Last-modified: Thu, 6 Sep 2006 20:42:33 JST

AYUMS is a useful software tool for the proteome analysis of LC/MS/MS. The software is developed using Java and runs on Linux, Windows, and Mac OS X.

Availability

There are two types of version, Java jar file and binary file for Windows. Now, AYUMS software jar file is available from authors at ayums@ims.u-tokyo.ac.jp. Please contact if you want the file. For evaluation, Windows version is available from here. Windows version ensure the compatibility with Java version and, you can all function of AYUMS.

AYUMS 071005 for Windows (20 MBytes)

AYUMS 1.00 for Windows (24 MBytes)

Download sample data

Sample [060314A431] zip package (573 MBytes)

Sample [060314A431] self-extracting exe (149 MBytes; super compression)

The size of sample files, Mascot HTML file and the raw data file in ayums format,is 1,414 Mbytes when unpacked.

Requirements

Java version

Operating system: Java platform independent
Java requirements: Java 1.4.2 or higher

Windows version

Operating system: Windows (may be) 98 or higher

Updates

2007-10-5 Version 071005 Released
2006-9-1 Version 1.00 Released
2006-1-25 Version 0.10 Privity released

Instructions

AYUMS is a console-based software tool. Both Java and Windows version are controled same descriptions on your console. Excution is typed as follows.

ayums <-switch> [parameters]... [-options [paremeters]]...

If you enter only "ayums", you can see the brief explanation.

Option Switches

All switches are letter-insensitive.

-C

-C <rawTextfile>

AYUMS with -C switch performs converting a ASCII style raw data to the ayums format. For an analyzing, you need the ayums format raw data. You have to convert your raw data in ASCII style format by using Databrige before you can make this AYUMS conversion.

ayusm -C Sample060314A431.txt

You will be able to get a raw data in ayums format of "Sample060314A431.txt.dat".

-Run

-Run <mascotFile> <ayumsRawfile> [options]...

This is the main function. You can set sub-onptions for your convinience.

ayusm -Run mascotFileSample060314A431.htm Sample060314A431.txt.dat

You will be able to get a result file in csv format of "Sample060314A431.txt.csv" at the same location as "Sample060314A431.txt.dat".

-ScorePeptides

-Run <mascotFile> <ayumsRawfile> -ScorePiptides <thresholdValue> [options]...

-ScorePeptides option is used in setting a threshold value of the Query Score of each peptides in protein list of Mascot html file. When the score is greater than <thresholdValue>, the Query is tested by AYUMS. If you run AYUMS without -ScorePeptides, the threshold value of the Query Score is applied 25 as a default value. This option is used with -Run option switch.

ayusm -Run mascotFileSample060314A431.htm Sample060314A431.txt.dat -ScorePeptides 20

-check

AYUMS includes some instant tools.

-check <ayumsRawfile>

You can check quickly whether a file in ayums format is correct or not.

ayusm -check Sample060314A431.txt.dat

-scanlist

-scanlist <functionNumber> <ayumsRawfile>

Display a scan list for the specified function number (scan = spectrum). The list provides values of the Scan number, Retention time, SetMass, Colision energy, and number of samples for each scan (The SetMass and Colision energy do not exist in Function 1).

ayusm -scanlist 2 Sample060314A431.txt.dat

The scan list of FUNCTION 2 is shown.

-scanlistall

-scanlistall <ayumsRawfile>

Show scan lists of all function number.

ayusm -scanlistall Sample060314A431.txt.dat

The all scan are listed.

-p

-p <functionNumber> <scanNumber> <ayumsRawfile>

Show only one scan information in a function number without the sample details.

ayusm -p 2 100 Sample060314A431.txt.dat

FUNCTION 2
Scan    Ret.T.  SetMass         Col.E.  Samples
100     49.842  455.2871        30.0000 923

-ps

-ps <functionNumber> <scanNumber> <ayumsRawfile>

Show only one scan information in a function number with the sample details of all. A sample consist of m/z value and its intensity.

ayusm -ps 2 100 Sample060314A431.txt.dat

FUNCTION 2
Scan    Ret.T.  SetMass         Col.E.  Samples
100     49.842  455.2871        30.0000 923

m/z             Intensity
49.5864         0
84.0902         0
84.0939         1
84.0977         0
84.1014         1
.

