
Peptides
The peptides table contains information on the identified peptides in the processed raw-files.
Name
Sequence
N-term cleavage window
C-term cleavage window
Amino acid before
First amino acid
Second amino acid
Second last amino acid
Last amino acid
Amino acid after
A Count
R Count
N Count
D Count
C Count
Q Count
E Count
G Count
H Count
I Count
L Count
K Count
M Count
F Count
P Count
S Count
T Count
W Count
Y Count
V Count
U Count
Length
Missed cleavages
Mass
Proteins
Leading razor protein
Start position
End position
Unique (Groups)
Separator
Description
The amino acid sequence of the identified peptide.
Sequence window from -8 to 8 around the N-terminal cleavage
site of this peptide.
Sequence window from -8 to 8 around the C-terminal cleavage
site of this peptide.
The amino acid in the protein sequence before the peptide.
The amino acid in the first position of the peptide sequence.
The amino acid in the first position of the peptide sequence.
The amino acid in the last position of the peptide sequence.
The amino acid in the last position of the peptide sequence.
The amino acid in the protein sequence after the peptide.
The number of instances of the 'A' amino acid contained within
the sequence.
The number of instances of the 'R' amino acid contained within
the sequence.
The number of instances of the 'N' amino acid contained within
the sequence.
The number of instances of the 'D' amino acid contained within
the sequence.
The number of instances of the 'C' amino acid contained within
the sequence.
The number of instances of the 'Q' amino acid contained within
the sequence.
The number of instances of the 'E' amino acid contained within
the sequence.
The number of instances of the 'G' amino acid contained within
the sequence.
The number of instances of the 'H' amino acid contained within
the sequence.
The number of instances of the 'I' amino acid contained within
the sequence.
The number of instances of the 'L' amino acid contained within
the sequence.
The number of instances of the 'K' amino acid contained within
the sequence.
The number of instances of the 'M' amino acid contained within
the sequence.
The number of instances of the 'F' amino acid contained within
the sequence.
The number of instances of the 'P' amino acid contained within
the sequence.
The number of instances of the 'S' amino acid contained within
the sequence.
The number of instances of the 'T' amino acid contained within
the sequence.
The number of instances of the 'W' amino acid contained within
the sequence.
The number of instances of the 'Y' amino acid contained within
the sequence.
The number of instances of the 'V' amino acid contained within
the sequence.
The number of instances of the 'U' amino acid contained within
the sequence.
The length of the sequence stored in the column "Sequence".
Monoisotopic mass of the peptide.
Identifiers of proteins this peptide is associated with.
Identifiers of the best scoring protein this peptide is associated
with.
Position of the first amino acid of this peptide in the protein
sequence. (one-based)
Position of the last amino acid of this peptide in the protein
sequence. (one-based)
When marked with '+', this particular peptide is unique to a
single protein group in the proteinGroups file.
Unique (Proteins)
Charges
PEP
Score
Identification type IP1
Identification type IP3_ctrl
Experiment IP1
Experiment IP2
Experiment IP3_ctrl
Intensity
Intensity IP1
Intensity IP2
Intensity IP3_ctrl
Reverse
id
Protein group IDs

Mod. peptide IDs
Evidence IDs
MS/MS IDs
Best MS/MS
MS/MS Count

single protein sequence in the fasta file(s).
All charge states that have been observed.
significant.
Highest Andromeda score for the associated MS/MS spectra.
Indicates whether this experiment was identified by MS/MS or
only by matching between runs.
Number of evidence entries for this 'Experiment'.
A unique (consecutive) identifier for each row in the peptides
table, which is used to cross-link the information in this table
with the information stored in the other tables.
The identifiers of the protein groups this peptide was linked to,
referenced against the proteinGroups table.
Identifier(s) for peptide sequence(s), associated with the
peptide, referenced against the corresponding modified
peptides table.
Identifier(s) for analyzed peptide evidence associated with the
protein group referenced against the evidences table.
The identifiers of the MS/MS scans identifying this peptide,
referenced against the msms table.
The identifier of the best (in terms of quality) MS/MS scan
identifying this peptide, referenced against the msms table.
Identifier(s) for site(s) associated with the protein group, which
show(s) evidence of the modification, referenced against the
appropriate modification site file.
Modification-specific peptides
Name
Sequence
Modifications
Mass
Mass Fractional Part
Protein Groups
Proteins
Unique (Groups)
Unique (Proteins)
Oxidation (M)
Missed cleavages
Experiment IP1
Experiment IP2
Experiment IP3_ctrl
Retention time
Calibrated retention time
Charges
PEP
MS/MS scan number
Raw file
Score
Delta score
Intensity
Intensity IP1
Intensity IP2
Intensity IP3_ctrl
Reverse
id
Protein group IDs
Separator
Description
Post-translational modifications contained within the sequence.
When no modifications exist, this is set to 'unmodified'.
Charge corrected mass of the precursor ion.
The values after the decimal point (ie value - floor(value)).
IDs of the protein groups to whoch this peptide belongs.
The identifiers of the proteins this particular peptide is
associated with.
single protein group in the proteinGroups file.
single protein sequence in the fasta file(s).
Number of Acetyl (Protein N-term) on this peptide.
Number of Oxidation (M) on this peptide.
Retention time in minutes averaged over the evidence entries
belonging to this modification-specific peptide.
Calibrated retention time averaged over the evidence entries
belonging to this modification-specific peptide. Obviously this
only makes sense if retention time recalibration has been
performed which is the case when matching between run is
selected.
All charge states that have been observed.
significant.
The RAW-file derived scan number of the MS/MS with the
highest peptide identification score (the highest score is stored
in the column 'Score').
from.
Andromeda score for the best identified among the associated
MS/MS spectra.
A unique (consecutive) identifier for each row in the peptides
table, which is used to cross-link the information in this table
with the information stored in the other tables.
The identifiers of the protein groups this peptide was linked to,
referenced against the proteinGroups table.
Peptide ID
Evidence IDs
MS/MS IDs
Best MS/MS
MS/MS Count
Identifier of the associated peptide sequence summary, which

can be found in the file 'peptides.txt'.
The identifier of the best (in terms of quality) MS/MS scan
identifying this peptide, referenced against the msms table.
Identifier(s) for site(s) associated with this peptide, which
Oxidation (M)Sites
Name
Proteins
Positions within proteins
Leading proteins
Protein
Fasta headers
Localization prob
Score diff
PEP
Score
Delta score
Score for localization
Localization prob IP1
Score diff IP1
PEP IP1
Score IP1
Localization prob IP2
Score diff IP2
PEP IP2
Score IP2
Localization prob IP3_ctrl
Score diff IP3_ctrl
PEP IP3_ctrl
Score IP3_ctrl
Diagnostic peak
Number of Oxidation (M)
Amino acid
Sequence window
Modification window
Peptide window coverage
Oxidation (M) Score diffs
Position in peptide
Charge
Mass error [ppm]

Intensity
Intensity___1
Intensity___2
Intensity___3
Separator
Description
Identifiers of proteins this site is associated with.
For each protein identifier in the 'Proteins' column you find here
the psoition of the site in the respective protein sequence. The
index of the first amino acid in the sequence is 1.
Identifier of the protein this peptide is associated with.
Descriptions of proteins this peptide is associated with.
The posterior error probability (PEP) of the best identified

modified peptide containing this site.
The Andromeda score of the best identified modified peptide
containing this site.
The Andromeda delta score of the best identified modified
peptide containing this site.
The Andromeda score of the MS/MS spectrum used for
calculating the localization score for this site.
Different numbers of Oxidation (M) on peptides that this site is

involved in.
Charge state of the precursor ion.

Ratio mod/base
Intensity IP1
Intensity IP2
Intensity IP3_ctrl
Ratio mod/base IP1

Ratio mod/base IP2
Ratio mod/base IP3_ctrl
Intensity IP1___1
Intensity IP1___2
Intensity IP1___3
Intensity IP2___1
Intensity IP2___2
Intensity IP2___3
Intensity IP3_ctrl___1
Reverse
id
Protein group IDs
Positions
Position
Peptide IDs
Mod. peptide IDs
Evidence IDs
MS/MS IDs


part of a protein derived from the reversed part of the protein
sequence database. These should be removed for further data
analysis.
A unique (consecutive) identifier for each row in the site table,
which is used to cross-link the information in this file with the
information stored in the other files.
The identifier of the protein-group this peptide sequence is
associated with, which can be used to look up the extended
protein information in the file 'proteinGroups.txt'.
The positions of the modifications in the protein amino acid
sequence.
The position of the modification in the protein amino acid
sequence.
Identifier(s) of the associated peptide sequence(s) summary,
which can be found in the file 'peptides.txt'.
which can be found in the file 'modificationSpecificPeptides.txt'.
Best localization evidence ID