-ps2

-ps2 <functionNumber> <scanNumber> <m/zFrom> <m/zTo> <ayumsRawfile>

Show the part of a scan (spectrum) for the specified function and scan number. The part of scan is specified by a renge of m/z value.

ayusm -ps2 1 1 460.7200 460.8000 Sample060314A431.txt.dat

FUNCTION 1
Scan    Ret.T.  Samples
1       0.026   22766

(460.7200 - 460.8000)
m/z             Intensity
460.7258        11
460.7346        15
460.7433        21
460.7521        18
460.7608        23
460.7696        18
460.7784        14
460.7871        17
460.7958        11

-MQUERYLIST

-MQUERYLIST <mascotFile>

Show the query list in the Mascot file.

ayusm -MQUERYLIST mascotFileSample060314A431.htm

Query   Experi. Cycles  ScanNum Ident.L Homol.L E_from  E_to    Period
1       2       1       782     20              9999.99 9999.99 0
2       2       1       885     27              9999.99 9999.99 0
3       5       1       35                      9999.99 9999.99 0
4       5       1       13      35              9999.99 9999.99 0
5       4       1       52      16              9999.99 9999.99 0
6       5       1       25      20      15      9999.99 9999.99 0
7       4       1       12      33              9999.99 9999.99 0
.

-MHITLIST

-MHITLIST <mascotFile>

Show the hit list in the Mascot file.

ayusm -MHITLIST mascotFileSample060314A431.htm

1. gi|61743954|ref|NP_001611.1|	Mass: 628699 Score: 1083 Queries Matched: 79
AHNAK nucleoprotein isoform 1 [Homo sapiens]
2. gi|21614499|ref|NP_003370.2|	Mass: 69370 Score: 304 Queries Matched: 12
villin 2 [Homo sapiens]
3. gi|29725609|ref|NP_005219.2|	Mass: 134190 Score: 289 Queries Matched: 18
epidermal growth factor receptor isoform a [Homo sapiens]
4. gi|55770844|ref|NP_001894.2|	Mass: 100009 Score: 256 Queries Matched: 11
catenin, alpha 1 [Homo sapiens]
.

-MHITLISTD

-MHITLISTD <mascotFile>

Show the hit list with the supporting peptides query list in the Mascot file.

ayusm -MHITLISTD mascotFileSample060314A431.htm

1. gi|61743954|ref|NP_001611.1|	Mass: 628699 Score: 1083 Queries Matched: 79
AHNAK nucleoprotein isoform 1 [Homo sapiens]
Query	Observ.	Mr(exp)	Mr(cal)	Delta	Miss	Score	Expect	Rank	Peptide
53	480.32	958.63	958.6	0.03	3	12	41.0	7	K.KSKIKMPK.F
89	518.79	1035.56	1035.51	0.05	0	53	0.0037	1	K.MPTFSTPGAK.G
112	536.82	1071.62	1071.56	0.06	0	36	0.16	1	K.MPSLEISAPK.V
.
.

2. gi|21614499|ref|NP_003370.2|	Mass: 69370 Score: 304 Queries Matched: 12
villin 2 [Homo sapiens]
Query	Observ.	Mr(exp)	Mr(cal)	Delta	Miss	Score	Expect	Rank	Peptide
53	480.32	958.63	958.59	0.04	0	18	9.8	1	K.FVIKPIDK.K
95	527.31	1052.61	1052.56	0.05	1	44	0.026	1	R.EKEELMLR.L + Arginine-13C6  (R-13C6)
.