Best localization MS/MS ID
Best localization raw file
Best localization scan number
Best score evidence ID
Best score MS/MS ID
Best score raw file
Best score scan number
Best PEP evidence ID
Best PEP MS/MS ID
Best PEP raw file
Best PEP scan number
Protein groups
The Protein Groups table contains information on the identified proteins in the processed raw-files. Each
single row contains the group of proteins that could be reconstructed from a set of peptides.
Name
Protein IDs
Majority protein IDs

Peptide counts (all)
Peptide counts (razor+unique)
Peptide counts (unique)
Fasta headers
Number of proteins
Peptides
Razor + unique peptides
Unique peptides
Peptides IP1
Peptides IP2
Peptides IP3_ctrl
Razor + unique peptides IP1
Razor + unique peptides IP2
Razor + unique peptides IP3_ctrl
Unique peptides IP1
Unique peptides IP2
Unique peptides IP3_ctrl
Sequence coverage [%]
Unique + razor sequence coverage
[%]
Unique sequence coverage [%]
Mol. weight [kDa]

Sequence length
Sequence lengths
Q-value
Score
Separator
Description
Identifier(s) of protein(s) contained in the protein group. They
are sorted by number of identified peptides in descending
order.
These are the IDs of those proteins that have at least half of
the peptides that the leading protein has.
Number of peptides associated with each protein in protein
group, occuring in the order as the protein IDs occur in the
'Protein IDs' column. Here distinct peptide sequences are
counted. Modified forms or different charges are counted as
one peptide.
one peptide.
one peptide.
Fasta headers(s) of protein(s) contained within the group.
Number of proteins contained within the group. This
corresponds to the number of entries in the colum 'Protein IDs'.
The total number of peptide sequences associated with the
protein group (i.e. for all the proteins in the group).
The total number of razor + unique peptides associated with
the protein group (i.e. these peptides are shared with another
protein group).
The total number of unique peptides associated with the
protein group (i.e. these peptides are not shared with another
protein group).
Number of peptides (distinct peptide sequences) in experiment
IP1
IP2
IP3_ctrl
Number of razor + unique peptides (distinct peptide
sequences) in experiment IP1
sequences) in experiment IP2
sequences) in experiment IP3_ctrl
Number of unique peptides (distinct peptide sequences) in
experiment IP1
experiment IP2
experiment IP3_ctrl
Percentage of the sequence that is covered by the identified
peptides of the best protein sequence contained in the group.
unique and razor peptides of the best protein sequence
contained in the group.
unique peptides of the best protein sequence contained in the
group.
Molecular weight of the leading protein sequence contained in
the protein group.
The length of the leading protein sequence contained in the
group.
The length of all sequences of the proteins contained in the
group.
This is the ratio of reverse to forward protein groups.
Protein score which is derived from peptide posterior error
probabilities.

Sequence coverage IP1 [%]
Sequence coverage IP2 [%]
Sequence coverage IP3_ctrl [%]
Intensity
Intensity IP1
Intensity IP2
Intensity IP3_ctrl
MS/MS Count
Only identified by site
Reverse
id
Peptide IDs
Peptide is razor
Mod. peptide IDs
Evidence IDs
MS/MS IDs
Best MS/MS
Oxidation (M) site positions

peptides in this sample of the longest protein sequence
contained within the group.
When marked with '+', this particular protein group was
identified only by a modification site.
When marked with '+', this particular protein group contains no
protein, made up of at least 50% of the peptides of the leading
protein, with a peptide derived from the reversed part of the
decoy database. These should be removed for further data
analysis. The 50% rule is in place to prevent spurious protein
hits to erroneously flag the protein group as reverse.
When marked with '+', this particular protein group was found
to be a commonly occurring contaminant. These should be
A unique (consecutive) identifier for each row in the
proteinGroups table, which is used to cross-link the information
in this file with the information stored in the other files.
which can be found in the file 'peptides.txt'.
Indicates for each peptide ID if it is a razor or group unique
peptide (true) or a non unique non razor peptide (false).
The identifier of the best (in terms of quality) MS/MS scans

identifying the peptides of this protein, referenced against the
msms table.
Identifier(s) for site(s) associated with the protein group, which
Positions of the sites in the leading protein of this group.
All peptides
Name
Raw file
Type
Charge
m/z
Mass
Uncalibrated m/z
Resolution
Number of data points
Number of scans
Number of isotopic peaks
PIF
Mass fractional part
Mass deficit
Mass precision [ppm]

Max intensity m/z 0
Retention time
Retention Length
Retention Length (FWHM)
Min scan number
Max scan number
Identified
MS/MS IDs
Sequence
Length
Modifications
Modified sequence
Separator
Description
Name of the raw file the spectral data was extracted from.
The type of detection for the peptide. SILAC A SILAC pair
was detected.
ISO An isotope pattern was detected.
The charge state of the peptide.
The mass divided by the charge of the charged peptide.
The mass of the neutral peptide ((m/z-proton) * charge).
m/z before recalibrations have been applied.
The resolution of the peak detected for the peptide measured
in Full Width at Half Maximum (FWHM).
The number of data points (peak centroids) collected for this
peptide feature.
The number of MS scans that the 3d peaks of this peptide
feature are overlapping with.
The number of isotopic peaks contained in this peptide feature.
The values after the radix point (ie value - floor(value)).
Empirically derived deviation measure to the next nearest
integer scaled to center around 0. Can be used to visually
detect contaminants in a plot setting Mass against this value.
m*a+b round(m*a+b)
m: the peptide mass
a: 0.999555
b: -0.10
The precision of the mass detection of the peptide in parts-permillion.
The retention time of the peak detected for the peptide
measured in minutes.
The total retention time width of the peak (last timepoint first
timepoint) in seconds.
The full width at half maximum value retention time width of the
peak in seconds.
The first scan-number at which the peak was encountered.
The last scan-number at which the peak was encountered.
When marked with '+' this particular MS/MS scan was
identified as a peptide; when marked with - no identification
was made.
Unique identifier linking this identification to the MS/MS scans.
The length of the sequence stored in the column Sequence.
When no modifications exist, this is set to unmodified.
Note: This column only set when this MS/MS spectrum has
been identified.
Sequence representation of the peptide including location(s) of
modified AAs.
Proteins
been identified.
Score
been identified.
The score of the identification (higher is better).
Intensity
Intensities
MS/MS Count
been identified.
The intensity values of the isotopes.
The number of MS/MS spectra recorded for the peptide.
MSMS Scan Numbers

MSMS Isotope Indices
The scan numbers where the MS/MS spectra were recorded.

Indices of the isotopic peaks that the MS/MS spectra reside on.
A value of 0 corresponds to the monoisotopic peak.
MS scans
The msScans table contains information about the full scans, which can be used to verify data quality and
generated useful statistics about the interaction between the samples and LC.
Name
Raw file
Scan number
Scan index
Retention time
Cycle time
Ion injection time
Base peak intensity