-MHIT

-MHIT <hitNumber> <mascotFile>

Show a predicted protein with the supporting peptides query list in the Mascot file. The Protein is specified by the hit number.

ayusm -MHIT 3 mascotFileSample060314A431.htm

3. gi|29725609|ref|NP_005219.2|	Mass: 134190 Score: 289 Queries Matched: 18
epidermal growth factor receptor isoform a [Homo sapiens]
Query	Observ.	Mr(exp)	Mr(cal)	Delta	Miss	Score	Expect	Rank	Peptide
63	489.8	977.59	977.54	0.05	0	27	1.2	1	R.ELIIEFSK.M
122	549.82	1097.63	1097.58	0.05	0	49	0.0091	1	R.YLVIQGDER.M + Arginine-13C6  (R-13C6)
124	551.82	1101.62	1101.59	0.02	0	50	0.0068	1	R.YLVIQGDER.M + Arginine-13C615N4  (R-full)
186	599.84	1197.66	1197.64	0.03	0	74	3.5E-5	1	K.VLGSGAFGTVYK.G
207	610.82	1219.63	1219.6	0.03	0	59	9.5E-4	1	K.GSTAENAEYLR.V + Arginine-13C615N4  (R-full)
242	628.38	1254.75	1254.7	0.05	1	30	0.9	1	K.GLWIPEGEKVK.I
251	631.37	1260.73	1260.67	0.06	0	61	6.5E-4	1	K.WMALESILHR.I + Arginine-13C6  (R-13C6)
255	633.37	1264.73	1264.69	0.05	0	47	0.018	1	K.WMALESILHR.I + Arginine-13C615N4  (R-full)
282	648.82	1295.62	1295.55	0.07	0	44	0.036	1	K.GSTAENAEYLR.V + Phospho (STY);  Arginine-13C6 (R-13C6)
308	664.38	1326.74	1326.69	0.05	1	48	0.013	1	K.EYHAEGGKVPIK.W
451	785.92	1569.82	1569.73	0.09	0	37	0.23	1	R.MHLPSPTDSNFYR.A + Arginine-13C6  (R-13C6)
452	787.9	1573.79	1573.75	0.04	0	45	0.035	1	R.MHLPSPTDSNFYR.A +  Arginine-13C615N4 (R-full)
487	827.9	1653.78	1653.71	0.07	0	19	17.0	1	R.MHLPSPTDSNFYR.A + Phospho (STY);  Arginine-13C615N4 (R-full)
613	1020.59	2039.16	2039.1	0.07	0	48	0.047	1	R.ELVEPLTPSGEAPNQALLR.I +  Arginine-13C6 (R-13C6)
618	1022.59	2043.17	2043.11	0.05	0	42	0.19	1	R.ELVEPLTPSGEAPNQALLR.I +  Arginine-13C615N4 (R-full)
672	746.04	2235.11	2235.02	0.08	0	59	0.0044	1	K.GSHQISLDNPDYQQDFFPK.E
673	1118.57	2235.12	2235.02	0.1	0	47	0.075	1	K.GSHQISLDNPDYQQDFFPK.E
923	1205.94	3614.81	3616.6	-1.79	0	17	150.0	2	R.ALMDEEDMDDVVDADEYLIPQQGFFSSPSTSR.T + Arginine-13C615N4  (R-full)

-MHITD

-MHITD <hitNumber> <mascotFile>

Show each query additional data as well as information of -MHIT switch.