Total ion current
MS/MS count
Mass calibration
Experiment
Peak length
Isotope pattern length
Multiplet length
Peaks / s
Single peaks / s
Isotope patterns / s
Single isotope patterns / s
Multiplets / s
Identified multiplets / s
Multiplet identification rate [%]
MS/MS / s
Identified MS/MS / s
MS/MS identification rate [%]
Intens Comp Factor
CTCD Comp
RawOvFtT
AGC Fill
Separator
Description
The name of the RAW-file the mass spectral data originates
from.
The scan number (defined in the raw-file) at which the full scan
was made.
The consecutive index of this full scan.
The retention time at which the full scan was made.
The total time (full scan including the tandem MS scans) this
full scan has taken up.
The total injection time that was required to capture the
specified amount of ions. This value is limited by a maximum,
which can be used to determine whether the time has maxed
out (indicative of a bad acquisition).
The intensity of the most intense ion in the spectrum.
The total intensity acquired in the full scan.
The number of tandem MS scans that were made based on
this full scan (e.g. a top 10 method selects the top 10 most
intense ions in the scan and fragments those).
The applied mass correction in Th to the full scan.
The average time between the start and the end of the peaks
detected in the full scan.
The average time between the start and the end of the isotope
patterns detected in the full scan.
The average time between the start and the end of the isotope
patterns of the labeling multiplets detected in the full scan.
The average number of peaks detected per second of
chromatography.
The average number of single peaks detected per second of
chromatography.
The average number of isotope patterns detected per second
of chromatography.
The average number of single isotope patterns detected per of
second chromatography.
The average number of labeling multiplets detected per of
second chromatography.
The percentage of labeling multiplets actually identified.
The percentage of the detected labeling multiplets that were
identified.
The average number of MS/MS events per second of
chromatography.
The average number of identified MS/MS events per second of
chromatography.
The percentage of tandem MS scans that were identified.
Taken from the Thermo RAW file.
For Thermo Fisher only. TIC estimation done with the orbitrap
cell.
MZ range
Name
Raw file
m/z
Peaks / Da
Single peaks / Da
Isotope patterns / Da
Single isotope patterns / Da
SILAC pairs / Da
Identified SILAC pairs / Da
SILAC identification rate [%]
MS/MS / Da
Identified MS/MS / Da
Identification rate [%]
Separator
Description
from.
The mass-over-charge value.
The average number of peaks detected per Dalton.
The average number of single peaks detected per Dalton.
The average number of isotope patterns detected per Dalton.
The average number of single isotope patterns detected per
Dalton.
The average number of SILAC pairs detected per Dalton.
The percentage of SILAC pairs actually identified.
The percentage of the detected SILAC pairs that were
identified.
The average number of MS/MS events per Dalton.
The average number of identified MS/MS events per Dalton.
The percentage of tandem MS scans that were identified.
MS/MS scans
Name
Raw file
Scan number
Retention time
Ion injection time
Total ion current
Collision energy
Summations
Base peak intensity
Elapsed time
Identified
MS/MS IDs
Sequence
Length
Filtered peaks
m/z
Mass
Charge
Type
Fragmentation
Mass analyzer
Parent intensity fraction

Base peak fraction
Precursor full scan number
Precursor intensity
Precursor apex fraction
Precursor apex offset
Precursor apex offset time
Scan event number
Modifications
Modified sequence
Separator
Description
Name of the RAW file the spectral MS/MS data was extracted
from.
RAW file derived scan number for the MS/MS spectrum.
Time point along the elution profile at which the MS/MS data
was recorded.
The ion inject time for the MS/MS scan. This can be used to
determine if this time equals to the maximum ion inject time,
general indicative of a lower quality spectrum.
The total ion current of the MS/MS scan. For Thermo data this
value is calculated by summing all the intensity values found in
the mass spectral data, which is different from the Xcalibur
reported TIC (Xcalibur TIC is about 25% of the value reported
here).
The collision energy used for the fragmentation that resulted in
this MS/MS scan.
For time of flight instruments only.
The intensity of the most intense ion in the spectrum.
The time the MS/MS scan took to complete.
When marked with '+' this particular MS/MS scan was
identified as a peptide; when marked with - no identification
was made.
Unique identifier linking this identification to the MS/MS scans.
The length of the sequence stored in the column Sequence.
Number of peaks after the 'top X per 100 Da' filtering.
Recalibrated m/z of the precursor ion.
Charge corrected mass of the precursor ion.
Charge state of the precursor ion.
The type of precursor ion as identified by MaxQuant. ISO
isotopic cluster.
PEAK single peak.
MULTI labeling cluster.
The type of fragmentation used to create the MS/MS spectrum.
CID Collision Induced Dissociation.
HCD High energy Collision induced Dissociation.
ETD Electron Transfer Dissociation.
The mass analyzer used to record the MS/MS spectrum. ITMS
Ion trap.
FTMS Fourier transform ICR or orbitrap cell.
TOF Time of flight.
The percentage the parent ion intensity makes up of the total
intensity in the selection window.
intensity of the whole MS spectrum.
highest peak in he MS spectrum.
The full scan number where the precursor ion was selected for
fragmentation.
The intensity of the precursor ion at the scannumber it was
selected.
The fraction the intensity of the precursor ion makes up of the
peak (apex) intensity.
How many full scans the precursor ion is offset from the peak
(apex) position.
How much time the precursor ion is offset from the peak (apex)
position.
This number indicates which MS/MS scan this one is in the
consecutive order of the MS/MS scans that are acquired after
an MS scan.
When no modifications exist, this is set to unmodified.
been identified.
modified AAs.
been identified.
Proteins
Score
been identified.
The score of the identification (higher is better).
been identified.
Experiment
Intens Comp Factor
CTCD Comp
RawOvFtT
AGC Fill
Scan index
MS scan index
MS scan number

For Thermo Fisher only. TIC estimation done with the orbitrap
cell.
Consecutive index of the MS/MS spectrum.
Consecutive index of the MS spectrum prior to this MS/MS
spectrum.
Scan number of the MS spectrum prior to this MS/MS
spectrum.
MS/MS
Name
Raw file
Scan number
Scan index
Sequence
Length
Missed cleavages
Modifications
Modified sequence

Oxidation (M)
Proteins
Charge
Fragmentation
Mass analyzer
Type
Scan event number

Isotope index
m/z
Mass
Mass Error [ppm]
Simple Mass Error [ppm]

Retention time
PEP
Score
Delta score
Score diff
Localization prob
Combinatorics
PIF
Base peak fraction
Precursor Full ScanNumber
Precursor Intensity
Precursor Apex Fraction
Separator
Description
The name of the RAW file the mass spectral data was read
from.
The RAW-file derived scan number of the MS/MS spectrum.
The consecutive index of the MS/MS spectrum.
Post-translational modifications contained within the identified
peptide sequence.
Sequence representation including the post-translational
modifications (abbreviation of the modification in brackets
before the modified AA). The sequence is always surrounded
by underscore characters ('_').
Sequence representation of the peptide including PTM
positioning probabilities ([0..1], where 1 is best match) for
'Oxidation (M)'.
The identifiers of the proteins the identified peptide is

associated with.
The charge state of the precursor ion.
The type of fragmentation used to create the MS/MS spectrum.
CID Collision Induced Dissociation.
HCD High energy Collision induced Dissociation.
ETD Electron Transfer Dissociation.
The mass analyzer used to record the MS/MS spectrum. ITMS
Ion trap.
FTMS Fourier transform ICR or orbitrap cell.
TOF Time of flight.
The type of precursor ion as identified by MaxQuant. ISO
isotopic cluster.
PEAK single peak.
MULTI labeling cluster.
The mass-over-charge of the precursor ion.

The charge corrected mass of the precursor ion.
The uncalibrated retention time in minutes where the MS/MS
spectrum has been acquired.
significant.
Andromeda score for the best associated MS/MS spectrum.
Score difference to the second best identified peptide with a
different amino acid sequence.
Score difference to the second best positioning of modifications
identified peptide with the same amino acid sequence.
peptide sequence.
intensity of the whole spectrum.
highest peak in he MS spectrum.
The full scannumber where the precursor ion was selected for
fragmentation.
The intensity of the precursor ion at the scannumber it was
selected.
The fraction the intensity of the precursor ion makes up of the
peak (apex) intensity.
Precursor Apex Offset

Precursor Apex Offset Time
Matches
Intensities
Mass Deviations [Da]
Mass Deviations [ppm]
Masses
Number of Matches
Intensity coverage
Peak coverage
Neutral loss level
ETD identification type
Reverse
All scores
All sequences
All modified sequences
id
Protein group IDs
Peptide ID
Mod. peptide ID
Evidence ID
How many full scans the precursor ion is offset from the peak
(apex) position.
How much time the precursor ion is offset from the peak (apex)
position.
The species of the peaks in the fragmentation spectrum after
TopN filtering.
The intensities of the peaks in the fragmentation spectrum after
TopN filtering.
The mass deviation of each peak in the fragmentation
spectrum in absolute mass units.
The mass deviation of each peak in the fragmentation
spectrum in parts per million.
The masses-over-charge of the peaks in the fragmentation
spectrum.
The number of peaks matching to the predicted fragmentation
spectrum.
The fraction of intensity in the MS/MS spectrum that is
annotated.
The fraction of peaks in the MS/MS spectrum that are
annotated.
How many neutral losses were applied to each fragment in the
Andromeda scoring.
For ETD spectra several different combinations of ion series
are scored. Here the highest scoring combination is indicated
A unique (consecutive) identifier for each row in the msms