ayusm -MHITD 3 mascotFileSample060314A431.htm

3. gi|29725609|ref|NP_005219.2|	Mass: 134190 Score: 289 Queries Matched: 18
epidermal growth factor receptor isoform a [Homo sapiens]
Query	Observ.	Mr(exp)	Mr(cal)	Delta	Miss	Score	Expect	Rank	Peptide
	Experi.	Cycles	ScanNum	Ident.L	Homol.L	E_from	E_to	Period
63	489.8	977.59	977.59	0.05	0	27	1.2	1	R.ELIIEFSK.M
	5	1	91	41	37	9999.99	9999.99	0
122	549.82	1097.63	1097.63	0.05	0	49	0.0091	1	R.YLVIQGDER.M + Arginine-13C6 (R-13C6)
	2	1	142	41	30	9999.99	9999.99	0
124	551.82	1101.62	1101.62	0.02	0	50	0.0068	1	R.YLVIQGDER.M + Arginine-13C615N4 (R-full)
	2	1	141	41	29	9999.99	9999.99	0
186	599.84	1197.66	1197.66	0.03	0	74	3.5E-5	1	K.VLGSGAFGTVYK.G
	2	1	173	42		9999.99	9999.99	0
207	610.82	1219.63	1219.63	0.03	0	59	9.5E-4	1	K.GSTAENAEYLR.V + Arginine-13C615N4 (R-full)
	2	1	30	42	38	9999.99	9999.99	0
.

-MHITkimo

-MHITkimo <hitNumber> <mascotFile>

Show minimal view in comparison with the -MHITD switch.

ayusm -MHITkimo 3 mascotFileSample060314A431.htm

3. gi|29725609|ref|NP_005219.2|	Mass: 134190 Score: 289 Queries Matched: 18
epidermal growth factor receptor isoform a [Homo sapiens]
Query	Observ.	Mr(exp)	Mr(cal)	Score	Charge	Pos.	Experi.	ScanNum	Ident.L	Peptide
63	489.8	977.59	977.59	27	2	0	5	91	41	ELIIEFSK
122	549.82	1097.63	1097.63	49	2	1	2	142	41	YLVIQGDER
124	551.82	1101.62	1101.62	50	2	2	2	141	41	YLVIQGDER
186	599.84	1197.66	1197.66	74	2	0	2	173	42	VLGSGAFGTVYK
207	610.82	1219.63	1219.63	59	2	2	2	30	42	GSTAENAEYLR
242	628.38	1254.75	1254.75	30	2	0	2	164	42	GLWIPEGEKVK
.

-MHITQUERY2

-MHITQUERY2 <hitNumber> <queryNumber> <mascotFile> <ayumsRawfile>

Try to analysis a single query in a hit.

ayusm -MHITQUERY2 3 122 mascotFileSample060314A431.htm Sample060314A431.txt.dat

3. gi|29725609|ref|NP_005219.2|	Mass: 134190 Score: 289 Queries Matched: 18
epidermal growth factor receptor isoform a [Homo sapiens]
Query	Observ.	Mr(exp)	Mr(cal)	Score	Charge	Pos.	Experi.	ScanNum	Ident.L	Peptide
122	549.82	1097.63	1097.63	49	2	1	2	142	41	YLVIQGDER
FUNCTION 2
Scan	Ret.T.	SetMass		Col.E.	Samples
142	47.371	549.8292	30.0000	6939
FUNCTION 1
Scan	Ret.T.	Samples
2067	47.612	71080

2064 6813/11280 = 0.60398936
2065 6397/11337 = 0.56425864
2066 6288/11234 = 0.5597294
2067 1618/5163 = 0.3133837
2068 1555/5346 = 0.29087168
2069 949/4191 = 0.2264376
2070 898/4386 = 0.20474236
2064 is selected as center. i/w: 5.73 hi/w: 4.94
2063 7864/13587 = 0.5787885
2063 0.58 OK i/w: 13.31 hi/w: 10.58 
2062 6944/11687 = 0.59416443
2062 0.59 OK i/w: 12.88 hi/w: 11.47 
2061 400/3582 = 0.11166946
2061 0.11 --
2065 0.56 OK i/w: 4.99 hi/w: 4.02 
2066 0.56 OK i/w: 4.20 hi/w: 3.68 
2067 0.31 --
scan range: 2062 - 2066
Position is 1 (R=1).

Members

Ayumu Saito, Researcher
Masao Nagasaki, Assistant Professor

Contact

ayums@ims.u-tokyo.ac.jp