table, which is used to cross-link the information in this file with
the information stored in the other files.
The identifier of the protein-group this redundant peptide
Identifier of the associated evidence stored in the file
'evidence.txt'.
Identifier of the oxidation summary stored in the file 'Oxidation
(M)Sites.txt'.
AIF MS/MS
Name
id
Protein group IDs
Peptide ID
Mod. peptide ID
Evidence ID
Raw file
Sequence
Length
Missed Cleavages
Modifications
Modified Sequence

Oxidation (M)
Proteins
Charge
m/z
Mass
Retention time
Precursor intensity
PEP
Score
Delta score
Combinatorics
Matches
Intensities
Mass Deviations
Masses
Charges
Correlations
Number of Matches
Reverse
Separator
Description
A unique (consecutive) identifier for each row in the AIF
MS/MS table, which is used to cross-link the information in this
file with the information stored in the other files.
The identifier of the protein group this redundant peptide
the case of razor-proteins), multiple id's can be stored here
Identifier for analyzed peptide evidence associated with the
Name of the RAW file the spectral data was extracted from,
which led to the identification of this peptide.
When no modifications exist, this is set to 'unmodified'. Note:
This column only set when this MS/MS spectrum has been
identified.
modified AAs.
been identified.
The IPI identifiers of the proteins the identified peptide is

associated with.
The charge of the precursor ion.
The mass-over-charge of the precursor ion.
The charge corrected mass of the precursor ion.
The uncalibrated retention time in minutes in the elution profile
The intensity of the precursor ion.
significant.
Andromeda identification score for the MS/MS spectrum.
peptide sequence.
The intensities of the peaks in the fragmentation spectrum after
top-N filtering.
The search engine allowed mass deviations of the peaks in the
fragmentation spectrum.
The masses-over-charge of the peaks in the fragmentation
spectrum.


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Summary

MS/MS Submitted (ISO)

Isotope Patterns Sequenced

The total number of isotope patterns sequenced by tandem

Oxidation (M) Probabilities

Oxidation (M) Score Diffs

Acetyl (Protein N-term)

Leading Razor Protein

Uncalibrated - Calibrated m/z [Da]

Mass Error [ppm]

Mass Error [Da]

Uncalibrated Mass Error [ppm]

Uncalibrated Mass Error [Da]

Max intensity m/z 0

Match time difference

Match m/z difference

MS/MS Scan Number

Mass error of the uncalibrated mass-over-charge value of the

Protein group IDs

The identifier of the protein-group this redundant peptide

Protein group IDs

When marked with '+', this particular peptide is unique to a

MS/MS scan number

Protein group IDs

Identifier of the associated peptide sequence summary, which

Identification type IP1

The posterior error probability (PEP) of the best identified

Different numbers of Oxidation (M) on peptides that this site is

Charge state of the precursor ion.

Ratio mod/base IP1

Protein group IDs

Summed up eXtracted Ion Current (XIC) of all isotopic clusters

Summed up eXtracted Ion Current (XIC) of all isotopic clusters

Best localization evidence ID

Majority protein IDs

Peptide counts (razor+unique)

Peptide counts (unique)

Mol. weight [kDa]

Identification type IP2

Sequence coverage IP2 [%]

Sequence coverage IP3_ctrl [%]

Oxidation (M) site IDs

Oxidation (M) site positions

Indicates whether this experiment was identified by MS/MS or

The identifier of the best (in terms of quality) MS/MS scans

Mass precision [ppm]

MSMS Scan Numbers

The scan numbers where the MS/MS spectra were recorded.

Base peak intensity

Total ion current

Parent intensity fraction

Identifiers of proteins this peptide is associated with.

Taken from the Thermo RAW file.

Oxidation (M) Probabilities

Oxidation (M) Score Diffs

Scan event number

Simple Mass Error [ppm]

The identifiers of the proteins the identified peptide is

The mass-over-charge of the precursor ion.